I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 29 00:47:36 +14 2020 I: pbuilder-time-stamp: 1593341256 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [python-cogent_1.9-14.dsc] I: copying [./python-cogent_1.9.orig.tar.gz] I: copying [./python-cogent_1.9-14.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Jan 11 04:35:50 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./python-cogent_1.9-14.dsc dpkg-source: info: extracting python-cogent in python-cogent-1.9 dpkg-source: info: unpacking python-cogent_1.9.orig.tar.gz dpkg-source: info: unpacking python-cogent_1.9-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying accept_newer_cdhit.patch dpkg-source: info: applying fix_python_shebang_line.patch dpkg-source: info: applying parsinsert_not_in_caps.patch dpkg-source: info: applying fasttree_not_in_caps.patch dpkg-source: info: applying raxml_unsupported_version.patch dpkg-source: info: applying cd-hit-test.patch dpkg-source: info: applying rdp_classifier.patch dpkg-source: info: applying skip_weak_tests.patch dpkg-source: info: applying adapt_to_ncbi-data_201609.patch dpkg-source: info: applying ignore_numpy_test_issue.patch dpkg-source: info: applying usr_bin_ls.patch dpkg-source: info: applying numpy_xor.patch dpkg-source: info: applying numpy-doctests.patch dpkg-source: info: applying privacy.patch dpkg-source: info: applying matplotlib-2.2.3.patch dpkg-source: info: applying sphinx.ext.pngmath.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/18050/tmp/hooks/D01_modify_environment starting debug: Running on profitbricks-build12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/18050/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/18050/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=2f8b6ad10a984a56bf131e4f6787f318 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=18050 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Cm7FC7TsEL/pbuilderrc_F5tF --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Cm7FC7TsEL/b2 --logfile b2/build.log python-cogent_1.9-14.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 GNU/Linux I: ls -l /bin total 5484 -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash -rwxr-xr-x 1 root root 120676 Mar 1 2019 date -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd -rwxr-xr-x 1 root root 100620 Mar 1 2019 df -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 34532 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln -rwxr-xr-x 1 root root 55400 Jul 27 2018 login -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 10 2019 more -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 29 00:50 sh -> bash lrwxrwxrwx 1 root root 4 Jun 28 22:28 sh.distrib -> dash -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty -rwsr-xr-x 1 root root 71072 Jan 10 2019 su -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch -rwxr-xr-x 1 root root 34532 Mar 1 2019 true -rwxr-xr-x 1 root root 17768 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/18050/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, python-all-dev, python-matplotlib, python-numpy, python-setuptools, python3-sphinx, cython, blast2, cd-hit, cdbfasta, clearcut, clustalw, dialign, fasttree, infernal, mafft, mothur, muscle, parsinsert, raxml, rdp-classifier, rtax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python-all-dev; however: Package python-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python-matplotlib; however: Package python-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on cython; however: Package cython is not installed. pbuilder-satisfydepends-dummy depends on blast2; however: Package blast2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on cdbfasta; however: Package cdbfasta is not installed. pbuilder-satisfydepends-dummy depends on clearcut; however: Package clearcut is not installed. pbuilder-satisfydepends-dummy depends on clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on dialign; however: Package dialign is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on infernal; however: Package infernal is not installed. pbuilder-satisfydepends-dummy depends on mafft; however: Package mafft is not installed. pbuilder-satisfydepends-dummy depends on mothur; however: Package mothur is not installed. pbuilder-satisfydepends-dummy depends on muscle; however: Package muscle is not installed. pbuilder-satisfydepends-dummy depends on parsinsert; however: Package parsinsert is not installed. pbuilder-satisfydepends-dummy depends on raxml; however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on rdp-classifier; however: Package rdp-classifier is not installed. pbuilder-satisfydepends-dummy depends on rtax; however: Package rtax is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blast2{a} bsdmainutils{a} ca-certificates{a} ca-certificates-java{a} cd-hit{a} cdbfasta{a} clearcut{a} clustalw{a} cython{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dialign{a} docutils-common{a} dwz{a} fasttree{a} file{a} fontconfig-config{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} infernal{a} intltool-debian{a} java-common{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasound2{a} libasound2-data{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libbsd0{a} libcdi-api-java{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-parent-java{a} libcroco3{a} libcups2{a} libdbus-1-3{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfastinfoset-java{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgssapi-krb5-2{a} libguava-java{a} libguice-java{a} libhttpclient-java{a} libhttpcore-java{a} libicu63{a} libistack-commons-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoup-java{a} libjsr305-java{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} libllvm7{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libmpdec2{a} libncurses6{a} libnspr4{a} libnss3{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} librdp-taxonomy-tree-java{a} libreadline7{a} librelaxng-datatype-java{a} librngom-java{a} libsensors-config{a} libsensors5{a} libsigsegv2{a} libsisu-guice-java{a} libsisu-inject-java{a} libsisu-ioc-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssl1.1{a} libstax-ex-java{a} libstreambuffer-java{a} libtool{a} libtxw2-java{a} libuchardet0{a} libwagon-http-java{a} libwagon-provider-api-java{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-sync1{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} lsb-base{a} m4{a} mafft{a} man-db{a} mime-support{a} mothur{a} muscle{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} parsinsert{a} po-debconf{a} python{a} python-all{a} python-all-dev{a} python-babel-localedata{a} python-backports.functools-lru-cache{a} python-cycler{a} python-dateutil{a} python-dev{a} python-kiwisolver{a} python-matplotlib{a} python-matplotlib2-data{a} python-minimal{a} python-numpy{a} python-pkg-resources{a} python-pyparsing{a} python-setuptools{a} python-six{a} python-subprocess32{a} python-tz{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-requests{a} python3-roman{a} python3-six{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.7{a} python3.7-minimal{a} raxml{a} rdp-classifier{a} rdp-readseq{a} readline-common{a} rtax{a} sensible-utils{a} sgml-base{a} sphinx-common{a} ttf-bitstream-vera{a} ucf{a} x11-common{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: curl dbus fonts-dejavu-extra javascript-common krb5-locales libarchive-cpio-perl libasm-java libatk-wrapper-java-jni libcglib-java libglib2.0-data libgpm2 libjansi-java libltdl-dev libmail-sendmail-perl libpaper-utils libwww-perl lynx python-pil python-tk python3-pil rdp-classifier-doc ruby shared-mime-info wget xdg-user-dirs 0 packages upgraded, 274 newly installed, 0 to remove and 0 not upgraded. Need to get 219 MB of archives. After unpacking 858 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 libpython2.7-minimal i386 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main i386 python2.7-minimal i386 2.7.16-2+deb10u1 [1381 kB] Get: 9 http://deb.debian.org/debian buster/main i386 python2-minimal i386 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python-minimal i386 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython2.7-stdlib i386 2.7.16-2+deb10u1 [1934 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python2.7 i386 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython2-stdlib i386 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main i386 libpython-stdlib i386 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main i386 python2 i386 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main i386 python i386 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 libpython3.7-minimal i386 3.7.3-2+deb10u1 [590 kB] Get: 23 http://deb.debian.org/debian buster/main i386 python3.7-minimal i386 3.7.3-2+deb10u1 [1745 kB] Get: 24 http://deb.debian.org/debian buster/main i386 python3-minimal i386 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libmpdec2 i386 2.4.2-2 [83.2 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libpython3.7-stdlib i386 3.7.3-2+deb10u1 [1750 kB] Get: 27 http://deb.debian.org/debian buster/main i386 python3.7 i386 3.7.3-2+deb10u1 [330 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libpython3-stdlib i386 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main i386 python3 i386 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main i386 sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 33 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 34 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 35 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 36 http://deb.debian.org/debian buster/main i386 ucf all 3.0038+nmu1 [69.0 kB] Get: 37 http://deb.debian.org/debian buster/main i386 openssl i386 1.1.1d-0+deb10u3 [853 kB] Get: 38 http://deb.debian.org/debian buster/main i386 ca-certificates all 20190110 [157 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libnspr4 i386 2:4.20-1 [122 kB] Get: 40 http://deb.debian.org/debian buster/main i386 libnss3 i386 2:3.42.1-1+deb10u2 [1237 kB] Get: 41 http://deb.debian.org/debian buster/main i386 ca-certificates-java all 20190405 [15.7 kB] Get: 42 http://deb.debian.org/debian buster/main i386 java-common all 0.71 [14.4 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libavahi-common-data i386 0.7-4+b1 [122 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libavahi-common3 i386 0.7-4+b1 [56.2 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libdbus-1-3 i386 1.12.16-1 [226 kB] Get: 46 http://deb.debian.org/debian buster/main i386 libavahi-client3 i386 0.7-4+b1 [60.1 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libkeyutils1 i386 1.6-6 [15.4 kB] Get: 48 http://deb.debian.org/debian buster/main i386 libkrb5support0 i386 1.17-3 [68.6 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libk5crypto3 i386 1.17-3 [126 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libkrb5-3 i386 1.17-3 [396 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libgssapi-krb5-2 i386 1.17-3 [168 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libcups2 i386 2.2.10-6+deb10u3 [338 kB] Get: 53 http://deb.debian.org/debian buster/main i386 liblcms2-2 i386 2.9-3 [156 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo i386 1:1.5.2-2+b1 [142 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libpng16-16 i386 1.6.36-6 [301 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libfreetype6 i386 2.9.1-3+deb10u1 [395 kB] Get: 57 http://deb.debian.org/debian buster/main i386 ttf-bitstream-vera all 1.10-8 [352 kB] Get: 58 http://deb.debian.org/debian buster/main i386 fontconfig-config all 2.13.1-2 [280 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libfontconfig1 i386 2.13.1-2 [357 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libasound2-data all 1.1.8-1 [59.6 kB] Get: 61 http://deb.debian.org/debian buster/main i386 libasound2 i386 1.1.8-1 [382 kB] Get: 62 http://deb.debian.org/debian buster/main i386 libpcsclite1 i386 1.8.24-1 [60.0 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libxau6 i386 1:1.0.8-1+b2 [20.3 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 65 http://deb.debian.org/debian buster/main i386 libxcb1 i386 1.13.1-2 [141 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libx11-data all 2:1.6.7-1 [298 kB] Get: 67 http://deb.debian.org/debian buster/main i386 libx11-6 i386 2:1.6.7-1 [778 kB] Get: 68 http://deb.debian.org/debian buster/main i386 libxext6 i386 2:1.3.3-1+b2 [55.2 kB] Get: 69 http://deb.debian.org/debian buster/main i386 libxi6 i386 2:1.7.9-1 [85.2 kB] Get: 70 http://deb.debian.org/debian buster/main i386 libxrender1 i386 1:0.9.10-1 [34.1 kB] Get: 71 http://deb.debian.org/debian buster/main i386 lsb-base all 10.2019051400 [28.4 kB] Get: 72 http://deb.debian.org/debian buster/main i386 x11-common all 1:7.7+19 [251 kB] Get: 73 http://deb.debian.org/debian buster/main i386 libxtst6 i386 2:1.2.3-1 [28.3 kB] Get: 74 http://deb.debian.org/debian buster/main i386 openjdk-11-jre-headless i386 11.0.6+10-1~deb10u1 [36.9 MB] Get: 75 http://deb.debian.org/debian buster/main i386 default-jre-headless i386 2:1.11-71 [10.9 kB] Get: 76 http://deb.debian.org/debian buster/main i386 ant all 1.10.5-2 [2082 kB] Get: 77 http://deb.debian.org/debian buster/main i386 ant-optional all 1.10.5-2 [379 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 79 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 80 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 81 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 82 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 83 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 84 http://deb.debian.org/debian buster/main i386 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 85 http://deb.debian.org/debian buster/main i386 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 86 http://deb.debian.org/debian buster/main i386 liblmdb0 i386 0.9.22-1 [46.3 kB] Get: 87 http://deb.debian.org/debian buster/main i386 libmbedcrypto3 i386 2.16.0-1 [222 kB] Get: 88 http://deb.debian.org/debian buster/main i386 libmbedx509-0 i386 2.16.0-1 [93.0 kB] Get: 89 http://deb.debian.org/debian buster/main i386 libmbedtls12 i386 2.16.0-1 [133 kB] Get: 90 http://deb.debian.org/debian buster/main i386 ncbi-blast+ i386 2.8.1-1+deb10u1 [11.7 MB] Get: 91 http://deb.debian.org/debian buster/main i386 ncbi-blast+-legacy all 2.8.1-1+deb10u1 [10.6 kB] Get: 92 http://deb.debian.org/debian buster/main i386 blast2 all 1:2.8.1-1+deb10u1 [10.1 kB] Get: 93 http://deb.debian.org/debian buster/main i386 cd-hit i386 4.6.8-2 [520 kB] Get: 94 http://deb.debian.org/debian buster/main i386 cdbfasta i386 0.99-20100722-5 [60.0 kB] Get: 95 http://deb.debian.org/debian buster/main i386 clearcut i386 1.0.9-3 [280 kB] Get: 96 http://deb.debian.org/debian buster/main i386 clustalw i386 2.1+lgpl-6 [301 kB] Get: 97 http://deb.debian.org/debian buster/main i386 cython i386 0.29.2-2 [1275 kB] Get: 98 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 99 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 100 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 101 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 102 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 103 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 104 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 105 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 106 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 107 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 108 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 109 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 110 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 111 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 112 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 113 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 114 http://deb.debian.org/debian buster/main i386 libglvnd0 i386 1.1.0-1 [41.9 kB] Get: 115 http://deb.debian.org/debian buster/main i386 libdrm-common all 2.4.97-1 [13.8 kB] Get: 116 http://deb.debian.org/debian buster/main i386 libdrm2 i386 2.4.97-1 [42.5 kB] Get: 117 http://deb.debian.org/debian buster/main i386 libglapi-mesa i386 18.3.6-2+deb10u1 [66.9 kB] Get: 118 http://deb.debian.org/debian buster/main i386 libx11-xcb1 i386 2:1.6.7-1 [190 kB] Get: 119 http://deb.debian.org/debian buster/main i386 libxcb-dri2-0 i386 1.13.1-2 [101 kB] Get: 120 http://deb.debian.org/debian buster/main i386 libxcb-dri3-0 i386 1.13.1-2 [101 kB] Get: 121 http://deb.debian.org/debian buster/main i386 libxcb-glx0 i386 1.13.1-2 [117 kB] Get: 122 http://deb.debian.org/debian buster/main i386 libxcb-present0 i386 1.13.1-2 [99.4 kB] Get: 123 http://deb.debian.org/debian buster/main i386 libxcb-sync1 i386 1.13.1-2 [103 kB] Get: 124 http://deb.debian.org/debian buster/main i386 libxfixes3 i386 1:5.0.3-1 [22.4 kB] Get: 125 http://deb.debian.org/debian buster/main i386 libxdamage1 i386 1:1.1.4-3+b3 [15.0 kB] Get: 126 http://deb.debian.org/debian buster/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 127 http://deb.debian.org/debian buster/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 128 http://deb.debian.org/debian buster/main i386 libdrm-amdgpu1 i386 2.4.97-1 [30.1 kB] Get: 129 http://deb.debian.org/debian buster/main i386 libpciaccess0 i386 0.14-1 [55.7 kB] Get: 130 http://deb.debian.org/debian buster/main i386 libdrm-intel1 i386 2.4.97-1 [72.9 kB] Get: 131 http://deb.debian.org/debian buster/main i386 libdrm-nouveau2 i386 2.4.97-1 [28.0 kB] Get: 132 http://deb.debian.org/debian buster/main i386 libdrm-radeon1 i386 2.4.97-1 [32.5 kB] Get: 133 http://deb.debian.org/debian buster/main i386 libedit2 i386 3.1-20181209-1 [98.2 kB] Get: 134 http://deb.debian.org/debian buster/main i386 libllvm7 i386 1:7.0.1-8 [13.0 MB] Get: 135 http://deb.debian.org/debian buster/main i386 libsensors-config all 1:3.5.0-3 [31.6 kB] Get: 136 http://deb.debian.org/debian buster/main i386 libsensors5 i386 1:3.5.0-3 [53.5 kB] Get: 137 http://deb.debian.org/debian buster/main i386 libgl1-mesa-dri i386 18.3.6-2+deb10u1 [7102 kB] Get: 138 http://deb.debian.org/debian buster/main i386 libglx-mesa0 i386 18.3.6-2+deb10u1 [187 kB] Get: 139 http://deb.debian.org/debian buster/main i386 libglx0 i386 1.1.0-1 [31.3 kB] Get: 140 http://deb.debian.org/debian buster/main i386 libgl1 i386 1.1.0-1 [83.1 kB] Get: 141 http://deb.debian.org/debian buster/main i386 libgif7 i386 5.1.4-3 [44.4 kB] Get: 142 http://deb.debian.org/debian buster/main i386 openjdk-11-jre i386 11.0.6+10-1~deb10u1 [34.8 kB] Get: 143 http://deb.debian.org/debian buster/main i386 default-jre i386 2:1.11-71 [1044 B] Get: 144 http://deb.debian.org/debian buster/main i386 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 145 http://deb.debian.org/debian buster/main i386 python3-distutils all 3.7.3-1 [142 kB] Get: 146 http://deb.debian.org/debian buster/main i386 dh-python all 3.20190308 [99.3 kB] Get: 147 http://deb.debian.org/debian buster/main i386 dialign i386 2.2.1-10 [141 kB] Get: 148 http://deb.debian.org/debian buster/main i386 xml-core all 0.18+nmu1 [23.8 kB] Get: 149 http://deb.debian.org/debian buster/main i386 docutils-common all 0.14+dfsg-4 [167 kB] Get: 150 http://deb.debian.org/debian buster/main i386 fasttree i386 2.1.10-2 [177 kB] Get: 151 http://deb.debian.org/debian buster/main i386 fonts-lyx all 2.3.2-1 [199 kB] Get: 152 http://deb.debian.org/debian buster/main i386 infernal i386 1.1.2-2 [19.9 MB] Get: 153 http://deb.debian.org/debian buster/main i386 libactivation-java all 1.2.0-2 [84.7 kB] Get: 154 http://deb.debian.org/debian buster/main i386 libaopalliance-java all 20070526-6 [9048 B] Get: 155 http://deb.debian.org/debian buster/main i386 libapache-pom-java all 18-1 [4676 B] Get: 156 http://deb.debian.org/debian buster/main i386 libargs4j-java all 2.33-1 [139 kB] Get: 157 http://deb.debian.org/debian buster/main i386 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 158 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 159 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 160 http://deb.debian.org/debian buster/main i386 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 161 http://deb.debian.org/debian buster/main i386 libcdi-api-java all 1.2-2 [54.5 kB] Get: 162 http://deb.debian.org/debian buster/main i386 libjaxen-java all 1.1.6-4 [214 kB] Get: 163 http://deb.debian.org/debian buster/main i386 libdom4j-java all 2.1.1-2 [310 kB] Get: 164 http://deb.debian.org/debian buster/main i386 libcommons-parent-java all 43-1 [10.8 kB] Get: 165 http://deb.debian.org/debian buster/main i386 libcommons-io-java all 2.6-2 [213 kB] Get: 166 http://deb.debian.org/debian buster/main i386 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get: 167 http://deb.debian.org/debian buster/main i386 libcommons-cli-java all 1.4-1 [55.2 kB] Get: 168 http://deb.debian.org/debian buster/main i386 libcommons-lang3-java all 3.8-2 [478 kB] Get: 169 http://deb.debian.org/debian buster/main i386 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get: 170 http://deb.debian.org/debian buster/main i386 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 171 http://deb.debian.org/debian buster/main i386 libguava-java all 19.0-1 [2028 kB] Get: 172 http://deb.debian.org/debian buster/main i386 libguice-java all 4.2.1-1 [962 kB] Get: 173 http://deb.debian.org/debian buster/main i386 libmaven-parent-java all 31-2 [5100 B] Get: 174 http://deb.debian.org/debian buster/main i386 libplexus-utils2-java all 3.1.1-1 [249 kB] Get: 175 http://deb.debian.org/debian buster/main i386 libwagon-provider-api-java all 3.3.1-2 [50.1 kB] Get: 176 http://deb.debian.org/debian buster/main i386 libmaven-resolver-java all 1.3.1-1 [549 kB] Get: 177 http://deb.debian.org/debian buster/main i386 libplexus-cipher-java all 1.7-3 [15.0 kB] Get: 178 http://deb.debian.org/debian buster/main i386 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 179 http://deb.debian.org/debian buster/main i386 libplexus-component-annotations-java all 1.7.1-7 [7536 B] Get: 180 http://deb.debian.org/debian buster/main i386 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get: 181 http://deb.debian.org/debian buster/main i386 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 182 http://deb.debian.org/debian buster/main i386 libslf4j-java all 1.7.25-3 [143 kB] Get: 183 http://deb.debian.org/debian buster/main i386 libsisu-inject-java all 0.3.3-1 [347 kB] Get: 184 http://deb.debian.org/debian buster/main i386 libsisu-plexus-java all 0.3.3-3 [182 kB] Get: 185 http://deb.debian.org/debian buster/main i386 libmaven3-core-java all 3.6.0-1 [1465 kB] Get: 186 http://deb.debian.org/debian buster/main i386 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 187 http://deb.debian.org/debian buster/main i386 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 188 http://deb.debian.org/debian buster/main i386 libcommons-compress-java all 1.18-2 [530 kB] Get: 189 http://deb.debian.org/debian buster/main i386 libplexus-io-java all 3.1.1-1 [64.6 kB] Get: 190 http://deb.debian.org/debian buster/main i386 libsnappy1v5 i386 1.1.7-1 [18.0 kB] Get: 191 http://deb.debian.org/debian buster/main i386 libsnappy-jni i386 1.1.7.2-1 [7236 B] Get: 192 http://deb.debian.org/debian buster/main i386 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get: 193 http://deb.debian.org/debian buster/main i386 libxz-java all 1.8-2 [141 kB] Get: 194 http://deb.debian.org/debian buster/main i386 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 195 http://deb.debian.org/debian buster/main i386 libsisu-guice-java all 4.2.0-1 [785 kB] Get: 196 http://deb.debian.org/debian buster/main i386 libsisu-ioc-java all 2.3.0-11 [492 kB] Get: 197 http://deb.debian.org/debian buster/main i386 libhttpcore-java all 4.4.11-1 [625 kB] Get: 198 http://deb.debian.org/debian buster/main i386 libcommons-codec-java all 1.11-1 [271 kB] Get: 199 http://deb.debian.org/debian buster/main i386 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 200 http://deb.debian.org/debian buster/main i386 libhttpclient-java all 4.5.7-1 [721 kB] Get: 201 http://deb.debian.org/debian buster/main i386 libjsoup-java all 1.10.2-2 [350 kB] Get: 202 http://deb.debian.org/debian buster/main i386 libwagon-http-java all 3.3.1-2 [50.5 kB] Get: 203 http://deb.debian.org/debian buster/main i386 libistack-commons-java all 3.0.6-3 [144 kB] Get: 204 http://deb.debian.org/debian buster/main i386 libcodemodel-java all 2.6+jaxb2.3.0.1-8 [163 kB] Get: 205 http://deb.debian.org/debian buster/main i386 libcommons-lang-java all 2.6-8 [273 kB] Get: 206 http://deb.debian.org/debian buster/main i386 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get: 207 http://deb.debian.org/debian buster/main i386 libexpat1-dev i386 2.2.6-2+deb10u1 [156 kB] Get: 208 http://deb.debian.org/debian buster/main i386 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 209 http://deb.debian.org/debian buster/main i386 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 210 http://deb.debian.org/debian buster/main i386 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get: 211 http://deb.debian.org/debian buster/main i386 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get: 212 http://deb.debian.org/debian buster/main i386 libxsom-java all 2.3.0.1-8 [396 kB] Get: 213 http://deb.debian.org/debian buster/main i386 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 214 http://deb.debian.org/debian buster/main i386 librngom-java all 2.3.0.1-8 [288 kB] Get: 215 http://deb.debian.org/debian buster/main i386 libtxw2-java all 2.3.0.1-8 [134 kB] Get: 216 http://deb.debian.org/debian buster/main i386 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get: 217 http://deb.debian.org/debian buster/main i386 libjaxb-java all 2.3.0.1-8 [1966 kB] Get: 218 http://deb.debian.org/debian buster/main i386 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 219 http://deb.debian.org/debian buster/main i386 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get: 220 http://deb.debian.org/debian buster/main i386 libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 221 http://deb.debian.org/debian buster/main i386 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 222 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 223 http://deb.debian.org/debian buster/main i386 libpython2.7 i386 2.7.16-2+deb10u1 [1059 kB] Get: 224 http://deb.debian.org/debian buster/main i386 libpython2.7-dev i386 2.7.16-2+deb10u1 [31.4 MB] Get: 225 http://deb.debian.org/debian buster/main i386 libpython2-dev i386 2.7.16-1 [20.9 kB] Get: 226 http://deb.debian.org/debian buster/main i386 libpython-dev i386 2.7.16-1 [20.9 kB] Get: 227 http://deb.debian.org/debian buster/main i386 libpython-all-dev i386 2.7.16-1 [1068 B] Get: 228 http://deb.debian.org/debian buster/main i386 librdp-taxonomy-tree-java all 1.2.0-3 [17.8 kB] Get: 229 http://deb.debian.org/debian buster/main i386 mafft i386 7.407-2 [908 kB] Get: 230 http://deb.debian.org/debian buster/main i386 mothur i386 1.41.21-1 [5158 kB] Get: 231 http://deb.debian.org/debian buster/main i386 muscle i386 1:3.8.1551-2 [232 kB] Get: 232 http://deb.debian.org/debian buster/main i386 parsinsert i386 1.04-4 [69.2 kB] Get: 233 http://deb.debian.org/debian buster/main i386 python-all i386 2.7.16-1 [1044 B] Get: 234 http://deb.debian.org/debian buster/main i386 python2.7-dev i386 2.7.16-2+deb10u1 [295 kB] Get: 235 http://deb.debian.org/debian buster/main i386 python2-dev i386 2.7.16-1 [1208 B] Get: 236 http://deb.debian.org/debian buster/main i386 python-dev i386 2.7.16-1 [1184 B] Get: 237 http://deb.debian.org/debian buster/main i386 python-all-dev i386 2.7.16-1 [1068 B] Get: 238 http://deb.debian.org/debian buster/main i386 python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 239 http://deb.debian.org/debian buster/main i386 python-backports.functools-lru-cache all 1.5-3 [6704 B] Get: 240 http://deb.debian.org/debian buster/main i386 python-six all 1.12.0-1 [15.7 kB] Get: 241 http://deb.debian.org/debian buster/main i386 python-cycler all 0.10.0-1 [7448 B] Get: 242 http://deb.debian.org/debian buster/main i386 python-dateutil all 2.7.3-3 [76.8 kB] Get: 243 http://deb.debian.org/debian buster/main i386 python-pkg-resources all 40.8.0-1 [182 kB] Get: 244 http://deb.debian.org/debian buster/main i386 python-kiwisolver i386 1.0.1-2+b1 [76.3 kB] Get: 245 http://deb.debian.org/debian buster/main i386 python-matplotlib2-data all 2.2.3-6 [4124 kB] Get: 246 http://deb.debian.org/debian buster/main i386 python-pyparsing all 2.2.0+dfsg1-2 [89.5 kB] Get: 247 http://deb.debian.org/debian buster/main i386 python-tz all 2019.1-1 [33.6 kB] Get: 248 http://deb.debian.org/debian buster/main i386 python-numpy i386 1:1.16.2-1 [2096 kB] Get: 249 http://deb.debian.org/debian buster/main i386 python-subprocess32 i386 3.5.3-1 [30.1 kB] Get: 250 http://deb.debian.org/debian buster/main i386 python-matplotlib i386 2.2.3-6 [5092 kB] Get: 251 http://deb.debian.org/debian buster/main i386 python-setuptools all 40.8.0-1 [382 kB] Get: 252 http://deb.debian.org/debian buster/main i386 python3-alabaster all 0.7.8-1 [18.4 kB] Get: 253 http://deb.debian.org/debian buster/main i386 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 254 http://deb.debian.org/debian buster/main i386 python3-tz all 2019.1-1 [27.1 kB] Get: 255 http://deb.debian.org/debian buster/main i386 python3-babel all 2.6.0+dfsg.1-1 [96.7 kB] Get: 256 http://deb.debian.org/debian buster/main i386 python3-certifi all 2018.8.24-1 [140 kB] Get: 257 http://deb.debian.org/debian buster/main i386 python3-chardet all 3.0.4-3 [80.5 kB] Get: 258 http://deb.debian.org/debian buster/main i386 python3-roman all 2.0.0-3 [8768 B] Get: 259 http://deb.debian.org/debian buster/main i386 python3-docutils all 0.14+dfsg-4 [378 kB] Get: 260 http://deb.debian.org/debian buster/main i386 python3-idna all 2.6-1 [34.3 kB] Get: 261 http://deb.debian.org/debian buster/main i386 python3-imagesize all 1.0.0-1 [4960 B] Get: 262 http://deb.debian.org/debian buster/main i386 python3-markupsafe i386 1.1.0-1 [15.0 kB] Get: 263 http://deb.debian.org/debian buster/main i386 python3-jinja2 all 2.10-2 [106 kB] Get: 264 http://deb.debian.org/debian buster/main i386 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 265 http://deb.debian.org/debian buster/main i386 python3-six all 1.12.0-1 [15.7 kB] Get: 266 http://deb.debian.org/debian buster/main i386 python3-packaging all 19.0-1 [20.5 kB] Get: 267 http://deb.debian.org/debian buster/main i386 python3-pygments all 2.3.1+dfsg-1 [594 kB] Get: 268 http://deb.debian.org/debian buster/main i386 python3-urllib3 all 1.24.1-1 [97.1 kB] Get: 269 http://deb.debian.org/debian buster/main i386 python3-requests all 2.21.0-1 [66.9 kB] Get: 270 http://deb.debian.org/debian buster/main i386 sphinx-common all 1.8.4-1 [500 kB] Get: 271 http://deb.debian.org/debian buster/main i386 python3-sphinx all 1.8.4-1 [481 kB] Get: 272 http://deb.debian.org/debian buster/main i386 raxml i386 8.2.12+dfsg-1 [1199 kB] Get: 273 http://deb.debian.org/debian buster/main i386 rdp-readseq all 2.0.2-6 [453 kB] Get: 274 http://deb.debian.org/debian buster/main i386 rdp-classifier all 2.10.2-4 [227 kB] Get: 275 http://deb.debian.org/debian buster/main i386 rtax all 0.984-6 [26.2 kB] Fetched 218 MB in 36min 32s (99.3 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:i386. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking libpython2.7-minimal:i386 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_i386.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_i386.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_i386.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:i386. Preparing to unpack .../14-libreadline7_7.0-5_i386.deb ... Unpacking libreadline7:i386 (7.0-5) ... 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Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u1_i386.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libssl1.1:i386 (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:i386 (3.7.3-2+deb10u1) ... Setting up libexpat1:i386 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20986 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_i386.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../libmpdec2_2.4.2-2_i386.deb ... Unpacking libmpdec2:i386 (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:i386. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u1_i386.deb ... Unpacking libpython3.7-stdlib:i386 (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u1_i386.deb ... Unpacking python3.7 (3.7.3-2+deb10u1) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../libpython3-stdlib_3.7.3-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21398 files and directories currently installed.) Preparing to unpack .../000-python3_3.7.3-1_i386.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... 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Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.5.0-3) ... Setting up libmagic1:i386 (1:5.35-4+deb10u1) ... Setting up parsinsert (1.04-4) ... Setting up gettext-base (0.19.8.1-9) ... Setting up libplexus-component-annotations-java (1.7.1-7) ... Setting up file (1:5.35-4+deb10u1) ... Setting up muscle (1:3.8.1551-2) ... Setting up libicu63:i386 (63.1-6+deb10u1) ... Setting up python-babel-localedata (2.6.0+dfsg.1-1) ... Setting up libplexus-cipher-java (1.7-3) ... Setting up libsnappy1v5:i386 (1.1.7-1) ... Setting up libkrb5support0:i386 (1.17-3) ... Setting up libgeronimo-annotation-1.3-spec-java (1.0-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4) ... Setting up libasound2-data (1.1.8-1) ... Setting up cdbfasta (0.99-20100722-5) ... Setting up infernal (1.1.2-2) ... Setting up librdp-taxonomy-tree-java (1.2.0-3) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:i386 (2.2.6-2+deb10u1) ... Setting up libjpeg62-turbo:i386 (1:1.5.2-2+b1) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libnspr4:i386 (2:4.20-1) ... Setting up libapache-pom-java (18-1) ... Setting up libavahi-common-data:i386 (0.7-4+b1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libdbus-1-3:i386 (1.12.16-1) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libplexus-interpolation-java (1.25-1) ... Setting up libpng16-16:i386 (1.6.36-6) ... Setting up libxml-commons-resolver1.1-java (1.2-9) ... Setting up libxz-java (1.8-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libpcsclite1:i386 (1.8.24-1) ... Setting up libsensors5:i386 (1:3.5.0-3) ... Setting up libk5crypto3:i386 (1.17-3) ... Setting up libactivation-java (1.2.0-2) ... Setting up libglapi-mesa:i386 (18.3.6-2+deb10u1) ... Setting up libgfortran5:i386 (8.3.0-6) ... Setting up libgif7:i386 (5.1.4-3) ... Setting up python-matplotlib2-data (2.2.3-6) ... Setting up sensible-utils (0.0.12) ... Setting up libxshmfence1:i386 (1.3-1) ... Setting up libjsoup-java (1.10.2-2) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up libasound2:i386 (1.1.8-1) ... Setting up clustalw (2.1+lgpl-6) ... Setting up libmbedcrypto3:i386 (2.16.0-1) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up fasttree (2.1.10-2) ... Setting up sgml-base (1.29) ... Setting up libkrb5-3:i386 (1.17-3) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up libhttpcore-java (4.4.11-1) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up librelaxng-datatype-java (1.0+ds1-3) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libdrm-common (2.4.97-1) ... Setting up libcdi-api-java (1.2-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up libsnappy-jni (1.1.7.2-1) ... Setting up dialign (2.2.1-10) ... Setting up readline-common (7.0-5) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libargs4j-java (2.33-1) ... Setting up libreadline7:i386 (7.0-5) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up raxml (8.2.12+dfsg-1) ... Setting up clearcut (1.0.9-3) ... Setting up libdom4j-java (2.1.1-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up mothur (1.41.21-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libwagon-provider-api-java (3.3.1-2) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:i386 (3.7.3-2+deb10u1) ... Setting up libxcb1:i386 (1.13.1-2) ... Setting up libtool (2.4.6-9) ... Setting up libmbedx509-0:i386 (2.16.0-1) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:i386 (1.13.1-2) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:i386 (3.1-20181209-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libmbedtls12:i386 (2.16.0-1) ... Setting up libavahi-common3:i386 (0.7-4+b1) ... Setting up libcommons-logging-java (1.2-2) ... Setting up m4 (1.4.18-2) ... Setting up libnss3:i386 (2:3.42.1-1+deb10u2) ... Setting up libcommons-lang-java (2.6-8) ... Setting up libpython2.7-stdlib:i386 (2.7.16-2+deb10u1) ... Setting up libxcb-present0:i386 (1.13.1-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:i386 (2.9.1-3+deb10u1) ... Setting up libguava-java (19.0-1) ... Setting up libxcb-sync1:i386 (1.13.1-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libstreambuffer-java (1.5.4-1) ... Setting up libgssapi-krb5-2:i386 (1.17-3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up autoconf (2.69-11) ... Setting up libxcb-dri2-0:i386 (1.13.1-2) ... Setting up librngom-java (2.3.0.1-8) ... Setting up libdrm2:i386 (2.4.97-1) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up xml-core (0.18+nmu1) ... Setting up libllvm7:i386 (1:7.0.1-8) ... Setting up libx11-6:i386 (2:1.6.7-1) ... Setting up libsnappy-java (1.1.7.2-1) ... Setting up libxsom-java (2.3.0.1-8) ... Setting up libcommons-codec-java (1.11-1) ... Setting up libavahi-client3:i386 (0.7-4+b1) ... Setting up libpython3-stdlib:i386 (3.7.3-1) ... Setting up libdrm-amdgpu1:i386 (2.4.97-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:i386 (1.13.1-2) ... Setting up python3.7 (3.7.3-2+deb10u1) ... Setting up libpython2.7:i386 (2.7.16-2+deb10u1) ... Setting up liblapack3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libpython2.7-dev:i386 (2.7.16-2+deb10u1) ... Setting up libdrm-nouveau2:i386 (2.4.97-1) ... Setting up gettext (0.19.8.1-9) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:i386 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.18-2) ... Setting up libpython2-stdlib:i386 (2.7.16-1) ... Setting up libcommons-io-java (2.6-2) ... Setting up libdrm-radeon1:i386 (2.4.97-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libdrm-intel1:i386 (2.4.97-1) ... Setting up libgl1-mesa-dri:i386 (18.3.6-2+deb10u1) ... Setting up libxext6:i386 (2:1.3.3-1+b2) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (1.1.0-1) ... Setting up python2 (2.7.16-1) ... Setting up libguice-java (4.2.1-1) ... Setting up python3-tz (2019.1-1) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up libpython-stdlib:i386 (2.7.16-1) ... Setting up python3-roman (2.0.0-3) ... Setting up python3-jinja2 (2.10-2) ... Setting up python3-pygments (2.3.1+dfsg-1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-certifi (2018.8.24-1) ... Setting up libxfixes3:i386 (1:5.0.3-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up python3-idna (2.6-1) ... Setting up python3-urllib3 (1.24.1-1) ... Setting up libcups2:i386 (2.2.10-6+deb10u3) ... Setting up libhttpclient-java (4.5.7-1) ... Setting up libwagon-http-java (3.3.1-2) ... Setting up libpython2-dev:i386 (2.7.16-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfontconfig1:i386 (2.13.1-2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python (2.7.16-1) ... Setting up python3-imagesize (1.0.0-1) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up cython (0.29.2-2) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxdamage1:i386 (1:1.1.4-3+b3) ... Setting up python2-dev (2.7.16-1) ... Setting up libxi6:i386 (2:1.7.9-1) ... Setting up python3-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python-pkg-resources (40.8.0-1) ... Setting up python3-alabaster (0.7.8-1) ... Setting up libxtst6:i386 (2:1.2.3-1) ... Setting up po-debconf (1.0.21) ... Setting up libsisu-inject-java (0.3.3-1) ... Setting up python-all (2.7.16-1) ... Setting up libpython-dev:i386 (2.7.16-1) ... Setting up python-six (1.12.0-1) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up python-dateutil (2.7.3-3) ... Setting up python3-packaging (19.0-1) ... Setting up python3-chardet (3.0.4-3) ... Setting up python-subprocess32 (3.5.3-1) ... Setting up python3-requests (2.21.0-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python-backports.functools-lru-cache (1.5-3) ... Setting up python-tz (2019.1-1) ... Setting up python-kiwisolver (1.0.1-2+b1) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up python-dev (2.7.16-1) ... Setting up ncbi-blast+-legacy (2.8.1-1+deb10u1) ... Setting up libglx-mesa0:i386 (18.3.6-2+deb10u1) ... Setting up libglx0:i386 (1.1.0-1) ... Setting up libpython-all-dev:i386 (2.7.16-1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up libmaven3-core-java (3.6.0-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up python-cycler (0.10.0-1) ... Setting up libgl1:i386 (1.1.0-1) ... Setting up blast2 (1:2.8.1-1+deb10u1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up python-all-dev (2.7.16-1) ... Setting up python-matplotlib (2.2.3-6) ... Setting up dh-autoreconf (19) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre-headless:i386 (11.0.6+10-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode OpenJDK Client VM warning: Ignoring option PermSize; support was removed in 8.0 Setting up debhelper (12.1.1) ... Setting up openjdk-11-jre:i386 (11.0.6+10-1~deb10u1) ... Setting up default-jre (2:1.11-71) ... Setting up ant (1.10.5-2) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Comodo_AAA_Services_root.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:SecureTrust_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:DST_Root_CA_X3.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:Certigna.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Taiwan_GRCA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Izenpe.com.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:ACCVRAIZ1.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:ISRG_Root_X1.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:TrustCor_ECA-1.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:EC-ACC.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:AddTrust_External_Root.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem done. Setting up ant-optional (1.10.5-2) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-8) ... Setting up libtxw2-java (2.3.0.1-8) ... Setting up libjaxb-java (2.3.0.1-8) ... Setting up rdp-readseq (2.0.2-6) ... Setting up rdp-classifier (2.10.2-4) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/python-cogent-1.9/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 1.9-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with python2 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/evolve/_pairwise_distance.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/maths/_period.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/maths/spatial/ckd3.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/struct/_asa.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_asa.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/struct/_contact.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_contact.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' Compiling cogent/evolve/_pairwise_distance.pyx because it depends on /usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/struct/_asa.pyx because it depends on /usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/struct/_contact.pyx because it depends on /usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/maths/_period.pyx because it depends on /usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd. Compiling cogent/maths/spatial/ckd3.pyx because it depends on /usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd. [1/5] Cythonizing cogent/evolve/_pairwise_distance.pyx [2/5] Cythonizing cogent/maths/_period.pyx [3/5] Cythonizing cogent/maths/spatial/ckd3.pyx [4/5] Cythonizing cogent/struct/_asa.pyx [5/5] Cythonizing cogent/struct/_contact.pyx running clean removing '/build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build' (and everything under it) 'build/bdist.linux-i386' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/python-cogent-1.9' #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$f" | grep -q '^/\* Generated by Cython' && rm "$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean make[1]: Leaving directory '/build/python-cogent-1.9' debian/rules build dh build --with python2 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/align/_compare.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/align/_pairwise_pogs.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/align/_pairwise_seqs.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/evolve/_likelihood_tree.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/evolve/_pairwise_distance.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/evolve/_solved_models.pyx tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/evolve/_solved_models.pyx:15:23: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/evolve/_solved_models.pyx:15:33: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/evolve/_solved_models.pyx:15:40: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/evolve/_solved_models.pyx:15:51: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/evolve/_solved_models.pyx:16:26: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/maths/_period.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/maths/spatial/ckd3.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pyx:14:0: 'stdlib' is deprecated, use 'libc.stdlib' /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/struct/_asa.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_asa.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-cogent-1.9/cogent/struct/_contact.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cogent/maths/spatial/ckd3.pxd:17:11: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:17:18: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: cogent/maths/spatial/ckd3.pxd:19:21: Declarations should not be declared inline. warning: cogent/maths/spatial/ckd3.pxd:23:24: Declarations should not be declared inline. warning: cogent/struct/_contact.pyx:6:0: 'stdlib' is deprecated, use 'libc.stdlib' Compiling cogent/align/_compare.pyx because it changed. Compiling cogent/align/_pairwise_seqs.pyx because it changed. Compiling cogent/align/_pairwise_pogs.pyx because it changed. Compiling cogent/evolve/_solved_models.pyx because it changed. Compiling cogent/evolve/_likelihood_tree.pyx because it changed. Compiling cogent/evolve/_pairwise_distance.pyx because it changed. Compiling cogent/struct/_asa.pyx because it changed. Compiling cogent/struct/_contact.pyx because it changed. Compiling cogent/maths/_period.pyx because it changed. Compiling cogent/maths/spatial/ckd3.pyx because it changed. [ 1/10] Cythonizing cogent/align/_compare.pyx [ 2/10] Cythonizing cogent/align/_pairwise_pogs.pyx [ 3/10] Cythonizing cogent/align/_pairwise_seqs.pyx [ 4/10] Cythonizing cogent/evolve/_likelihood_tree.pyx [ 5/10] Cythonizing cogent/evolve/_pairwise_distance.pyx [ 6/10] Cythonizing cogent/evolve/_solved_models.pyx [ 7/10] Cythonizing cogent/maths/_period.pyx [ 8/10] Cythonizing cogent/maths/spatial/ckd3.pyx [ 9/10] Cythonizing cogent/struct/_asa.pyx [10/10] Cythonizing cogent/struct/_contact.pyx running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/python-cogent-1.9' dh_auto_build I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent copying cogent/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/align.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/algorithm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/indel_model.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/indel_positions.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/pairwise.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/pycompare.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/dp_calculation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/traceback.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align copying cogent/align/progressive.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights copying cogent/align/weights/methods.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights copying cogent/align/weights/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights copying cogent/align/weights/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/sffinfo.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/fastq_join.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/cmfinder.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/knetfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/carnac.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/dynalign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rtax.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/vienna_package.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/mothur.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/cdbfasta.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/flash.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/pplacer.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/comrna.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/seqprep.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/dialign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/formatdb.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/unafold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/raxml.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rnashapes.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/clearcut.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rdp_classifier.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/uclust.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rnaview.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/pknotsrg.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/msms.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/fasttree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/sfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/gctmpca.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/cd_hit.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/sfffile.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/muscle_v38.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/dotur.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/raxml_v730.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/usearch.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rnaalifold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/pfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rdp_classifier20.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/ilm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/consan.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/muscle.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/mafft.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/blat.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/clustalw.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/parsinsert.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/contrafold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/guppy.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/nupack.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/blast.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/rnaforester.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/fasttree_v1.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/pandaseq.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/infernal.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/parameters.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/foldalign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/mfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/stride.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/bwa.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app copying cogent/app/cove.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/approximate_mds.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/nmds.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/metric_scaling.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/goodness_of_fit.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/procrustes.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster copying cogent/cluster/UPGMA.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/location.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/usage.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/info.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/bitvector.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/entity.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/annotation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/alphabet.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/genetic_code.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/moltype.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/profile.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/alignment.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core copying cogent/core/sequence.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/nucleic_properties.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/energy_params.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/protein_properties.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/ligand_properties.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/molecular_weight.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data copying cogent/data/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db copying cogent/db/pdb.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db copying cogent/db/rfam.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db copying cogent/db/ncbi.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db copying cogent/db/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db copying cogent/db/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/feature_level.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/genome.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/related_region.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/assembly.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/region.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/species.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/host.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/name.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/compara.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/database.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/sequence.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl copying cogent/db/ensembl/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/dotplot.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/distribution_plots.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/rlg2mpl.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/compatibility.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/linear.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/fancy_arrow.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/arrow_rates.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/legend.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/codon_usage.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/dinuc.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/dendrogram.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw copying cogent/draw/multivariate_plot.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/solved_models.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/simulate.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/pairwise_distance.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/best_likelihood.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/coevolution.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/models.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/substitution_calculation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/likelihood_calculation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/motif_prob_model.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/substitution_model.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/bootstrap.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/parameter_controller.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/predicate.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/likelihood_tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/discrete_markov.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve copying cogent/evolve/likelihood_function.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/pdb_color.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/motif.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/phylip.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/table.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/fasta.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/pdb.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/clustal.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/bedgraph.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/structure.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/text_tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/alignment.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/xyzrn.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/nexus.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/rna_struct.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/stockholm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format copying cogent/format/mage.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/matrix_exponentiation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/fit_function.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/simannealingoptimiser.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/distance_transform.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/matrix_logarithm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/matrix_exponential_integration.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/optimisers.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/svd.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/scipy_optimisers.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/function_optimisation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/markov.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/period.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/solve.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/scipy_optimize.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths copying cogent/maths/geometry.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix copying cogent/maths/matrix/distance.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix copying cogent/maths/matrix/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/jackknife.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/distribution.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/rarefaction.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/alpha_diversity.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/kendall.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/test.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/period.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/histogram.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/information_criteria.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/ks.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats copying cogent/maths/stats/special.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai copying cogent/maths/stats/cai/adaptor.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai copying cogent/maths/stats/cai/get_by_cai.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai copying cogent/maths/stats/cai/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai copying cogent/maths/stats/cai/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac copying cogent/maths/unifrac/fast_tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac copying cogent/maths/unifrac/fast_unifrac.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac copying cogent/maths/unifrac/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/spatial copying cogent/maths/spatial/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/spatial creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif copying cogent/motif/k_word.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif copying cogent/motif/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif copying cogent/motif/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/kegg_pos.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/bowtie.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/locuslink.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/cmfinder.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/column.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/knetfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/flowgram.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/flowgram_collection.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/hmmscan.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/carnac.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/dynalign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/cigar.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/binary_sff.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/mothur.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/phylip.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/fastq.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/comrna.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/dialign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/unafold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/table.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/macsim.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/bpseq.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/tree_xml.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rnashapes.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/fasta.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/pdb.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rnaview.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rfam.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/pknotsrg.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/msms.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/cut.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/greengenes.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/sfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/clustal.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/kegg_fasta.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/gcg.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/aaindex.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rna_fold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/unigene.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/gbseq.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/kegg_taxonomy.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/ncbi_taxonomy.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/structure.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/dotur.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/gibbs.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/record.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rnaalifold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/pfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/tinyseq.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/meme.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/gff.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/psl.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/ilm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/consan.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/cutg.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/flowgram_parser.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/ct.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/ebi.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rdb.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/contrafold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/nupack.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/paml_matrix.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rna_plot.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/newick.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/blast.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/rnaforester.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/sequence.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/sprinzl.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/agilent_microarray.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/blast_xml.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/infernal.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/nexus.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/record_finder.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/stockholm.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/foldalign.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/kegg_ko.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/paml.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/mfold.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/stride.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/genbank.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/cove.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/mage.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse copying cogent/parse/illumina_sequence.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/consensus.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/nj.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/least_squares.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/tree_space.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/maximum_likelihood.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/distance.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo copying cogent/phylo/tree_collection.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation copying cogent/recalculation/setting.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation copying cogent/recalculation/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation copying cogent/recalculation/scope.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation copying cogent/recalculation/calculation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation copying cogent/recalculation/definition.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/usage.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/analysis.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/birth_death.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/markov.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/randomization.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/searchpath.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/microarray_normalize.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/tree.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/microarray.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim copying cogent/seqsim/sequence_generators.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/pairs_util.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/dihedral.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/rna2d.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/manipulation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/annotation.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/selection.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/contact.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/knots.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct copying cogent/struct/asa.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct creating /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/option_parsing.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/progress_display.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/dict_array.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/trie.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/table.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/dict2d.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/recode_alignment.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/parallel.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/transform.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/checkpointing.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/warning.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/modules.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/terminal.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/__init__.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/datatypes.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/update_version.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/misc.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/unit_test.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/array.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util copying cogent/util/organizer.py -> /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util running build_ext building 'cogent.align._compare' extension creating build creating build/temp.linux-i386-2.7 creating build/temp.linux-i386-2.7/cogent creating build/temp.linux-i386-2.7/cogent/align i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_compare.c -o build/temp.linux-i386-2.7/cogent/align/_compare.o i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/align/_compare.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_compare.so building 'cogent.align._pairwise_seqs' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_seqs.c -o build/temp.linux-i386-2.7/cogent/align/_pairwise_seqs.o cogent/align/_pairwise_seqs.c:2425:12: warning: '__pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:2295:12: warning: '__pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c: In function '__pyx_pw_6cogent_5align_14_pairwise_seqs_3calc_rows': cogent/align/_pairwise_seqs.c:6323:103: warning: '__pyx_v_max_exponent' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_seqs_SCALE_STEP) * __pyx_v_max_exponent)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3772:8: note: '__pyx_v_max_exponent' was declared here long __pyx_v_max_exponent; ^~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:6323:22: warning: '__pyx_v_mantissa' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_seqs_SCALE_STEP) * __pyx_v_max_exponent)); ^~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3766:10: note: '__pyx_v_mantissa' was declared here double __pyx_v_mantissa; ^~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:24225:20: warning: '__pyx_v_state' may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3734:7: note: '__pyx_v_state' was declared here int __pyx_v_state; ^~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:5822:295: warning: '__pyx_v_pointer_b' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_53 * __pyx_v_track.strides[0]) ) + __pyx_t_54 * __pyx_v_track.strides[1]) )) + __pyx_t_55)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3777:8: note: '__pyx_v_pointer_b' was declared here long __pyx_v_pointer_b; ^~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:5822:254: warning: '__pyx_v_pointer_a' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_53 * __pyx_v_track.strides[0]) ) + __pyx_t_54 * __pyx_v_track.strides[1]) )) + __pyx_t_55)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3776:8: note: '__pyx_v_pointer_a' was declared here long __pyx_v_pointer_a; ^~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/align/_pairwise_seqs.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_pairwise_seqs.so building 'cogent.align._pairwise_pogs' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_pogs.c -o build/temp.linux-i386-2.7/cogent/align/_pairwise_pogs.o cogent/align/_pairwise_pogs.c:2458:12: warning: '__pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:2328:12: warning: '__pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c: In function '__pyx_pw_6cogent_5align_14_pairwise_pogs_3calc_rows': cogent/align/_pairwise_pogs.c:6976:103: warning: '__pyx_v_max_exponent' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_pogs_SCALE_STEP) * __pyx_v_max_exponent)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3815:8: note: '__pyx_v_max_exponent' was declared here long __pyx_v_max_exponent; ^~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6976:22: warning: '__pyx_v_mantissa' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_pogs_SCALE_STEP) * __pyx_v_max_exponent)); ^~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3809:10: note: '__pyx_v_mantissa' was declared here double __pyx_v_mantissa; ^~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:24921:20: warning: '__pyx_v_state' may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3768:7: note: '__pyx_v_state' was declared here int __pyx_v_state; ^~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6476:295: warning: '__pyx_v_pointer_b' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_74 * __pyx_v_track.strides[0]) ) + __pyx_t_75 * __pyx_v_track.strides[1]) )) + __pyx_t_76)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3820:8: note: '__pyx_v_pointer_b' was declared here long __pyx_v_pointer_b; ^~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6476:254: warning: '__pyx_v_pointer_a' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_74 * __pyx_v_track.strides[0]) ) + __pyx_t_75 * __pyx_v_track.strides[1]) )) + __pyx_t_76)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3819:8: note: '__pyx_v_pointer_a' was declared here long __pyx_v_pointer_a; ^~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/align/_pairwise_pogs.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_pairwise_pogs.so building 'cogent.evolve._solved_models' extension creating build/temp.linux-i386-2.7/cogent/evolve i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_solved_models.c -o build/temp.linux-i386-2.7/cogent/evolve/_solved_models.o cogent/evolve/_solved_models.c:2426:12: warning: '__pyx_fuse_2__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_2__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, int *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_solved_models.c:2250:12: warning: '__pyx_fuse_1__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_solved_models.c:2120:12: warning: '__pyx_fuse_0__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/evolve/_solved_models.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_solved_models.so building 'cogent.evolve._likelihood_tree' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_likelihood_tree.c -o build/temp.linux-i386-2.7/cogent/evolve/_likelihood_tree.o cogent/evolve/_likelihood_tree.c:2307:12: warning: '__pyx_fuse_1__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_likelihood_tree.c:2177:12: warning: '__pyx_fuse_0__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/evolve/_likelihood_tree.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_likelihood_tree.so building 'cogent.evolve._pairwise_distance' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_pairwise_distance.c -o build/temp.linux-i386-2.7/cogent/evolve/_pairwise_distance.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/evolve/_pairwise_distance.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/evolve/_pairwise_distance.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_pairwise_distance.so building 'cogent.struct._asa' extension creating build/temp.linux-i386-2.7/cogent/struct i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_asa.c -o build/temp.linux-i386-2.7/cogent/struct/_asa.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_asa.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/struct/_asa.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/_asa.so building 'cogent.struct._contact' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_contact.c -o build/temp.linux-i386-2.7/cogent/struct/_contact.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_contact.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/struct/_contact.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/_contact.so building 'cogent.maths._period' extension creating build/temp.linux-i386-2.7/cogent/maths i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/_period.c -o build/temp.linux-i386-2.7/cogent/maths/_period.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/_period.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/maths/_period.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/_period.so building 'cogent.maths.spatial.ckd3' extension creating build/temp.linux-i386-2.7/cogent/maths/spatial i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/spatial/ckd3.c -o build/temp.linux-i386-2.7/cogent/maths/spatial/ckd3.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/spatial/ckd3.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-2.7/cogent/maths/spatial/ckd3.o -o /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/spatial/ckd3.so cd doc; /usr/bin/make html make[2]: Entering directory '/build/python-cogent-1.9/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.8.4 making output directory... building [mo]: targets for 0 po files that are out of date building [html]: targets for 95 source files that are out of date updating environment: 95 added, 0 changed, 0 removed reading sources... 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[100%] data/count_seqs.py copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in _build/html. Build finished. The HTML pages are in _build/html. make[2]: Leaving directory '/build/python-cogent-1.9/doc' # remove superfluous files and dirs find doc/_build -name "*.doctree*" -delete rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ make[1]: Leaving directory '/build/python-cogent-1.9' debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-cogent-1.9' cp -a tests/alltests.py tests/alltests.py~ # exclude tests known to fail for tst in test_infernal test_mothur test_parsinsert test_raxml_v730 test_rtax test_clustalw test_mafft test_unifrac test_seqsim.test_analysis test_seqsim.test_usage ; do sed -i "/${tst}/d" tests/alltests.py ; done for tst in test_bwa ; do sed -i "/${tst}/d" tests/alltests.py ; done for tst in test_maths.test_stats.test_test test_seqsim.test_sequence_generators ; do sed -i "/${tst}/d" tests/alltests.py ; done BLASTMAT=/usr/share/ncbi/data/ RDP_JAR_PATH=/usr/share/java/rdp_classifier.jar /build/python-cogent-1.9/run_tests -v # --debug running build_ext building 'cogent.align._compare' extension creating build/temp.linux-i686-2.7 creating build/temp.linux-i686-2.7/cogent creating build/temp.linux-i686-2.7/cogent/align i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_compare.c -o build/temp.linux-i686-2.7/cogent/align/_compare.o creating build/lib.linux-i686-2.7 creating build/lib.linux-i686-2.7/cogent creating build/lib.linux-i686-2.7/cogent/align i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_compare.o -o build/lib.linux-i686-2.7/cogent/align/_compare.so building 'cogent.align._pairwise_seqs' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_seqs.c -o build/temp.linux-i686-2.7/cogent/align/_pairwise_seqs.o cogent/align/_pairwise_seqs.c:2425:12: warning: '__pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:2295:12: warning: '__pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_seqs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c: In function '__pyx_pw_6cogent_5align_14_pairwise_seqs_3calc_rows': cogent/align/_pairwise_seqs.c:6323:103: warning: '__pyx_v_max_exponent' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_seqs_SCALE_STEP) * __pyx_v_max_exponent)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3772:8: note: '__pyx_v_max_exponent' was declared here long __pyx_v_max_exponent; ^~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:6323:22: warning: '__pyx_v_mantissa' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_seqs_SCALE_STEP) * __pyx_v_max_exponent)); ^~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3766:10: note: '__pyx_v_mantissa' was declared here double __pyx_v_mantissa; ^~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:24225:20: warning: '__pyx_v_state' may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3734:7: note: '__pyx_v_state' was declared here int __pyx_v_state; ^~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:5822:295: warning: '__pyx_v_pointer_b' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_53 * __pyx_v_track.strides[0]) ) + __pyx_t_54 * __pyx_v_track.strides[1]) )) + __pyx_t_55)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3777:8: note: '__pyx_v_pointer_b' was declared here long __pyx_v_pointer_b; ^~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:5822:254: warning: '__pyx_v_pointer_a' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_53 * __pyx_v_track.strides[0]) ) + __pyx_t_54 * __pyx_v_track.strides[1]) )) + __pyx_t_55)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_seqs.c:3776:8: note: '__pyx_v_pointer_a' was declared here long __pyx_v_pointer_a; ^~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_pairwise_seqs.o -o build/lib.linux-i686-2.7/cogent/align/_pairwise_seqs.so building 'cogent.align._pairwise_pogs' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/align/_pairwise_pogs.c -o build/temp.linux-i686-2.7/cogent/align/_pairwise_pogs.o cogent/align/_pairwise_pogs.c:2458:12: warning: '__pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:2328:12: warning: '__pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_5align_14_pairwise_pogs_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c: In function '__pyx_pw_6cogent_5align_14_pairwise_pogs_3calc_rows': cogent/align/_pairwise_pogs.c:6976:103: warning: '__pyx_v_max_exponent' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_pogs_SCALE_STEP) * __pyx_v_max_exponent)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3815:8: note: '__pyx_v_max_exponent' was declared here long __pyx_v_max_exponent; ^~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6976:22: warning: '__pyx_v_mantissa' may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_v_score = (log(__pyx_v_mantissa) + (log(__pyx_v_6cogent_5align_14_pairwise_pogs_SCALE_STEP) * __pyx_v_max_exponent)); ^~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3809:10: note: '__pyx_v_mantissa' was declared here double __pyx_v_mantissa; ^~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:24921:20: warning: '__pyx_v_state' may be used uninitialized in this function [-Wmaybe-uninitialized] return PyInt_FromLong((long) value); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3768:7: note: '__pyx_v_state' was declared here int __pyx_v_state; ^~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6476:295: warning: '__pyx_v_pointer_b' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_74 * __pyx_v_track.strides[0]) ) + __pyx_t_75 * __pyx_v_track.strides[1]) )) + __pyx_t_76)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3820:8: note: '__pyx_v_pointer_b' was declared here long __pyx_v_pointer_b; ^~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:6476:254: warning: '__pyx_v_pointer_a' may be used uninitialized in this function [-Wmaybe-uninitialized] *((unsigned char *) ( /* dim=2 */ ((char *) (((unsigned char *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_track.data + __pyx_t_74 * __pyx_v_track.strides[0]) ) + __pyx_t_75 * __pyx_v_track.strides[1]) )) + __pyx_t_76)) )) = (((__pyx_v_pointer_a << __pyx_v_tcode_x) | (__pyx_v_pointer_b << __pyx_v_tcode_y)) | (__pyx_v_pointer_state << __pyx_v_tcode_s)); ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ cogent/align/_pairwise_pogs.c:3819:8: note: '__pyx_v_pointer_a' was declared here long __pyx_v_pointer_a; ^~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/align/_pairwise_pogs.o -o build/lib.linux-i686-2.7/cogent/align/_pairwise_pogs.so building 'cogent.evolve._solved_models' extension creating build/temp.linux-i686-2.7/cogent/evolve i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_solved_models.c -o build/temp.linux-i686-2.7/cogent/evolve/_solved_models.o cogent/evolve/_solved_models.c:2426:12: warning: '__pyx_fuse_2__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_2__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, int *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_solved_models.c:2250:12: warning: '__pyx_fuse_1__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_solved_models.c:2120:12: warning: '__pyx_fuse_0__pyx_f_6cogent_6evolve_14_solved_models_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_6evolve_14_solved_models_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ creating build/lib.linux-i686-2.7/cogent/evolve i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_solved_models.o -o build/lib.linux-i686-2.7/cogent/evolve/_solved_models.so building 'cogent.evolve._likelihood_tree' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_likelihood_tree.c -o build/temp.linux-i686-2.7/cogent/evolve/_likelihood_tree.o cogent/evolve/_likelihood_tree.c:2307:12: warning: '__pyx_fuse_1__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_1__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, long *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cogent/evolve/_likelihood_tree.c:2177:12: warning: '__pyx_fuse_0__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim' defined but not used [-Wunused-function] static int __pyx_fuse_0__pyx_f_6cogent_6evolve_16_likelihood_tree_checkDim(PyObject *__pyx_v_dimension, Py_ssize_t __pyx_v_val, Py_ssize_t *__pyx_v_var) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_likelihood_tree.o -o build/lib.linux-i686-2.7/cogent/evolve/_likelihood_tree.so building 'cogent.evolve._pairwise_distance' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/evolve/_pairwise_distance.c -o build/temp.linux-i686-2.7/cogent/evolve/_pairwise_distance.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/evolve/_pairwise_distance.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/evolve/_pairwise_distance.o -o build/lib.linux-i686-2.7/cogent/evolve/_pairwise_distance.so building 'cogent.struct._asa' extension creating build/temp.linux-i686-2.7/cogent/struct i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_asa.c -o build/temp.linux-i686-2.7/cogent/struct/_asa.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_asa.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ creating build/lib.linux-i686-2.7/cogent/struct i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/struct/_asa.o -o build/lib.linux-i686-2.7/cogent/struct/_asa.so building 'cogent.struct._contact' extension i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/struct/_contact.c -o build/temp.linux-i686-2.7/cogent/struct/_contact.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/struct/_contact.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/struct/_contact.o -o build/lib.linux-i686-2.7/cogent/struct/_contact.so building 'cogent.maths._period' extension creating build/temp.linux-i686-2.7/cogent/maths i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/_period.c -o build/temp.linux-i686-2.7/cogent/maths/_period.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/_period.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ creating build/lib.linux-i686-2.7/cogent/maths i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/maths/_period.o -o build/lib.linux-i686-2.7/cogent/maths/_period.so building 'cogent.maths.spatial.ckd3' extension creating build/temp.linux-i686-2.7/cogent/maths/spatial i686-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cogent/maths/spatial/ckd3.c -o build/temp.linux-i686-2.7/cogent/maths/spatial/ckd3.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cogent/maths/spatial/ckd3.c:626: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ creating build/lib.linux-i686-2.7/cogent/maths/spatial i686-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-EBAgX8/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-cogent-1.9=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-2.7/cogent/maths/spatial/ckd3.o -o build/lib.linux-i686-2.7/cogent/maths/spatial/ckd3.so copying build/lib.linux-i686-2.7/cogent/align/_compare.so -> cogent/align copying build/lib.linux-i686-2.7/cogent/align/_pairwise_seqs.so -> cogent/align copying build/lib.linux-i686-2.7/cogent/align/_pairwise_pogs.so -> cogent/align copying build/lib.linux-i686-2.7/cogent/evolve/_solved_models.so -> cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/_likelihood_tree.so -> cogent/evolve copying build/lib.linux-i686-2.7/cogent/evolve/_pairwise_distance.so -> cogent/evolve copying build/lib.linux-i686-2.7/cogent/struct/_asa.so -> cogent/struct copying build/lib.linux-i686-2.7/cogent/struct/_contact.so -> cogent/struct copying build/lib.linux-i686-2.7/cogent/maths/_period.so -> cogent/maths copying build/lib.linux-i686-2.7/cogent/maths/spatial/ckd3.so -> cogent/maths/spatial Can't find blat executable: skipping test Can't find carnac executable: skipping test Can't find cmfinder.pl executable: skipping test Can't find comrna executable: skipping test Can't find contrafold executable: skipping test Can't find covea executable: skipping test Can't find dynalign executable: skipping test Can't find foldalign executable: skipping test Can't find guppy executable: skipping test Can't find ilm executable: skipping test Can't find knetfold.pl executable: skipping test Can't find mfold executable: skipping test Can't find msms executable: skipping test Can't find pplacer executable: skipping test Can't find rdp_classifier-2.2.jar executable: skipping test Can't find rdp_classifier-2.0.jar executable: skipping test Can't find Fold.out executable: skipping test Can't find findphyl executable: skipping test Can't find pknotsRG-1.2-i386-linux-static executable: skipping test Can't find RNAalifold executable: skipping test Can't find rnaview executable: skipping test Can't find RNAfold executable: skipping test Can't find sfold.X86_64.LINUX executable: skipping test Can't find stride executable: skipping test Can't find hybrid-ss-min executable: skipping test Can't find calculate_likelihood executable: skipping test Can't find sfffile executable: skipping test Can't find sffinfo executable: skipping test Can't find uclust executable: skipping test Can't find usearch executable: skipping test Environment variable TEST_DB=1 not set: skipping db tests test_recalculation.rst Doctest: test_recalculation.rst ... ok test_consensus_from_scored_trees_collection (test_phylo.ConsensusTests) tree collection should get same consensus as direct approach ... ok test_consensus_from_scored_trees_collection_ii (test_phylo.ConsensusTests) strict consensus should handle conflicting trees ... ok test_consensus_tree_branch_lengths (test_phylo.ConsensusTests) consensus trees should average branch lengths properly ... ok test_get_tree_get_splits (test_phylo.ConsensusTests) getTree should provide a reciprocal map of getSplits ... ok test_majorityRule (test_phylo.ConsensusTests) Tests for majority rule consensus trees ... ok test_tree_collection_read_write_file (test_phylo.ConsensusTests) should correctly read / write a collection from a file ... ok test_weighted_consensus_from_scored_trees_collection (test_phylo.ConsensusTests) weighted consensus from a tree collection should be different ... ok test_weighted_consensus_from_scored_trees_collection_ii (test_phylo.ConsensusTests) root positions in input tree collection should not effect result ... ok test_weighted_trees_satisyfing_cutoff (test_phylo.ConsensusTests) build consensus tree from those satisfying cutoff ... ok test_EstimateDistances (test_phylo.DistancesTests) testing (well, exercising at least), EstimateDistances ... ok test_EstimateDistancesWithMotifProbs (test_phylo.DistancesTests) EstimateDistances with supplied motif probs ... ok test_EstimateDistances_fromThreeway (test_phylo.DistancesTests) testing (well, exercising at least), EsimateDistances fromThreeway ... ok test_EstimateDistances_fromUnaligned (test_phylo.DistancesTests) Excercising estimate distances from unaligned sequences ... ok test_EstimateDistances_modify_lf (test_phylo.DistancesTests) tests modifying the lf ... ok test_EstimateDistances_other_model_params (test_phylo.DistancesTests) test getting other model params from EstimateDistances ... ok test_get_raw_estimates (test_phylo.DistancesTests) correctly return raw result object ... ok test_gnj (test_phylo.TreeReconstructionTests) testing gnj ... ok test_limited_wls (test_phylo.TreeReconstructionTests) testing (well, exercising at least), wls with constrained start ... ok test_nj (test_phylo.TreeReconstructionTests) testing nj ... ok test_truncated_wls (test_phylo.TreeReconstructionTests) testing wls with order option ... ok test_wls (test_phylo.TreeReconstructionTests) testing wls ... ok test_dictarray.rst Doctest: test_dictarray.rst ... ok test_codon (test_align.test_align.AlignmentTestCase) ... ok test_gap_at_one_end (test_align.test_align.AlignmentTestCase) ... ok test_gaps_at_both_ends (test_align.test_align.AlignmentTestCase) ... ok test_local (test_align.test_align.AlignmentTestCase) ... ok test_local_tiebreak (test_align.test_align.AlignmentTestCase) Should pick the first best-equal hit rather than the last one ... ok test_pairwise_returns_score (test_align.test_align.AlignmentTestCase) exercise pairwise local/global returns alignment score ... ok test_short (test_align.test_align.AlignmentTestCase) ... ok test_TreeAlign_does_pairs (test_align.test_align.HirschbergTestCase) test TreeAlign handles pairs of sequences ... ok test_difficult_end_gaps (test_align.test_align.HirschbergTestCase) ... ok test_gap_at_end (test_align.test_align.HirschbergTestCase) test progressive alignment, gaps at end ... ok test_gap_at_start (test_align.test_align.HirschbergTestCase) test progressive alignment, gaps at start ... ok test_gaps2 (test_align.test_align.HirschbergTestCase) Gaps have real costs, even end gaps ... ok test_progressive1 (test_align.test_align.HirschbergTestCase) test progressive alignment, gaps in middle ... ok test_progressive_est_tree (test_align.test_align.HirschbergTestCase) excercise progressive alignment without a guide tree ... ok test_progressive_params (test_align.test_align.HirschbergTestCase) excercise progressive alignment providing model params ... ok test_TreeAlign_does_pairs (test_align.test_align.MultipleAlignmentTestCase) test TreeAlign handles pairs of sequences ... ok test_difficult_end_gaps (test_align.test_align.MultipleAlignmentTestCase) ... ok test_gap_at_end (test_align.test_align.MultipleAlignmentTestCase) test progressive alignment, gaps at end ... ok test_gap_at_start (test_align.test_align.MultipleAlignmentTestCase) test progressive alignment, gaps at start ... ok test_gaps2 (test_align.test_align.MultipleAlignmentTestCase) Gaps have real costs, even end gaps ... ok test_progressive1 (test_align.test_align.MultipleAlignmentTestCase) test progressive alignment, gaps in middle ... ok test_progressive_est_tree (test_align.test_align.MultipleAlignmentTestCase) excercise progressive alignment without a guide tree ... ok test_progressive_params (test_align.test_align.MultipleAlignmentTestCase) excercise progressive alignment providing model params ... ok test_forward (test_align.test_align.UnalignedPairTestCase) ... ok test_scorer (test_align.test_algorithm.MatchScorerTests) Tests for MatchScorer function. ... ok test_fill (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix fill function. ... ok test_init_first_cell (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix _init_first_cell function. ... ok test_init_first_col (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix _init_first_col function. ... ok test_init_first_row (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix _init_first_row function. ... ok test_initialized_matrix (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix after full initialization. ... ok test_traceback (test_align.test_algorithm.NeedlemanWunschMatrixTests) Tests for NeedlemanWunschMatrix traceback function. ... ok test_nw_align (test_align.test_algorithm.NwAlignTests) Tests for nw_align function. ... ok test_nw_align_empty (test_align.test_algorithm.NwAlignTests) Tests for nw_align function. ... ok test_init (test_align.test_algorithm.ScoreCellTests) Tests for ScoreCell __init__ function. ... ok test_update (test_align.test_algorithm.ScoreCellTests) Tests for ScoreCell update function. ... ok test_alignment (test_align.test_algorithm.ScoreMatrixTests) Tests for ScoreMatrix alignment function. ... ok test_init (test_align.test_algorithm.ScoreMatrixTests) Tests for ScoreMatrix __init__ function. ... ok test_str (test_align.test_algorithm.ScoreMatrixTests) Tests for ScoreMatrix __str__ function. ... ok test_fill (test_align.test_algorithm.SmithWatermanMatrixTests) Tests for SmithWatermanMatrix fill function. ... ok test_traceback (test_align.test_algorithm.SmithWatermanMatrixTests) Tests for SmithWatermanMatrix traceback function. ... ok test_sw_align (test_align.test_algorithm.SwAlignTests) Tests for sw_align function. ... ok test_sw_align_empty (test_align.test_algorithm.SwAlignTests) Tests for sw_align function. ... ok test_ACL (test_align.test_weights.test_methods.AclTests) ACL: should return correct weights ... ok test_gsc (test_align.test_weights.test_methods.GscTests) GSC: should return correct weights ... ok test_PB (test_align.test_weights.test_methods.PositionBasedTests) PB: should return correct weights ... ok test_pos_char_weights (test_align.test_weights.test_methods.PositionBasedTests) pos_char_weights: should return correct contributions at each pos ... ok test_SS (test_align.test_weights.test_methods.SsTests) SS: should return the correct weights ... ok test_VA (test_align.test_weights.test_methods.VoronoiTests) VA: should return expected results. Results don't vary with runs ... ok test_VOR_exact (test_align.test_weights.test_methods.VoronoiTests) VOR: should give exact results when using pseudo_seqs_exact ... ok test_VOR_force_mc (test_align.test_weights.test_methods.VoronoiTests) VOR: should result in good approximation when using monte carlo ... ok test_VOR_mc_threshold (test_align.test_weights.test_methods.VoronoiTests) VOR: should apply monte carlo when # of pseudo seqs > mc_threshold ... ok test_AlignmentToProfile_basic (test_align.test_weights.test_util.UtilTests) AlignmentToProfile: should work under basic conditions ... ok test_AlignmentToProfile_ignore (test_align.test_weights.test_util.UtilTests) AlignmentToProfile: should raise an error if too many chars ignored ... ok test_AlignmentToProfile_weighted (test_align.test_weights.test_util.UtilTests) AlignmentToProfile: should work when sequences are weighted ... ok test_SeqToProfile (test_align.test_weights.test_util.UtilTests) SequenceToProfile: should work with different parameter settings ... ok test_distance_matrix (test_align.test_weights.test_util.UtilTests) distance_matrix should obey Names of alignment ... ok test_distance_to_closest (test_align.test_weights.test_util.UtilTests) distance_to_closest: should return closest distances ... ok test_eigenvector_for_largest_eigenvalue (test_align.test_weights.test_util.UtilTests) eigenvector_for_largest_eigenvalue: No idea how to test this ... ok test_number_of_pseudo_seqs (test_align.test_weights.test_util.UtilTests) number_of_pseudo_seqs: should return # of pseudo seqs ... ok test_pseudo_seqs_exact (test_align.test_weights.test_util.UtilTests) pseudo_seqs_exact: should generate expected pseudo sequences ... ok test_pseudo_seqs_monte_carlo (test_align.test_weights.test_util.UtilTests) pseudo_seqs_monte_carlo: random sample from all possible pseudo seqs ... ok test_row_to_vote (test_align.test_weights.test_util.UtilTests) row_to_vote: should return correct votes for int and float distances ... ok test_weights (test_align.test_weights.test_util.WeightsTests) Weights: should behave like a normal dict and can be normalized ... ok test_FilePath_identity_preserved (test_app.test_parameters.FilePathTests) FilePath: trivial actions on FilePaths yeild original FilePath ... ok test_add (test_app.test_parameters.FilePathTests) FilePath: add (or joining of paths) functions as expected ... ok test_init (test_app.test_parameters.FilePathTests) FilePath: initialization returns w/o error ... ok test_str (test_app.test_parameters.FilePathTests) FilePath: str wraps path in quotes ... ok test_str_path_is_None (test_app.test_parameters.FilePathTests) FilePath: str return empty string when path is None ... ok test_eq (test_app.test_parameters.FlagParameterTests) FlagParameter: eq functions as expected ... ok test_get_id (test_app.test_parameters.FlagParameterTests) FlagParameter: _get_id functions as expected ... ok test_init (test_app.test_parameters.FlagParameterTests) FlagParameter: init functions as expected ... ok test_init_defaults (test_app.test_parameters.FlagParameterTests) FlagParameter: init functions as expected with default values ... ok test_isOff_False (test_app.test_parameters.FlagParameterTests) FlagParameter: isOff functions as expected with False values ... ok test_isOff_True (test_app.test_parameters.FlagParameterTests) FlagParameter: isOff functions as expected with True values ... ok test_isOn_False (test_app.test_parameters.FlagParameterTests) FlagParameter: isOn functions as expected with False Values ... ok test_isOn_True (test_app.test_parameters.FlagParameterTests) FlagParameter: isOn functions as expected with True Values ... ok test_ne (test_app.test_parameters.FlagParameterTests) FlagParameter: ne functions as expected ... ok test_off (test_app.test_parameters.FlagParameterTests) FlagParameter: off functions as expected ... ok test_on (test_app.test_parameters.FlagParameterTests) FlagParameter: on functions as expected ... ok test_str_modify_name (test_app.test_parameters.FlagParameterTests) FlagParameter: str functions as expected with different names ... ok test_str_modify_prefix (test_app.test_parameters.FlagParameterTests) FlagParameter: str functions as expected with different prefixes ... ok test_eq (test_app.test_parameters.MixedParameterTests) Parameter: eq functions as expected ... ok test_get_default (test_app.test_parameters.MixedParameterTests) Parameter: default behaves as expected ... ok test_get_default_w_IsPath (test_app.test_parameters.MixedParameterTests) Parameter: default is a FilePath object when IsPath is set ... ok test_get_id (test_app.test_parameters.MixedParameterTests) Parameter: _get_id functions as expected ... ok test_init (test_app.test_parameters.MixedParameterTests) Parameter: init functions as expected ... ok test_init_defaults (test_app.test_parameters.MixedParameterTests) MixedParameter: init functions as expected with default values ... ok test_isOff_False (test_app.test_parameters.MixedParameterTests) Parameter: isOff functions as expected with False values ... ok test_isOff_True (test_app.test_parameters.MixedParameterTests) Parameter: isOff functions as expected with True values ... ok test_isOn_False (test_app.test_parameters.MixedParameterTests) Parameter: isOn functions as expected with False Values ... ok test_isOn_True (test_app.test_parameters.MixedParameterTests) Parameter: isOn functions as expected with True Values ... ok test_ne (test_app.test_parameters.MixedParameterTests) Parameter: ne functions as expected ... ok test_off (test_app.test_parameters.MixedParameterTests) Parameter: off functions as expected ... ok test_on (test_app.test_parameters.MixedParameterTests) Parameter: on functions as expected ... ok test_reset (test_app.test_parameters.MixedParameterTests) Parameter: reset correctly set Value to _default ... ok test_str_all_modes (test_app.test_parameters.MixedParameterTests) MixedParameter: str() functions in various modes ... ok test_str_full (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with all values non-default ... ok test_str_modify_delimiter (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with different delimiter ... ok test_str_modify_is_path (test_app.test_parameters.MixedParameterTests) MixedParameter: str functions as expected with different IsPath ... ok test_str_modify_name (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with different names ... ok test_str_modify_prefix (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with different prefixes ... ok test_str_modify_quotes (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with different quotes ... ok test_str_modify_values (test_app.test_parameters.MixedParameterTests) Parameter: str functions as expected with different values ... ok test_str_off (test_app.test_parameters.MixedParameterTests) Parameter: str() prints empty string when off ... ok test_all_off (test_app.test_parameters.ParametersTests) Parameters: all_off() should turn all parametes off ... ok test_immutability (test_app.test_parameters.ParametersTests) Parameters: attempt to modify object raises error ... ok test_init (test_app.test_parameters.ParametersTests) Parameters: init functions as expected ... ok test_lookup (test_app.test_parameters.ParametersTests) Parameters: test ability to lookup ... ok test_eq (test_app.test_parameters.ValuedParameterTests) Parameter: eq functions as expected ... ok test_get_default (test_app.test_parameters.ValuedParameterTests) Parameter: default behaves as expected ... ok test_get_default_w_IsPath (test_app.test_parameters.ValuedParameterTests) Parameter: default is a FilePath object when IsPath is set ... ok test_get_id (test_app.test_parameters.ValuedParameterTests) Parameter: _get_id functions as expected ... ok test_init (test_app.test_parameters.ValuedParameterTests) Parameter: init functions as expected ... ok test_init_defaults (test_app.test_parameters.ValuedParameterTests) Parameter: init functions as expected with default values ... ok test_isOff_False (test_app.test_parameters.ValuedParameterTests) Parameter: isOff functions as expected with False values ... ok test_isOff_True (test_app.test_parameters.ValuedParameterTests) Parameter: isOff functions as expected with True values ... ok test_isOn_False (test_app.test_parameters.ValuedParameterTests) Parameter: isOn functions as expected with False Values ... ok test_isOn_True (test_app.test_parameters.ValuedParameterTests) Parameter: isOn functions as expected with True Values ... ok test_ne (test_app.test_parameters.ValuedParameterTests) Parameter: ne functions as expected ... ok test_off (test_app.test_parameters.ValuedParameterTests) Parameter: off functions as expected ... ok test_on (test_app.test_parameters.ValuedParameterTests) Parameter: on functions as expected ... ok test_reset (test_app.test_parameters.ValuedParameterTests) Parameter: reset correctly set Value to _default ... ok test_str_full (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with all values non-default ... ok test_str_modify_delimiter (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different delimiter ... ok test_str_modify_is_path (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different IsPath ... ok test_str_modify_name (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different names ... ok test_str_modify_prefix (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different prefixes ... ok test_str_modify_quotes (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different quotes ... ok test_str_modify_values (test_app.test_parameters.ValuedParameterTests) Parameter: str functions as expected with different values ... ok test_str_off (test_app.test_parameters.ValuedParameterTests) Parameter: str() prints empty string when off ... ok test_TmpDir (test_app.test_util.CommandLineApplicationTests) CLAppTester: Alternative TmpDir functions as expected ... ok test_TmpDir_w_space (test_app.test_util.CommandLineApplicationTests) CLAppTester: TmpDir functions as expected w space in name ... ok test_WorkingDir (test_app.test_util.CommandLineApplicationTests) CLAppTester: WorkingDir functions as expected ... ok test_WorkingDir_w_space (test_app.test_util.CommandLineApplicationTests) CLAppTester: WorkingDir w/ space in path functions as expected ... ok test_absolute (test_app.test_util.CommandLineApplicationTests) CLAppTester: _absolute converts relative paths to absolute paths ... ok test_base_command (test_app.test_util.CommandLineApplicationTests) CLAppTester: BaseCommand correctly composed ... ok test_error_on_missing_executable (test_app.test_util.CommandLineApplicationTests) CLAppTester: Useful error message on executable not found ... ok test_error_raised_on_command_None (test_app.test_util.CommandLineApplicationTests) CLAppTester: An error is raises when _command == None ... ok test_getHelp (test_app.test_util.CommandLineApplicationTests) CLAppTester: getHelp() functions as expected ... ok test_getTmpFilename (test_app.test_util.CommandLineApplicationTests) TmpFilename should return filename of correct length ... ok test_getTmpFilename_defaults_to_no_class_id (test_app.test_util.CommandLineApplicationTests) CLAppTester: getTmpFilename doesn't include class id by default ... ok test_getTmpFilename_non_default (test_app.test_util.CommandLineApplicationTests) TmpFilename handles alt tmp_dir, prefix and suffix properly ... ok test_getTmpFilename_prefix_suffix_result_constructor (test_app.test_util.CommandLineApplicationTests) TmpFilename: result has correct prefix, suffix, type ... ok test_handle_app_result_build_failure (test_app.test_util.CommandLineApplicationTests) _handle_app_result_build_failure called when CommandLineAppResult() fails ... ok test_input_as_lines_from_list (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_lines functions as expected w/ data as list ... ok test_input_as_lines_from_list_single_entry (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_lines functions as expected w/ 1 element list ... ok test_input_as_lines_from_list_w_newlines (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_lines functions w/ data as list w/ newlines ... ok test_input_as_lines_from_string (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_lines functions as expected w/ data as str ... ok test_input_as_multiline_string (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_multiline_string functions as expected ... ok test_input_as_multiline_string_single_line (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_multiline_string functions w/ single line ... ok test_input_as_path (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_path casts data to FilePath ... ok test_input_as_paths (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_paths casts each input to FilePath ... ok test_input_as_string (test_app.test_util.CommandLineApplicationTests) CLAppTester: _input_as_string functions as expected ... ok test_no_p_data_as_str (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned off, data as string ... ok test_no_p_no_d (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned off, no data ... ok test_p_data_as_file (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, data as file ... ok test_p_data_as_str (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, data as str ... ok test_p_data_as_str_suppress_stderr (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, data as string, suppress stderr ... ok test_p_data_as_str_suppress_stdout (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, data as string, suppress stdout ... ok test_p_no_data (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, no data ... ok test_p_space_in_command (test_app.test_util.CommandLineApplicationTests) CLAppTester: parameters turned on, no data, space in command ... ok test_rejected_exit_status (test_app.test_util.CommandLineApplicationTests) CLAppTester_reject_exit_status results in useful error ... ok test_working_dir_setting (test_app.test_util.CommandLineApplicationTests) CLAppTester: WorkingDir is set correctly ... ok test_cmdline_generator_easy (test_app.test_util.CommandLineGeneratorTests) Returns parameter combinations commandlines ... ok test_cmdline_generator_hard (test_app.test_util.CommandLineGeneratorTests) Returns parameter combinations commandlines. Test stdin/stdout ... ok test_cmdline_generator_multiple_input_stdin (test_app.test_util.CommandLineGeneratorTests) Tests cmdline_generator for multiple inputs over stdin ... ok test_cmdline_generator_multiple_inputs (test_app.test_util.CommandLineGeneratorTests) Tests the cmdline_generator for multiple input support ... ok test_cmdline_generator_stdout_stderr_off (test_app.test_util.CommandLineGeneratorTests) Returns cmdlines with stdout and stderr disabled ... ok test_get_tmp_filename (test_app.test_util.ConvenienceFunctionTests) get_tmp_filename should return filename of correct length ... ok test_get_tmp_filename_prefix_suffix_constructor (test_app.test_util.ConvenienceFunctionTests) get_tmp_filename: result has correct prefix, suffix, type ... ok test_guess_input_handler (test_app.test_util.ConvenienceFunctionTests) guess_input_handler should correctly identify input ... ok test_init_generator (test_app.test_util.ParameterCombinationsTests) Tests generator capabilities ... ok test_reset (test_app.test_util.ParameterCombinationsTests) Resets the iterator ... ok test_init (test_app.test_util.ParameterIterBaseTests) Test constructor ... ok test_make_app_params (test_app.test_util.ParameterIterBaseTests) Returns app parameters with expected values set ... ok test_remove (test_app.test_util.RemoveTests) This will remove the test script. Not actually a test! ... ok test_argument_mixup_exception (test_cluster.test_goodness_of_fit.GoodnessOfFitTestCase) ... ok test_calc_pwdist (test_cluster.test_goodness_of_fit.GoodnessOfFitTestCase) ... ok test_kruskalstress1 (test_cluster.test_goodness_of_fit.GoodnessOfFitTestCase) ... ok test_size_exception (test_cluster.test_goodness_of_fit.GoodnessOfFitTestCase) ... ok test_sstress (test_cluster.test_goodness_of_fit.GoodnessOfFitTestCase) ... ok test_PCoA (test_cluster.test_metric_scaling.MetricScalingTests) PCoA returns a cogent Table result ... ok test_get_principal_coordinates (test_cluster.test_metric_scaling.MetricScalingTests) get_principal_coordinates normalizes eigvecs with eigvalues ... ok test_integration (test_cluster.test_metric_scaling.MetricScalingTests) Integration test of PCoA should work correctly ... ok test_make_E_matrix (test_cluster.test_metric_scaling.MetricScalingTests) make_E_matrix converts a distance matrix to an E matrix ... ok test_make_F_matrix (test_cluster.test_metric_scaling.MetricScalingTests) make_F_matrix converts an E_matrix to an F_matrix ... ok test_output_pca (test_cluster.test_metric_scaling.MetricScalingTests) output_pca1 creates a Table output for pcs results ... ok test_principal_coordinate_analysis (test_cluster.test_metric_scaling.MetricScalingTests) principal_coordinate_analysis returns array of principal coors ... ok test_run_eig (test_cluster.test_metric_scaling.MetricScalingTests) run_eig returns eigenvectors and values ... ok test_calc_matrix_a (test_cluster.test_approximate_mds.FastMetricNystromScalingTests) calc_matrix_a should calculate a k x k matrix of ... ok test_calc_matrix_b (test_cluster.test_approximate_mds.FastMetricNystromScalingTests) calc_matrix_b should calculate a k x n-k matrix of ... ok test_nystrom (test_cluster.test_approximate_mds.FastMetricNystromScalingTests) nystrom() should return an MDS approximation ... ok test_nystrom_build_seed_matrix (test_cluster.test_approximate_mds.FastMetricNystromScalingTests) build_seed_matrix() should return a seedmatrix and an order ... ok test_nystrom_seed_number (test_cluster.test_approximate_mds.FastMetricNystromScalingTests) nystrom() should give better MDS approximations the more ... ok test_scmds_adjust_mds_to_ref (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) adjust_mds_to_ref() should return an adjusted mds solutions ... ok test_scmds_affine_mapping (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) affine_mapping() should return a touple of two matrices of ... ok test_scmds_class_combinemds (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) class CombineMds() should be able to join MDS solutions ... ok test_scmds_cmds_tzeng (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) cmds_tzeng() should return eigenvectors and eigenvalues, ... ok test_scmds_combine_mds (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) combine_mds() should merge two mds solutions ... ok test_scmds_recenter (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) recenter() should recenter an mds solution ... ok test_scmds_rowmeans (test_cluster.test_approximate_mds.FastMetricScmdsScalingTests) rowmeans() should return a vector of row-means for a 2d matrix. ... ok test_center (test_cluster.test_procrustes.procrustesTests) ... ok test_get_disparity (test_cluster.test_procrustes.procrustesTests) tests get_disparity ... ok test_normalize (test_cluster.test_procrustes.procrustesTests) ... ok test_procrustes (test_cluster.test_procrustes.procrustesTests) tests procrustes' ability to match two matrices. ... ok test_procrustes2 (test_cluster.test_procrustes.procrustesTests) procrustes disparity should not depend on order of matrices ... ok test_UPGMA_cluster (test_cluster.test_UPGMA.UPGMATests) upgma works on pairwise distance dict ... ok test_UPGMA_cluster_diag (test_cluster.test_UPGMA.UPGMATests) UPGMA_cluster works when the diagonal has intermediate values ... ok test_condense_matrix (test_cluster.test_UPGMA.UPGMATests) condense_array joins two rows and columns identified by indices ... ok test_condense_node_order (test_cluster.test_UPGMA.UPGMATests) condense_node_order condenses nodes in list based on index info ... ok test_find_smallest_index (test_cluster.test_UPGMA.UPGMATests) find_smallest_index returns the index of smallest value in array ... ok test_inputs_from_dict2D (test_cluster.test_UPGMA.UPGMATests) inputs_from_dict2D makes an array object and PhyloNode list ... ok test_upgma_cluster (test_cluster.test_UPGMA.UPGMATests) UPGMA_cluster clusters nodes based on info in a matrix with UPGMA ... ok test_getPoints (test_cluster.test_nmds.NMDSTests) points should be of the right number and dimensionality ... ok test_getStress (test_cluster.test_nmds.NMDSTests) stress should be small ... ok test_metaNMDS (test_cluster.test_nmds.NMDSTests) l19 data should give stress below .13 ... ok test_fromArray (test_core.test_alphabet.CharAlphabetTests) CharAlphabet fromArray should return correct array ... ok test_fromString (test_core.test_alphabet.CharAlphabetTests) CharAlphabet fromString should return correct array ... ok test_init (test_core.test_alphabet.CharAlphabetTests) CharAlphabet init should make correct translation tables ... ok test_isValid (test_core.test_alphabet.CharAlphabetTests) CharAlphabet isValid should return True for valid sequence ... ok test_pairs (test_core.test_alphabet.CharAlphabetTests) pairs should cache the same object. ... ok test_toChars (test_core.test_alphabet.CharAlphabetTests) CharAlphabet toChars should convert an input array to chars ... ok test_toString (test_core.test_alphabet.CharAlphabetTests) CharAlphabet toString should convert an input array to string ... ok test_triples (test_core.test_alphabet.CharAlphabetTests) triples should cache the same object. ... ok test_counts (test_core.test_alphabet.EnumerationTests) Enumeration counts should count freqs in array ... ok test_fromIndices (test_core.test_alphabet.EnumerationTests) Enumeration fromIndices should return elements from indices ... ok test_getitem (test_core.test_alphabet.EnumerationTests) Enumeration[i] should return character at i ... ok test_index (test_core.test_alphabet.EnumerationTests) Enumeration index should return first index of item ... ok test_init (test_core.test_alphabet.EnumerationTests) Enumeration init should work from any sequence ... ok test_isValid (test_core.test_alphabet.EnumerationTests) Enumeration isValid should return True for valid sequence ... ok test_mul (test_core.test_alphabet.EnumerationTests) Enumeration mul should produce correct JointEnumeration ... ok test_pow (test_core.test_alphabet.EnumerationTests) Enumeration pow should produce JointEnumeration with n copies ... ok test_toIndices (test_core.test_alphabet.EnumerationTests) Enumeration toIndices should return indices from elements ... ok test_fromIndices (test_core.test_alphabet.JointEnumerationTests) JointEnumeration fromIndices should return correct tuples ... ok test_init (test_core.test_alphabet.JointEnumerationTests) JointEnumeration init should work as expected ... ok test_packArrays (test_core.test_alphabet.JointEnumerationTests) JointEnumeration packArrays should return correct array. ... ok test_toIndices (test_core.test_alphabet.JointEnumerationTests) JointEnumeration toIndices should convert tuples correctly ... ok test_unpackArrays (test_core.test_alphabet.JointEnumerationTests) JointEnumeration unpackArrays should return correct arrays. ... ok test_get_array_type (test_core.test_alphabet.get_array_type_tests) get_array_type should return unsigned type that fits elements. ... ok test_make_complement_array (test_core.test_alphabet.translation_table_tests) _make_complement_array should identify complements correctly ... ok test_make_translation_tables (test_core.test_alphabet.translation_table_tests) _make_translation_tables should translate from chars to indices ... ok test_IUPACConsensus_DNA (test_core.test_alignment.AlignmentTests) SequenceCollection IUPACConsensus should use DNA IUPAC symbols correctly ... ok test_IUPACConsensus_Protein (test_core.test_alignment.AlignmentTests) SequenceCollection IUPACConsensus should use protein IUPAC symbols correctly ... ok test_IUPACConsensus_RNA (test_core.test_alignment.AlignmentTests) SequenceCollection IUPACConsensus should use RNA IUPAC symbols correctly ... ok test_Items (test_core.test_alignment.AlignmentTests) SequenceCollection Items should iterate over items in specified order. ... ok test_Positions (test_core.test_alignment.AlignmentTests) SequenceCollection Positions property should iterate over positions, using self.Names ... ok test_SeqLen_get (test_core.test_alignment.AlignmentTests) SequenceCollection SeqLen should return length of longest seq ... ok test_Seqs (test_core.test_alignment.AlignmentTests) SequenceCollection Seqs property should return seqs in correct order. ... ok test_add (test_core.test_alignment.AlignmentTests) __add__ should concatenate sequence data, by name ... ok test_addFromReferenceAln (test_core.test_alignment.AlignmentTests) should add or insert seqs based on align to reference ... ok test_addSeqs (test_core.test_alignment.AlignmentTests) addSeqs should return an alignment with the new sequences appended or inserted ... ok test_aln_from_fasta (test_core.test_alignment.AlignmentTests) SequenceCollection should init from fasta-format string ... ok test_aln_from_fasta_parser (test_core.test_alignment.AlignmentTests) aln_from_fasta_parser should init from iterator ... ok test_annotateFromGff (test_core.test_alignment.AlignmentTests) SequenceCollection.annotateFromGff should read gff features ... ok test_columnFreqs (test_core.test_alignment.AlignmentTests) Alignment.columnFreqs should count symbols in each column ... ok test_columnProbs (test_core.test_alignment.AlignmentTests) SequenceCollection.columnProbs should find Pr(symbol) in each column ... ok test_consistent_gap_degen_handling (test_core.test_alignment.AlignmentTests) gap degen character should be treated consistently ... ok test_copy (test_core.test_alignment.AlignmentTests) correctly copy an alignment ... ok test_copyAnnotations (test_core.test_alignment.AlignmentTests) SequenceCollection copyAnnotations should copy from seq objects ... ok test_degap (test_core.test_alignment.AlignmentTests) SequenceCollection.degap should strip gaps from each seq ... ok test_distanceMatrix (test_core.test_alignment.AlignmentTests) SequenceCollection distanceMatrix should produce correct scores ... ok test_filtered (test_core.test_alignment.AlignmentTests) filtered should return new alignment with positions consistent with ... ok test_getDegappedRelativeTo (test_core.test_alignment.AlignmentTests) should remove all columns with a gap in sequence with given name ... ok test_getGappedSeq (test_core.test_alignment.AlignmentTests) SequenceCollection.getGappedSeq should return seq, with gaps ... ok test_getIntMap (test_core.test_alignment.AlignmentTests) SequenceCollection.getIntMap should return correct mapping. ... ok test_getItemIndices (test_core.test_alignment.AlignmentTests) SequenceCollection getItemIndices should return coordinates of matching items ... ok test_getItems (test_core.test_alignment.AlignmentTests) SequenceCollection getItems should return list of items from k,v pairs ... ok test_getItemsIf (test_core.test_alignment.AlignmentTests) SequenceCollection getItemsIf should return matching items ... ok test_getNumSeqs (test_core.test_alignment.AlignmentTests) SequenceCollection.getNumSeqs should count seqs. ... ok test_getPerSequenceAmbiguousPositions (test_core.test_alignment.AlignmentTests) SequenceCollection.getPerSequenceAmbiguousPositions should return pos ... ok test_getPosFreqs (test_core.test_alignment.AlignmentTests) Alignment getPosFreqs: should work with DnaSequences and strings ... ok test_getPositionIndices (test_core.test_alignment.AlignmentTests) SequenceCollection getPositionIndices should return names of cols where f(col) ... ok test_getSeq (test_core.test_alignment.AlignmentTests) SequenceCollection.getSeq should return specified seq ... ok test_getSeqFreqs (test_core.test_alignment.AlignmentTests) Alignment getSeqFreqs: should work with DnaSequences and strings ... ok test_getSeqIndices (test_core.test_alignment.AlignmentTests) SequenceCollection getSeqIndices should return names of seqs where f(row) is True ... ok test_getSimilar (test_core.test_alignment.AlignmentTests) SequenceCollection getSimilar should get all sequences close to target seq ... ok test_getTranslation (test_core.test_alignment.AlignmentTests) SequenceCollection.getTranslation translates each seq ... ok test_get_freqs (test_core.test_alignment.AlignmentTests) Alignment _get_freqs: should work on positions and sequences ... ok test_guess_input_type (test_core.test_alignment.AlignmentTests) SequenceCollection _guess_input_type should figure out data type correctly ... ok test_init_aln (test_core.test_alignment.AlignmentTests) SequenceCollection SequenceCollection should init from existing alignments ... ok test_init_ambig (test_core.test_alignment.AlignmentTests) SequenceCollection should tolerate ambiguous chars ... ok test_init_annotated_seq (test_core.test_alignment.AlignmentTests) SequenceCollection init from seqs w/ Info should preserve data ... ok test_init_dict (test_core.test_alignment.AlignmentTests) SequenceCollection init from dict should work as expected ... ok test_init_duplicate_keys (test_core.test_alignment.AlignmentTests) SequenceCollection init from (key, val) pairs should fail on dup. keys ... ok test_init_name_mapped (test_core.test_alignment.AlignmentTests) SequenceCollection init should allow name mapping function ... ok test_init_ordered (test_core.test_alignment.AlignmentTests) SequenceCollection should iterate over seqs correctly even if ordered ... ok test_init_pairs (test_core.test_alignment.AlignmentTests) SequenceCollection init from list of (key,val) pairs should work correctly ... ok test_init_seq (test_core.test_alignment.AlignmentTests) SequenceCollection init from list of sequences should use indices as keys ... ok test_isRagged (test_core.test_alignment.AlignmentTests) SequenceCollection isRagged should return true if ragged alignment ... ok test_iterItems (test_core.test_alignment.AlignmentTests) SequenceCollection iterItems() should iterate over items in correct order ... ok test_iterPositions (test_core.test_alignment.AlignmentTests) ... ok test_iterSeqs (test_core.test_alignment.AlignmentTests) SequenceCollection iterSeqs() method should support reordering of seqs ... ok test_len (test_core.test_alignment.AlignmentTests) len(SequenceCollection) returns length of longest sequence ... ok test_majorityConsensus (test_core.test_alignment.AlignmentTests) SequenceCollection.majorityConsensus should return commonest symbol per column ... ok test_make_gap_filter (test_core.test_alignment.AlignmentTests) make_gap_filter returns f(seq) -> True if aligned ok w/ query ... ok test_omitGapPositions (test_core.test_alignment.AlignmentTests) SequenceCollection omitGapPositions should return alignment w/o positions of gaps ... ok test_omitGapRuns (test_core.test_alignment.AlignmentTests) SequenceCollection omitGapRuns should return alignment w/o runs of gaps ... ok test_omitGapSeqs (test_core.test_alignment.AlignmentTests) SequenceCollection omitGapSeqs should return alignment w/o seqs with gaps ... ok test_omitSeqsTemplate (test_core.test_alignment.AlignmentTests) SequenceCollection.omitSeqsTemplate returns new aln with well-aln to temp ... ok test_padSeqs (test_core.test_alignment.AlignmentTests) SequenceCollection padSeqs should work on alignment. ... ok test_replaceSeqs (test_core.test_alignment.AlignmentTests) replaceSeqs should replace 1-letter w/ 3-letter seqs ... ok test_sample (test_core.test_alignment.AlignmentTests) Alignment.sample should permute alignment by default ... ok test_sample_tuples (test_core.test_alignment.AlignmentTests) ... ok test_sample_with_replacement (test_core.test_alignment.AlignmentTests) ... ok test_scoreMatrix (test_core.test_alignment.AlignmentTests) Alignment scoreMatrix should produce position specific score matrix. ... ok test_slidingWindows (test_core.test_alignment.AlignmentTests) slidingWindows should return slices of alignments. ... ok test_takePositions (test_core.test_alignment.AlignmentTests) SequenceCollection takePositions should return new alignment w/ specified pos ... ok test_takePositionsIf (test_core.test_alignment.AlignmentTests) SequenceCollection takePositionsIf should return cols where f(col) is True ... ok test_takeSeqs (test_core.test_alignment.AlignmentTests) SequenceCollection takeSeqs should return new SequenceCollection with selected seqs. ... ok test_takeSeqsIf (test_core.test_alignment.AlignmentTests) SequenceCollection takeSeqsIf should return seqs where f(row) is True ... ok test_takeSeqs_moltype (test_core.test_alignment.AlignmentTests) takeSeqs should preserve the MolType ... ok test_toFasta (test_core.test_alignment.AlignmentTests) SequenceCollection should return correct FASTA string ... ok test_toNexus (test_core.test_alignment.AlignmentTests) SequenceCollection should return correct Nexus string format ... ok test_toPhylip (test_core.test_alignment.AlignmentTests) SequenceCollection should return PHYLIP string format correctly ... ok test_toPretty (test_core.test_alignment.AlignmentTests) produce correct pretty print formatted text ... ok test_todict (test_core.test_alignment.AlignmentTests) SequenceCollection.todict should return dict of strings (not obj) ... ok test_uncertainties (test_core.test_alignment.AlignmentTests) SequenceCollection.uncertainties should match hand-calculated values ... ok test_withGapsFrom (test_core.test_alignment.AlignmentTests) withGapsFrom should overwrite with gaps. ... ok test_withModifiedTermini (test_core.test_alignment.AlignmentTests) SequenceCollection.withModifiedTermini should code trailing gaps as ? ... ok test_writeToFile (test_core.test_alignment.AlignmentTests) SequenceCollection.writeToFile should write in correct format ... ok test_getPosEntropy (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getPosEntropy should get entropy of each pos ... ok test_getPosFreqs (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getPosFreqs should get profile of freqs at each pos ... ok test_getSeqEntropy (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getSeqEntropy should get entropy of each seq ... ok test_getSeqFreqs (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getSeqFreqs should get profile of freqs in each seq ... ok test_getSubAlignment (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getSubAlignment should get requested part of alignment. ... ok test_get_alphabet_and_moltype (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment should figure out correct alphabet and moltype ... ok test_get_freqs (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment _get_freqs should get row or col freqs ... ok test_getitem (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment getitem should default to positions as chars ... ok test_guess_input_type (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment _guess_input_type should figure out data type correctly ... ok test_init (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should work from a sequence ... ok test_init_aln (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should work from another alignment. ... ok test_init_dict (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should work from dict. ... ok test_init_empty (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should fail if empty. ... ok test_init_generic (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should work from generic objects. ... ok test_init_seqs (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment init should work from ModelSequence objects. ... ok test_iter (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment iter should iterate over positions ... ok test_str (test_core.test_alignment.DenseAlignmentSpecificTests) DenseAlignment str should return FASTA representation of aln ... ok test_IUPACConsensus_DNA (test_core.test_alignment.DenseAlignmentTests) SequenceCollection IUPACConsensus should use DNA IUPAC symbols correctly ... ok test_IUPACConsensus_Protein (test_core.test_alignment.DenseAlignmentTests) SequenceCollection IUPACConsensus should use protein IUPAC symbols correctly ... ok test_IUPACConsensus_RNA (test_core.test_alignment.DenseAlignmentTests) SequenceCollection IUPACConsensus should use RNA IUPAC symbols correctly ... ok test_Items (test_core.test_alignment.DenseAlignmentTests) SequenceCollection Items should iterate over items in specified order. ... ok test_Positions (test_core.test_alignment.DenseAlignmentTests) SequenceCollection Positions property should iterate over positions, using self.Names ... ok test_SeqLen_get (test_core.test_alignment.DenseAlignmentTests) SequenceCollection SeqLen should return length of longest seq ... ok test_Seqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection Seqs property should return seqs in correct order. ... ok test_add (test_core.test_alignment.DenseAlignmentTests) __add__ should concatenate sequence data, by name ... ok test_addSeqs (test_core.test_alignment.DenseAlignmentTests) addSeqs should return an alignment with the new sequences appended or inserted ... ok test_aln_from_fasta (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should init from fasta-format string ... ok test_aln_from_fasta_parser (test_core.test_alignment.DenseAlignmentTests) aln_from_fasta_parser should init from iterator ... ok test_annotateFromGff (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.annotateFromGff should read gff features ... ok test_columnFreqs (test_core.test_alignment.DenseAlignmentTests) Alignment.columnFreqs should count symbols in each column ... ok test_columnProbs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.columnProbs should find Pr(symbol) in each column ... ok test_consistent_gap_degen_handling (test_core.test_alignment.DenseAlignmentTests) gap degen character should be treated consistently ... ok test_copy (test_core.test_alignment.DenseAlignmentTests) correctly copy an alignment ... ok test_copyAnnotations (test_core.test_alignment.DenseAlignmentTests) SequenceCollection copyAnnotations should copy from seq objects ... ok test_degap (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.degap should strip gaps from each seq ... ok test_distanceMatrix (test_core.test_alignment.DenseAlignmentTests) SequenceCollection distanceMatrix should produce correct scores ... ok test_getGappedSeq (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getGappedSeq should return seq, with gaps ... ok test_getIntMap (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getIntMap should return correct mapping. ... ok test_getItemIndices (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getItemIndices should return coordinates of matching items ... ok test_getItems (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getItems should return list of items from k,v pairs ... ok test_getItemsIf (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getItemsIf should return matching items ... ok test_getNumSeqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getNumSeqs should count seqs. ... ok test_getPerSequenceAmbiguousPositions (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getPerSequenceAmbiguousPositions should return pos ... ok test_getPosFreqs_sequence (test_core.test_alignment.DenseAlignmentTests) DenseAlignment getPosFreqs: should work with DnaSequences and strings ... ok test_getPositionIndices (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getPositionIndices should return names of cols where f(col) ... ok test_getSeq (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getSeq should return specified seq ... ok test_getSeqFreqs (test_core.test_alignment.DenseAlignmentTests) DenseAlignment getSeqFreqs: should work with DnaSequences and strings ... ok test_getSeqIndices (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getSeqIndices should return names of seqs where f(row) is True ... ok test_getSimilar (test_core.test_alignment.DenseAlignmentTests) SequenceCollection getSimilar should get all sequences close to target seq ... ok test_getTranslation (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.getTranslation translates each seq ... ok test_get_freqs (test_core.test_alignment.DenseAlignmentTests) DenseAlignment getSeqFreqs: should work on positions and sequences ... ok test_guess_input_type (test_core.test_alignment.DenseAlignmentTests) SequenceCollection _guess_input_type should figure out data type correctly ... ok test_init_aln (test_core.test_alignment.DenseAlignmentTests) SequenceCollection SequenceCollection should init from existing alignments ... ok test_init_ambig (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should tolerate ambiguous chars ... ok test_init_annotated_seq (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init from seqs w/ Info should preserve data ... ok test_init_dict (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init from dict should work as expected ... ok test_init_duplicate_keys (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init from (key, val) pairs should fail on dup. keys ... ok test_init_name_mapped (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init should allow name mapping function ... ok test_init_ordered (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should iterate over seqs correctly even if ordered ... ok test_init_pairs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init from list of (key,val) pairs should work correctly ... ok test_init_seq (test_core.test_alignment.DenseAlignmentTests) SequenceCollection init from list of sequences should use indices as keys ... ok test_isRagged (test_core.test_alignment.DenseAlignmentTests) SequenceCollection isRagged should return true if ragged alignment ... ok test_iterItems (test_core.test_alignment.DenseAlignmentTests) SequenceCollection iterItems() should iterate over items in correct order ... ok test_iterPositions (test_core.test_alignment.DenseAlignmentTests) ... ok test_iterSeqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection iterSeqs() method should support reordering of seqs ... ok test_len (test_core.test_alignment.DenseAlignmentTests) len(SequenceCollection) returns length of longest sequence ... ok test_majorityConsensus (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.majorityConsensus should return commonest symbol per column ... ok test_make_gap_filter (test_core.test_alignment.DenseAlignmentTests) make_gap_filter returns f(seq) -> True if aligned ok w/ query ... ok test_omitGapPositions (test_core.test_alignment.DenseAlignmentTests) SequenceCollection omitGapPositions should return alignment w/o positions of gaps ... ok test_omitGapRuns (test_core.test_alignment.DenseAlignmentTests) SequenceCollection omitGapRuns should return alignment w/o runs of gaps ... ok test_omitGapSeqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection omitGapSeqs should return alignment w/o seqs with gaps ... ok test_omitSeqsTemplate (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.omitSeqsTemplate returns new aln with well-aln to temp ... ok test_padSeqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection padSeqs should work on alignment. ... ok test_replaceSeqs (test_core.test_alignment.DenseAlignmentTests) replaceSeqs should replace 1-letter w/ 3-letter seqs ... ok test_sample (test_core.test_alignment.DenseAlignmentTests) Alignment.sample should permute alignment by default ... ok test_sample_tuples (test_core.test_alignment.DenseAlignmentTests) ... ok test_sample_with_replacement (test_core.test_alignment.DenseAlignmentTests) ... ok test_scoreMatrix (test_core.test_alignment.DenseAlignmentTests) Alignment scoreMatrix should produce position specific score matrix. ... ok test_takePositions (test_core.test_alignment.DenseAlignmentTests) SequenceCollection takePositions should return new alignment w/ specified pos ... ok test_takePositionsIf (test_core.test_alignment.DenseAlignmentTests) SequenceCollection takePositionsIf should return cols where f(col) is True ... ok test_takeSeqs (test_core.test_alignment.DenseAlignmentTests) SequenceCollection takeSeqs should return new SequenceCollection with selected seqs. ... ok test_takeSeqsIf (test_core.test_alignment.DenseAlignmentTests) SequenceCollection takeSeqsIf should return seqs where f(row) is True ... ok test_takeSeqs_moltype (test_core.test_alignment.DenseAlignmentTests) takeSeqs should preserve the MolType ... ok test_toFasta (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should return correct FASTA string ... ok test_toNexus (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should return correct Nexus string format ... ok test_toPhylip (test_core.test_alignment.DenseAlignmentTests) SequenceCollection should return PHYLIP string format correctly ... ok test_toPretty (test_core.test_alignment.DenseAlignmentTests) produce correct pretty print formatted text ... ok test_todict (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.todict should return dict of strings (not obj) ... ok test_uncertainties (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.uncertainties should match hand-calculated values ... ok test_withModifiedTermini (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.withModifiedTermini should code trailing gaps as ? ... ok test_writeToFile (test_core.test_alignment.DenseAlignmentTests) SequenceCollection.writeToFile should write in correct format ... ok test_model_aln_to_model_aln (test_core.test_alignment.IntegrationTests) Model aln should convert to model aln ... ok test_model_aln_to_regular_aln (test_core.test_alignment.IntegrationTests) Dense aln should convert to regular aln ... ok test_model_to_model (test_core.test_alignment.IntegrationTests) Model seq should work with dense alignment ... ok test_model_to_regular (test_core.test_alignment.IntegrationTests) Model seq should work with regular alignment ... ok test_regular_aln_to_model_aln (test_core.test_alignment.IntegrationTests) Regular aln should convert to model aln ... ok test_regular_aln_to_regular_aln (test_core.test_alignment.IntegrationTests) Regular aln should convert to regular aln ... ok test_regular_to_model (test_core.test_alignment.IntegrationTests) Regular seq should work with dense alignment ... ok test_regular_to_regular (test_core.test_alignment.IntegrationTests) Regular seq should work with regular alignment ... ok test_Items (test_core.test_alignment.SequenceCollectionTests) SequenceCollection Items should iterate over items in specified order. ... ok test_SeqLen_get (test_core.test_alignment.SequenceCollectionTests) SequenceCollection SeqLen should return length of longest seq ... ok test_SeqLen_get_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection SeqLen get should work for ragged seqs ... ok test_Seqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection Seqs property should return seqs in correct order. ... ok test_Seqs_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection Seqs should work on ragged alignment ... ok test_add (test_core.test_alignment.SequenceCollectionTests) __add__ should concatenate sequence data, by name ... ok test_addSeqs (test_core.test_alignment.SequenceCollectionTests) addSeqs should return an alignment with the new sequences appended or inserted ... ok test_aln_from_fasta (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should init from fasta-format string ... ok test_aln_from_fasta_parser (test_core.test_alignment.SequenceCollectionTests) aln_from_fasta_parser should init from iterator ... ok test_annotateFromGff (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.annotateFromGff should read gff features ... ok test_consistent_gap_degen_handling (test_core.test_alignment.SequenceCollectionTests) gap degen character should be treated consistently ... ok test_copyAnnotations (test_core.test_alignment.SequenceCollectionTests) SequenceCollection copyAnnotations should copy from seq objects ... ok test_degap (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.degap should strip gaps from each seq ... ok test_distanceMatrix (test_core.test_alignment.SequenceCollectionTests) SequenceCollection distanceMatrix should produce correct scores ... ok test_getGappedSeq (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getGappedSeq should return seq, with gaps ... ok test_getIntMap (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getIntMap should return correct mapping. ... ok test_getItemIndices (test_core.test_alignment.SequenceCollectionTests) SequenceCollection getItemIndices should return coordinates of matching items ... ok test_getItems (test_core.test_alignment.SequenceCollectionTests) SequenceCollection getItems should return list of items from k,v pairs ... ok test_getItemsIf (test_core.test_alignment.SequenceCollectionTests) SequenceCollection getItemsIf should return matching items ... ok test_getNumSeqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getNumSeqs should count seqs. ... ok test_getPerSequenceAmbiguousPositions (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getPerSequenceAmbiguousPositions should return pos ... ok test_getSeq (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getSeq should return specified seq ... ok test_getSeqIndices (test_core.test_alignment.SequenceCollectionTests) SequenceCollection getSeqIndices should return names of seqs where f(row) is True ... ok test_getSimilar (test_core.test_alignment.SequenceCollectionTests) SequenceCollection getSimilar should get all sequences close to target seq ... ok test_getTranslation (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.getTranslation translates each seq ... ok test_guess_input_type (test_core.test_alignment.SequenceCollectionTests) SequenceCollection _guess_input_type should figure out data type correctly ... ok test_init_aln (test_core.test_alignment.SequenceCollectionTests) SequenceCollection SequenceCollection should init from existing alignments ... ok test_init_ambig (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should tolerate ambiguous chars ... ok test_init_annotated_seq (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init from seqs w/ Info should preserve data ... ok test_init_dict (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init from dict should work as expected ... ok test_init_duplicate_keys (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init from (key, val) pairs should fail on dup. keys ... ok test_init_name_mapped (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init should allow name mapping function ... ok test_init_ordered (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should iterate over seqs correctly even if ordered ... ok test_init_pairs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init from list of (key,val) pairs should work correctly ... ok test_init_seq (test_core.test_alignment.SequenceCollectionTests) SequenceCollection init from list of sequences should use indices as keys ... ok test_isRagged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection isRagged should return true if ragged alignment ... ok test_isRagged_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection isRagged should return True if ragged ... ok test_iterItems (test_core.test_alignment.SequenceCollectionTests) SequenceCollection iterItems() should iterate over items in correct order ... ok test_iterSeqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection iterSeqs() method should support reordering of seqs ... ok test_iterSeqs_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection iterSeqs() method should support reordering of seqs ... ok test_len (test_core.test_alignment.SequenceCollectionTests) len(SequenceCollection) returns length of longest sequence ... ok test_make_gap_filter (test_core.test_alignment.SequenceCollectionTests) make_gap_filter returns f(seq) -> True if aligned ok w/ query ... ok test_omitGapRuns (test_core.test_alignment.SequenceCollectionTests) SequenceCollection omitGapRuns should return alignment w/o runs of gaps ... ok test_omitGapSeqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection omitGapSeqs should return alignment w/o seqs with gaps ... ok test_omitSeqsTemplate (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.omitSeqsTemplate returns new aln with well-aln to temp ... ok test_padSeqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection padSeqs should work on alignment. ... ok test_padSeqs_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection padSeqs should work on ragged alignment. ... ok test_replaceSeqs (test_core.test_alignment.SequenceCollectionTests) replaceSeqs should replace 1-letter w/ 3-letter seqs ... ok test_takeSeqs (test_core.test_alignment.SequenceCollectionTests) SequenceCollection takeSeqs should return new SequenceCollection with selected seqs. ... ok test_takeSeqsIf (test_core.test_alignment.SequenceCollectionTests) SequenceCollection takeSeqsIf should return seqs where f(row) is True ... ok test_takeSeqs_moltype (test_core.test_alignment.SequenceCollectionTests) takeSeqs should preserve the MolType ... ok test_toFasta (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should return correct FASTA string ... ok test_toNexus (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should return correct Nexus string format ... ok test_toPHYLIP_ragged (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should refuse to convert ragged seqs to phylip ... ok test_toPhylip (test_core.test_alignment.SequenceCollectionTests) SequenceCollection should return PHYLIP string format correctly ... ok test_todict (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.todict should return dict of strings (not obj) ... ok test_withModifiedTermini (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.withModifiedTermini should code trailing gaps as ? ... ok test_writeToFile (test_core.test_alignment.SequenceCollectionTests) SequenceCollection.writeToFile should write in correct format ... ok test_aln_from_array (test_core.test_alignment.alignment_tests) aln_from_array should return same array, and successive indices. ... ok test_aln_from_collection (test_core.test_alignment.alignment_tests) aln_from_collection should initialize from existing alignment ... ok test_aln_from_dense_aln (test_core.test_alignment.alignment_tests) aln_from_dense_aln should initialize from existing alignment ... ok test_aln_from_empty (test_core.test_alignment.alignment_tests) aln_from_empty should always raise ValueError ... ok test_aln_from_fasta (test_core.test_alignment.alignment_tests) aln_from_fasta should initialize aln from fasta-format string ... ok test_aln_from_generic (test_core.test_alignment.alignment_tests) aln_from_generic should initialize aln from list of lists, etc. ... ok test_aln_from_model_seqs (test_core.test_alignment.alignment_tests) aln_from_model_seqs should initialize aln from sequence objects. ... ok test_seqs_from_aln (test_core.test_alignment.alignment_tests) seqs_from_aln should initialize from existing alignment ... ok test_seqs_from_array (test_core.test_alignment.alignment_tests) seqs_from_array should return chars, and successive indices. ... ok test_seqs_from_empty (test_core.test_alignment.alignment_tests) seqs_from_empty should always raise ValueError ... ok test_seqs_from_fasta (test_core.test_alignment.alignment_tests) seqs_from_fasta should initialize seqs from fasta-format string ... ok test_seqs_from_generic (test_core.test_alignment.alignment_tests) seqs_from_generic should initialize seqs from list of lists, etc. ... ok test_seqs_from_kv_pairs (test_core.test_alignment.alignment_tests) seqs_from_kv_pairs should initialize from key-value pairs ... ok test_seqs_from_model_seqs (test_core.test_alignment.alignment_tests) seqs_from_model_seqs should return model seqs + names. ... ok test_aln_annotations (test_core.test_annotation.TestAnnotations) test that annotations to alignment and its' sequences ... ok test_feature_projection (test_core.test_annotation.TestAnnotations) ... ok test_inherit_feature (test_core.test_annotation.TestAnnotations) should be able to subclass and extend _Feature ... ok test_reversecomplement (test_core.test_annotation.TestAnnotations) test correct translation of annotations on reverse complement. ... ok test_slice_aln_with_annotations (test_core.test_annotation.TestAnnotations) test that annotations of sequences and alignments survive alignment ... ok test_slice_seq_with_annotations (test_core.test_annotation.TestAnnotations) ... ok test_map (test_core.test_annotation.TestMapSpans) reversing a map with multiple spans should preserve span relative ... ok test_span (test_core.test_annotation.TestMapSpans) ... ok test_and (test_core.test_bitvector.BitvectorClassTests) Bitwise and should work between short and long bitvectors ... ok test_or (test_core.test_bitvector.BitvectorClassTests) Bitwise or should work between short and long bitvectors ... ok test_and (test_core.test_bitvector.BitvectorTests) Bitvector A&B should return 0 for each position that is 0 in A and B ... ok test_bitcount (test_core.test_bitvector.BitvectorTests) Bitvector bitcount should correctly count 1's or 0's ... ok test_divideSequence (test_core.test_bitvector.BitvectorTests) Bitvector divideSequence should cut sequence at state changes ... ok test_freeze (test_core.test_bitvector.BitvectorTests) Bitvector freeze should return same object ... ok test_getitem (test_core.test_bitvector.BitvectorTests) Bitvector getitem should return states at specified position(s) ... ok test_init (test_core.test_bitvector.BitvectorTests) Bitvector init should give expected results. ... ok test_invert (test_core.test_bitvector.BitvectorTests) Bitvector ~A should return a vector exchanging 1's for 0's ... ok test_len (test_core.test_bitvector.BitvectorTests) Bitvector len should match initialized length ... ok test_or (test_core.test_bitvector.BitvectorTests) Bitvector A|B should return 1 for each position that is 1 in A or B ... ok test_repr (test_core.test_bitvector.BitvectorTests) Bitvector repr should look like a normal object ... ok test_stateChanges (test_core.test_bitvector.BitvectorTests) Bitvector stateChanges should return indices where state changes ... ok test_str (test_core.test_bitvector.BitvectorTests) Bitvector str should match expected results ... ok test_thaw (test_core.test_bitvector.BitvectorTests) Bitvector thaw should return mutable bitvector with same data ... ok test_xor (test_core.test_bitvector.BitvectorTests) Bitvector A^B should return 0 for each identical position in A and B ... ok test_and (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector A&B should return 0 for each position 0 in both ... ok test_bitcount (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector bitcount should correctly count 1's or 0's ... ok test_divideSequence (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector divideSequence should cut sequence at state changes ... ok test_freeze (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector freeze should return immutable bv with same data ... ok test_getitem (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector getitem should return states at specified position(s) ... ok test_init (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector init should give expected results. ... ok test_invert (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector ~A should return a vector exchanging 1's for 0's ... ok test_len (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector len should match initialized length ... ok test_or (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector A|B should return 1 at 1 positions in A or B ... ok test_repr (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector repr should look like a normal object ... ok test_setitem (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector setitem should change positions correctly ... ok test_stateChanges (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector stateChanges should return indices where state changes ... ok test_str (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector str should match expected results ... ok test_thaw (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector thaw should return same object ... ok test_xor (test_core.test_bitvector.MutableBitvectorTests) MutableBitvector A^B should return 0 at identical positions in A, B ... ok test_bit_ops (test_core.test_bitvector.PackedBasesTests) PackedBases xor and bitcount should give correct # differences ... ok test_init (test_core.test_bitvector.PackedBasesTests) PackedBases init should allow sequence recovery ... ok test_str (test_core.test_bitvector.PackedBasesTests) PackedBases str should respect RNA/DNA ... ok test_init (test_core.test_bitvector.VectorFromCasesTests) VectorFromCases should return vector with 1 where string is ucase ... ok testBothEmpty (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches empty string/pattern should return empty vector ... ok testEmptyPattern (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches empty pattern should return zeroes for len(string) ... ok testMultiBasePattern (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches should match multi-char string matches ... ok testMultiBaseRegex (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches should match every matching combination of chars ... ok testSingleBasePattern (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches should match every matching char in string ... ok testSingleBaseRegex (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches should match every matching character in regex ... ok test_type (test_core.test_bitvector.VectorFromMatchesTests) VectorFromMatches should return correct type of vector ... ok test_init (test_core.test_bitvector.VectorFromPositionsTests) VectorFromPositions should return correct vector ... ok test_init (test_core.test_bitvector.VectorFromRunsTests) VectorFromRuns should return vector with 1 where string is ucase ... ok test_init (test_core.test_bitvector.VectorFromSpansTests) VectorFromSpans hould return vector with 1 in correct spans ... ok test_bitcount (test_core.test_bitvector.bitvectorTests) bitcount should provide expected results ... ok test_is_nonzero_char (test_core.test_bitvector.bitvectorTests) is_nonzero_char should return '0' for any False item or '0' ... ok test_is_nonzero_int (test_core.test_bitvector.bitvectorTests) is_nonzero_int should return 0 for any False item or '0' ... ok test_is_nonzero_string_char (test_core.test_bitvector.bitvectorTests) is_nonzero_string_char should return '1' for anything but '0', '' ... ok test_is_nonzero_string_int (test_core.test_bitvector.bitvectorTests) is_nonzero_string_int should return 1 for anything but '0', '' ... ok test_number_to_bitstring (test_core.test_bitvector.bitvectorTests) number_to_bitstring should provide expected results ... ok test_seq_to_bitlist (test_core.test_bitvector.bitvectorTests) seq_to_bitlist should provide expected results ... ok test_seq_to_bitstring (test_core.test_bitvector.bitvectorTests) seq_to_bitstring should provide expected results ... ok test_DnaRna_interconversion (test_core.test_core_standalone.AlignmentTestMethods) test interconversion between Rna and Dna by SequenceCollection and ... ok test_alignadd (test_core.test_core_standalone.AlignmentTestMethods) testing adding one alignment to another. ... ok test_alignlsength (test_core.test_core_standalone.AlignmentTestMethods) testing the alignment length ... ok test_degap (test_core.test_core_standalone.AlignmentTestMethods) test stripping gaps from collections and alignments ... ok test_empty_seq (test_core.test_core_standalone.AlignmentTestMethods) test creation of an alignment from scratch, with one sequence pure gap ... ok test_getNumSeqs (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_getSubAlignment (test_core.test_core_standalone.AlignmentTestMethods) test slicing otus, and return of new alignment ... ok test_get_motifprobs (test_core.test_core_standalone.AlignmentTestMethods) calculation of motif probs ... ok test_getasdict (test_core.test_core_standalone.AlignmentTestMethods) getting the alignment as a dictionary ... ok test_hasTerminalStops (test_core.test_core_standalone.AlignmentTestMethods) test truth values for terminal stops ... ok test_init_from_strings (test_core.test_core_standalone.AlignmentTestMethods) testing constructing an alignment from a dictionary of strings ... ok test_numberseqs (test_core.test_core_standalone.AlignmentTestMethods) testing the number of sequences ... ok test_picklability (test_core.test_core_standalone.AlignmentTestMethods) Pickle an alignment containing an annotated sequence ... ok test_replaceSeqs (test_core.test_core_standalone.AlignmentTestMethods) synchronize gaps between protein seqs and codon seqs ... ok test_reversecomplement (test_core.test_core_standalone.AlignmentTestMethods) test reverse complementing of Alignments and SequenceCollection. ... ok test_reversecomplement_with_ambig (test_core.test_core_standalone.AlignmentTestMethods) correctly reverse complement with ambiguous bases ... ok test_sample (test_core.test_core_standalone.AlignmentTestMethods) Test sample generation ... ok test_sample_tuples (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_sample_with_replacement (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_seqnames (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_slice (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_slice_align (test_core.test_core_standalone.AlignmentTestMethods) test slicing of sequences ... ok test_slidingWindows (test_core.test_core_standalone.AlignmentTestMethods) test slicing of sequences ... ok test_translate (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_variablePositions (test_core.test_core_standalone.AlignmentTestMethods) ... ok test_withoutAnyGaps (test_core.test_core_standalone.AlignmentTestMethods) test removal of all gaps (any entries in alignment column are gaps) ... ok test_withoutRedundantGaps (test_core.test_core_standalone.AlignmentTestMethods) test removal of redundant gaps (all entries in alignment column are gaps) ... ok test_withoutTerminalStopCodons (test_core.test_core_standalone.AlignmentTestMethods) test without terminal stop handling ... ok test_clustal (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_fasta (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_gde (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_msf (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_paml (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_phylip_interleaved (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_phylipsequential (test_core.test_core_standalone.ReadingWritingFileFormats) ... ok test_write_unknown_raises (test_core.test_core_standalone.ReadingWritingFileFormats) writing unknown format raises FileFormatError ... ok test_ambig_translate (test_core.test_core_standalone.SequenceTestMethods) test of translating seqs ... ok test_getInMotifSize (test_core.test_core_standalone.SequenceTestMethods) test accuracy of chunking various sizes ... ok test_getlength (test_core.test_core_standalone.SequenceTestMethods) testing getting length ... ok test_hasTerminalStop (test_core.test_core_standalone.SequenceTestMethods) test check for terminal stop codons ... ok test_reversecomplement (test_core.test_core_standalone.SequenceTestMethods) testing reversal and complementing of a sequence ... ok test_slidingWindows (test_core.test_core_standalone.SequenceTestMethods) test sliding window along sequences ... ok test_translate (test_core.test_core_standalone.SequenceTestMethods) test of translating seqs ... ok test_withoutTerminalStopCodon (test_core.test_core_standalone.SequenceTestMethods) testing deleting terminal stop ... ok test_core/test_features.rst Doctest: test_features.rst ... ok test__link (test_core.test_entity.EntityTests) Tests linking for cPickle. ... ok test_child (test_core.test_entity.EntityTests) Test child manipulation ... ok test_coords (test_core.test_entity.EntityTests) ... ok test_coords2 (test_core.test_entity.EntityTests) ... ok test_copy (test_core.test_entity.EntityTests) ... ok test_del_parent (test_core.test_entity.EntityTests) tests parent removal ... ok test_dispatch (test_core.test_entity.EntityTests) Tests method dispatching. ... ok test_getChildren (test_core.test_entity.EntityTests) Tests if can retrieve children. ... ok test_getMasked (test_core.test_entity.EntityTests) tests if masking works. ... ok test_getSeq (test_core.test_entity.EntityTests) ... ok test_iter (test_core.test_entity.EntityTests) Tests iterations. ... ok test_maskChildren (test_core.test_entity.EntityTests) ... ok test_masking (test_core.test_entity.EntityTests) Test entity masking. ... ok test_modif (test_core.test_entity.EntityTests) Tests modifications. ... ok test_moveRecursively (test_core.test_entity.EntityTests) ... ok test_parent (test_core.test_entity.EntityTests) Test parent manipulation ... ok test_pickle (test_core.test_entity.EntityTests) ... ok test_propagateData (test_core.test_entity.EntityTests) ... ok test_removeHydrogens (test_core.test_entity.EntityTests) ... ok test_selectChildren (test_core.test_entity.EntityTests) ... ok test_setId (test_core.test_entity.EntityTests) Test setting an id. ... ok test_sorted (test_core.test_entity.EntityTests) ... ok test_stripChildren (test_core.test_entity.EntityTests) Tests if removing children works. ... ok test_table (test_core.test_entity.EntityTests) Tests the creation of the SMCRA table. ... ok test_table_set_del_get (test_core.test_entity.EntityTests) test table creation ... ok test_updateIds (test_core.test_entity.EntityTests) Test if ids get updated. ... ok test_Anticodons (test_core.test_genetic_code.GeneticCodeTests) GeneticCode Anticodons should return correct list ... ok test_Blocks (test_core.test_genetic_code.GeneticCodeTests) GeneticCode Blocks should return correct list ... ok test_Synonyms (test_core.test_genetic_code.GeneticCodeTests) GeneticCode Synonyms should return aa -> codon set mapping. ... ok test_cmp (test_core.test_genetic_code.GeneticCodeTests) GeneticCode cmp() should act on code strings ... ok test_getitem_aa (test_core.test_genetic_code.GeneticCodeTests) GeneticCode getitem should return codon set for aa ... ok test_getitem_codon (test_core.test_genetic_code.GeneticCodeTests) GeneticCode getitem should return amino acid for codon ... ok test_getitem_invalid_length (test_core.test_genetic_code.GeneticCodeTests) GeneticCode getitem should raise InvalidCodonError on wrong length ... ok test_init (test_core.test_genetic_code.GeneticCodeTests) GeneticCode init should work with correct-length sequences ... ok test_sixframes (test_core.test_genetic_code.GeneticCodeTests) GeneticCode sixframes should provide six-frame translation ... ok test_standard_code (test_core.test_genetic_code.GeneticCodeTests) Standard genetic code from NCBI should have correct properties ... ok test_standard_code_lookup (test_core.test_genetic_code.GeneticCodeTests) GeneticCodes should hold codes keyed by id as string and number ... ok test_stop_indexes (test_core.test_genetic_code.GeneticCodeTests) should return stop codon indexes for a specified frame ... ok test_str (test_core.test_genetic_code.GeneticCodeTests) GeneticCode str() should return its code string ... ok test_translate (test_core.test_genetic_code.GeneticCodeTests) GeneticCode translate should return correct amino acid string ... ok test_cmp (test_core.test_info.DbRefTests) DbRef cmp should first try numeric, then alphabetic, cmp. ... ok test_init (test_core.test_info.DbRefTests) DbRef init should insert correct data ... ok test_init_minimal (test_core.test_info.DbRefTests) DbRef minimal init should fill fields as expected ... ok test_int (test_core.test_info.DbRefTests) DbRef int should be the same as the accession int ... ok test_str (test_core.test_info.DbRefTests) DbRef str should be the same as the accession str ... ok test_init_data (test_core.test_info.DbRefsTests) DbRefs init with data should produce expected results ... ok test_init_empty (test_core.test_info.DbRefsTests) DbRefs empty init should work as expected ... ok test_identity (test_core.test_info.InfoTests) Info should get its own new Refs when created ... ok test_init_data (test_core.test_info.InfoTests) Info init with data should put items in correct places ... ok test_init_empty (test_core.test_info.InfoTests) Info empty init should work as expected ... ok test_make_list (test_core.test_info.infoTests) _make_list should always return a list ... ok test_get_coords (test_core.test_location.MapTests) getCoordinates should return raw coordinates matching input ... ok test_init (test_core.test_location.RangeFromStringTests) ... ok test_Extent (test_core.test_location.RangeTests) Range extent should span limits of range ... ok test_Reverse (test_core.test_location.RangeTests) Range Reverse property should return True if any span reversed ... ok test_cmp (test_core.test_location.RangeTests) Ranges should compare equal if they have the same spans ... ok test_contains (test_core.test_location.RangeTests) Range contains an item if any span contains it ... ok test_init (test_core.test_location.RangeTests) Range init from Spans, numbers, or Ranges should work OK. ... ok test_iter (test_core.test_location.RangeTests) Range iter should iterate through each span in turn ... ok test_len (test_core.test_location.RangeTests) Range len should sum span lengths ... ok test_overlaps (test_core.test_location.RangeTests) Range overlaps should return true if any component overlapping ... ok test_overlapsExtent (test_core.test_location.RangeTests) Range overlapsExtent should return true for interleaved ranges ... ok test_reverse (test_core.test_location.RangeTests) Range reverse method should reverse each span ... ok test_simplify (test_core.test_location.RangeTests) Range reduce should group overlapping ranges ... ok test_sort (test_core.test_location.RangeTests) Range sort should sort component spans ... ok test_start_end (test_core.test_location.RangeTests) Range Start and End should behave as expected ... ok test_str (test_core.test_location.RangeTests) Range str should print nested with parens ... ok test_cmp (test_core.test_location.SpanTests) Span cmp should support sort by 1st/2nd index and direction ... ok test_contains (test_core.test_location.SpanTests) Span object contains its start but not its end ... ok test_endsAfter (test_core.test_location.SpanTests) Span endsAfter should match hand-calculated results ... ok test_endsAt (test_core.test_location.SpanTests) Span endsAt should return True if input matches ... ok test_endsBefore (test_core.test_location.SpanTests) Span endsBefore should match hand-calculated results ... ok test_endsInside (test_core.test_location.SpanTests) Span endsInside should return True if input ends inside span ... ok test_init (test_core.test_location.SpanTests) Span object should init with Start, End, and Length ... ok test_iter (test_core.test_location.SpanTests) Span iter should loop through (integer) contents ... ok test_len (test_core.test_location.SpanTests) Span len should return difference between start and end ... ok test_overlaps (test_core.test_location.SpanTests) Span objects should be able to overlap points or spans ... ok test_reverse (test_core.test_location.SpanTests) Span reverse should change direction ... ok test_startsAfter (test_core.test_location.SpanTests) Span startsAfter should match hand-calculated results ... ok test_startsAt (test_core.test_location.SpanTests) Span startsAt should return True if input matches ... ok test_startsBefore (test_core.test_location.SpanTests) Span startsBefore should match hand-calculated results ... ok test_startsInside (test_core.test_location.SpanTests) Span startsInside should return True if input starts inside span ... ok test_str (test_core.test_location.SpanTests) Span str should print start, stop, reverse ... ok test_getByAnnotation (test_core.test_maps.MapTest) ... ok test_getBySequenceAnnotation (test_core.test_maps.MapTest) ... ok test_maps_on_maps (test_core.test_maps.MapTest) ... ok test_spans (test_core.test_maps.MapTest) ... ok test_init (test_core.test_moltype.AlphabetGroupTests) AlphabetGroup should initialize successfully ... ok test_ambiguous_gaps (test_core.test_moltype.CodonAlphabet) ... ok test_exclude (test_core.test_moltype.CodonAlphabet) testing excluding gap motif ... ok test_include (test_core.test_moltype.CodonAlphabet) testing including gap motif ... ok test_init (test_core.test_moltype.CoreObjectGroupTests) CoreObjectGroup should init with basic list of objects. ... ok test_exclude (test_core.test_moltype.DNAAlphabet) Nucleotide alphabet testing excluding gap motif ... ok test_include (test_core.test_moltype.DNAAlphabet) Nucleotide alphabet testing including gap motif ... ok test_usesubset (test_core.test_moltype.DNAAlphabet) testing using a subset of motifs. ... ok test_exclude (test_core.test_moltype.DinucAlphabet) Dinucleotide alphabet testing excluding gap motif ... ok test_include (test_core.test_moltype.DinucAlphabet) Dinucleotide alphabet testing including gap motif ... ok test_usesubset (test_core.test_moltype.DinucAlphabet) testing using a subset of motifs. ... ok test_usesubsetbyfreq (test_core.test_moltype.DinucAlphabet) testing using a subset of motifs by using motif probs. ... ok test_MW (test_core.test_moltype.MolTypeTests) MolType MW should return correct molecular weight ... ok test_canMatch (test_core.test_moltype.MolTypeTests) MolType canMatch should return True if all positions can match ... ok test_canMismatch (test_core.test_moltype.MolTypeTests) MolType canMismatch should return True on any possible mismatch ... ok test_canMispair (test_core.test_moltype.MolTypeTests) MolType canMispair should return True on any possible mispair ... ok test_canPair (test_core.test_moltype.MolTypeTests) MolType canPair should return True if all positions can pair ... ok test_complement (test_core.test_moltype.MolTypeTests) MolType complement should correctly complement sequence ... ok test_contains (test_core.test_moltype.MolTypeTests) MolType contains should return correct result ... ok test_countDegenerate (test_core.test_moltype.MolTypeTests) MolType countDegenerate should return correct degen base count ... ok test_countGaps (test_core.test_moltype.MolTypeTests) MolType countGaps should return correct gap count ... ok test_degap (test_core.test_moltype.MolTypeTests) MolType degap should remove all gaps from sequence ... ok test_disambiguate (test_core.test_moltype.MolTypeTests) MolType disambiguate should remove degenerate bases ... ok test_firstDegenerate (test_core.test_moltype.MolTypeTests) MolType firstDegenerate should return index of first degen symbol ... ok test_firstGap (test_core.test_moltype.MolTypeTests) MolType firstGap should return index of first gap symbol, or None ... ok test_firstInvalid (test_core.test_moltype.MolTypeTests) MolType firstInvalid should return index of first invalid symbol ... ok test_firstNonStrict (test_core.test_moltype.MolTypeTests) MolType firstNonStrict should return index of first non-strict symbol ... ok test_gapList (test_core.test_moltype.MolTypeTests) MolType gapList should return correct gap positions ... ok test_gapMaps (test_core.test_moltype.MolTypeTests) MolType gapMaps should return dicts mapping gapped/ungapped pos ... ok test_gapVector (test_core.test_moltype.MolTypeTests) MolType gapVector should return correct gap positions ... ok test_init_everything (test_core.test_moltype.MolTypeTests) MolType should init OK with all parameters set ... ok test_init_minimal (test_core.test_moltype.MolTypeTests) MolType should init OK with just monomers ... ok test_isDegenerate (test_core.test_moltype.MolTypeTests) MolType isDegenerate should return True if degen symbol in seq ... ok test_isGap (test_core.test_moltype.MolTypeTests) MolType isGap should return True if char is a gap ... ok test_isGapped (test_core.test_moltype.MolTypeTests) MolType isGapped should return True if gaps in seq ... ok test_isStrict (test_core.test_moltype.MolTypeTests) MolType isStrict should return True if all symbols in Monomers ... ok test_isValid (test_core.test_moltype.MolTypeTests) MolType isValid should return True if any unknown symbol in seq ... ok test_iter (test_core.test_moltype.MolTypeTests) MolType iter should iterate over monomer order ... ok test_mustMatch (test_core.test_moltype.MolTypeTests) MolType mustMatch should return True when no possible mismatches ... ok test_mustPair (test_core.test_moltype.MolTypeTests) MolType mustPair should return True when no possible mispairs ... ok test_possibilites (test_core.test_moltype.MolTypeTests) MolType possibilities should return correct # possible sequences ... ok test_rc (test_core.test_moltype.MolTypeTests) MolType rc should correctly reverse-complement sequence ... ok test_stripBad (test_core.test_moltype.MolTypeTests) MolType stripBad should remove any non-base, non-gap chars ... ok test_stripBadAndGaps (test_core.test_moltype.MolTypeTests) MolType stripBadAndGaps should remove gaps and bad chars ... ok test_stripDegenerate (test_core.test_moltype.MolTypeTests) MolType stripDegenerate should remove any degenerate bases ... ok test_contains (test_core.test_moltype.RnaMolTypeTests) RnaMolType should __contain__ the expected symbols. ... ok test_degenerateFromSequence (test_core.test_moltype.RnaMolTypeTests) RnaMolType degenerateFromSequence should give correct results ... ok test_init_all (test_core.test_moltype.make_matches_tests) make_matches with everything should produce correct dict ... ok test_init_degen (test_core.test_moltype.make_matches_tests) make_matches with only degen should work as expected ... ok test_init_empty (test_core.test_moltype.make_matches_tests) make_matches should init ok with no parameters ... ok test_init_gaps (test_core.test_moltype.make_matches_tests) make_matches with only gaps should match all gaps to each other ... ok test_init_monomers (test_core.test_moltype.make_matches_tests) make_matches with only monomers should produce {(i,i):True} ... ok test_init_degen (test_core.test_moltype.make_pairs_tests) make_pairs should add in degenerate combinations as weak pairs ... ok test_init_empty (test_core.test_moltype.make_pairs_tests) make_pairs should init ok with no parameters ... ok test_init_gaps (test_core.test_moltype.make_pairs_tests) make_pairs should add all combinations of gaps as weak pairs ... ok test_init_monomers (test_core.test_moltype.make_pairs_tests) make_pairs with pairs and monomers should equal just the pairs ... ok test_init_pairs (test_core.test_moltype.make_pairs_tests) make_pairs with just pairs should equal the original ... ok test_CharMeaningProfile (test_core.test_profile.ModuleLevelFunctionsTest) CharMeaningProfile: should work as expected ... ok test__add_ (test_core.test_profile.ProfileTests) __add__: should not normalize input or output, just add ... ok test__div_ (test_core.test_profile.ProfileTests) __div__ and __truediv__: always true division b/c __future__.division ... ok test__mul_ (test_core.test_profile.ProfileTests) __mul__: should multiply two profiles, no normalization ... ok test__score_indices (test_core.test_profile.ProfileTests) _score_indices: should work on valid input ... ok test__score_profile (test_core.test_profile.ProfileTests) _score_profile: should work on valid input ... ok test__sub_ (test_core.test_profile.ProfileTests) __sub__: should subtract two profiles, no normalization ... ok test_columnDegeneracy (test_core.test_profile.ProfileTests) columnDegeneracy: shoudl work as expected ... ok test_columnUncertainty (test_core.test_profile.ProfileTests) columnUncertainty: should handle full and empty profiles ... ok test_copy (test_core.test_profile.ProfileTests) copy: should act as expected while rebinding/modifying attributes ... ok test_dataAt (test_core.test_profile.ProfileTests) dataAt: should work on valid position and character ... ok test_distance (test_core.test_profile.ProfileTests) distance: should return correct distance between the profiles ... ok test_hasValidAttributes (test_core.test_profile.ProfileTests) hasValidAttributes: should work for different alphabets/char orders ... ok test_hasValidData (test_core.test_profile.ProfileTests) hasValidData: should work on full and empty profiles ... ok test_init (test_core.test_profile.ProfileTests) __init__: should set all attributed correctly ... ok test_isValid (test_core.test_profile.ProfileTests) isValid: should work as expected ... ok test_make_translation_table (test_core.test_profile.ProfileTests) _make_translation_table: should return correct table from char order ... ok test_normalizePositions (test_core.test_profile.ProfileTests) normalizePositions: should normalize or raise appropriate error ... ok test_normalizeSequences (test_core.test_profile.ProfileTests) normalizeSequences: should normalize or raise appropriate error ... ok test_prettyPrint_four_cases (test_core.test_profile.ProfileTests) prettyPrint: with/without header/transpose/limit ... ok test_prettyPrint_without_parameters (test_core.test_profile.ProfileTests) prettyPrint: should work without parameters passed in ... ok test_randomIndices (test_core.test_profile.ProfileTests) randomIndices: 99% of new frequencies should be within 3*SD ... ok test_randomSequence (test_core.test_profile.ProfileTests) randomSequence: 99% of new frequencies should be within 3*SD ... ok test_reduce_normalization_error (test_core.test_profile.ProfileTests) reduce: fails when input or output can't be normalized ... ok test_reduce_operators (test_core.test_profile.ProfileTests) reduce: should work fine with different operators ... ok test_reduce_wrong_size (test_core.test_profile.ProfileTests) reduce: should fail when profiles have different sizes ... ok test_rowDegeneracy (test_core.test_profile.ProfileTests) rowDegneracy: should work as expected ... ok test_rowMax (test_core.test_profile.ProfileTests) rowMax should return max value in each row ... ok test_rowUncertainty (test_core.test_profile.ProfileTests) rowUncertainty: should handle full and empty profiles ... ok test_score_no_trans_table (test_core.test_profile.ProfileTests) score: should work when no translation table is present ... ok test_score_profile (test_core.test_profile.ProfileTests) score: should work correctly for Profile as input ... ok test_score_sequence (test_core.test_profile.ProfileTests) score: should work correctly for Sequence as input ... ok test_score_sequence_object (test_core.test_profile.ProfileTests) score: should work correctly on Sequence object as input ... ok test_str (test_core.test_profile.ProfileTests) __str__: should return string representation of data in profile ... ok test_toConsensus (test_core.test_profile.ProfileTests) toConsensus: should work with all the different options ... ok test_toConsensus_include_all (test_core.test_profile.ProfileTests) toConsensus: Should include all possibilities when include_all=True ... ok test_toLogOddsMatrix (test_core.test_profile.ProfileTests) toLogOddsMatrix: should work as expected ... ok test_toOddsMatrix (test_core.test_profile.ProfileTests) toOddsMatrix: should work on valid data or raise an error ... ok test_DenseAlignment_without_moltype (test_core.test_seq_aln_integration.AllTests) Expect MolType to be picked up from the sequences. ... ok test_aln_equality (test_core.test_seq_aln_integration.AllTests) ... ok test_names (test_core.test_seq_aln_integration.AllTests) ... ok test_printing_named_seqs (test_core.test_seq_aln_integration.AllTests) Printing named seqs should work the same on Aln and DenseAln ... ok test_printing_unnamed_seqs (test_core.test_seq_aln_integration.AllTests) Printing unnamed sequences should work the same on Aln and DenseAln ... ok test_seqFreqs (test_core.test_seq_aln_integration.AllTests) seqFreqs should work the same on Alignment and DenseAlignment ... ok test_seq_equality (test_core.test_seq_aln_integration.AllTests) ... ok test_seq_ungapping (test_core.test_seq_aln_integration.AllTests) ... ok test_subset_positions_Alignment (test_core.test_seq_aln_integration.AllTests) ... ok test_subset_positions_DenseAlignment (test_core.test_seq_aln_integration.AllTests) ... ok test_subset_seqs_Alignment (test_core.test_seq_aln_integration.AllTests) ... ok test_subset_seqs_DenseAlignment (test_core.test_seq_aln_integration.AllTests) ... ok test_takePositions_sequence_order (test_core.test_seq_aln_integration.AllTests) Alignment takePositions should maintain seq order ... ok test_the_rest_of_ModelSequence (test_core.test_seq_aln_integration.AllTests) The class ModelSequence has 14 methods, but only 2 unittests. ... ok test_MW (test_core.test_sequence.CodonSequenceTests) Sequence MW should return correct molecular weight ... ok test_canMatch (test_core.test_sequence.CodonSequenceTests) Sequence canMatch should return True if all positions can match ... ok test_canMismatch (test_core.test_sequence.CodonSequenceTests) Sequence canMismatch should return True on any possible mismatch ... ok test_canMispair (test_core.test_sequence.CodonSequenceTests) Sequence canMispair should return True on any possible mispair ... ok test_canPair (test_core.test_sequence.CodonSequenceTests) Sequence canPair should return True if all positions can pair ... ok test_compare_to_string (test_core.test_sequence.CodonSequenceTests) Sequence should compare equal to same string. ... ok test_complement (test_core.test_sequence.CodonSequenceTests) Sequence complement should correctly complement sequence ... ok test_consistent_gap_degen_handling (test_core.test_sequence.CodonSequenceTests) gap degen character should be treated consistently ... ok test_contains (test_core.test_sequence.CodonSequenceTests) Sequence contains should return correct result ... ok test_conversion (test_core.test_sequence.CodonSequenceTests) Should convert t to u automatically ... ok test_countDegenerate (test_core.test_sequence.CodonSequenceTests) Sequence countDegenerate should return correct degen base count ... ok test_countGaps (test_core.test_sequence.CodonSequenceTests) Sequence countGaps should return correct gap count ... ok test_degap (test_core.test_sequence.CodonSequenceTests) Sequence degap should remove all gaps from sequence ... ok test_diff (test_core.test_sequence.CodonSequenceTests) Sequence diff should count 1 for each difference between sequences ... ok test_disambiguate (test_core.test_sequence.CodonSequenceTests) Sequence disambiguate should remove degenerate bases ... ok test_distance (test_core.test_sequence.CodonSequenceTests) Sequence distance should calculate correctly based on function ... ok test_firstDegenerate (test_core.test_sequence.CodonSequenceTests) Sequence firstDegenerate should return index of first degen symbol ... ok test_firstGap (test_core.test_sequence.CodonSequenceTests) Sequence firstGap should return index of first gap symbol, or None ... ok test_firstNonStrict (test_core.test_sequence.CodonSequenceTests) Sequence firstNonStrict should return index of first non-strict symbol ... ok test_fracDiff (test_core.test_sequence.CodonSequenceTests) Sequence fracDiff should return difference between sequences ... ok test_fracDiffGaps (test_core.test_sequence.CodonSequenceTests) Sequence fracDiffGaps should return difference in gap positions ... ok test_fracDiffNonGaps (test_core.test_sequence.CodonSequenceTests) Sequence fracDiffNonGaps should return differences at non-gaps ... ok test_fracSame (test_core.test_sequence.CodonSequenceTests) Sequence fracSame should return similarity between sequences ... ok test_fracSameGaps (test_core.test_sequence.CodonSequenceTests) Sequence fracSameGaps should return similarity in gap positions ... ok test_fracSameNonGaps (test_core.test_sequence.CodonSequenceTests) Sequence fracSameNonGaps should return similarities at non-gaps ... ok test_fracSimilar (test_core.test_sequence.CodonSequenceTests) Sequence fracSimilar should return the fraction similarity ... ok test_gapList (test_core.test_sequence.CodonSequenceTests) Sequence gapList should return correct gap positions ... ok test_gapMaps (test_core.test_sequence.CodonSequenceTests) Sequence gapMaps should return dicts mapping gapped/ungapped pos ... ok test_gapVector (test_core.test_sequence.CodonSequenceTests) Sequence gapVector should return correct gap positions ... ok test_init (test_core.test_sequence.CodonSequenceTests) Sequence should do round-trip from string ... ok test_init_data (test_core.test_sequence.CodonSequenceTests) Sequence init with data should set data in correct location ... ok test_init_empty (test_core.test_sequence.CodonSequenceTests) Sequence and subclasses should init correctly. ... ok test_init_other_seq (test_core.test_sequence.CodonSequenceTests) Sequence init with other seq should preserve name and info. ... ok test_isDegenerate (test_core.test_sequence.CodonSequenceTests) Sequence isDegenerate should return True if degen symbol in seq ... ok test_isGap (test_core.test_sequence.CodonSequenceTests) Sequence isGap should return True if char is a valid gap char ... ok test_isGapped (test_core.test_sequence.CodonSequenceTests) Sequence isGapped should return True if gaps in seq ... ok test_isStrict (test_core.test_sequence.CodonSequenceTests) Sequence isStrict should return True if all symbols in Monomers ... ok test_iter (test_core.test_sequence.CodonSequenceTests) Sequence iter should iterate over sequence ... ok test_matrixDistance (test_core.test_sequence.CodonSequenceTests) Sequence matrixDistance should look up distances from a matrix ... ok test_mustMatch (test_core.test_sequence.CodonSequenceTests) Sequence mustMatch should return True when no possible mismatches ... ok test_mustPair (test_core.test_sequence.CodonSequenceTests) Sequence mustPair should return True when no possible mispairs ... ok test_possibilites (test_core.test_sequence.CodonSequenceTests) Sequence possibilities should return correct # possible sequences ... ok test_rc (test_core.test_sequence.CodonSequenceTests) Sequence rc should correctly reverse-complement sequence ... ok test_serialize (test_core.test_sequence.CodonSequenceTests) Sequence should be serializable ... ok test_shuffle (test_core.test_sequence.CodonSequenceTests) Sequence shuffle should return new random sequence w/ same monomers ... ok test_slice (test_core.test_sequence.CodonSequenceTests) Sequence slicing should work as expected ... ok test_stripBad (test_core.test_sequence.CodonSequenceTests) Sequence stripBad should remove any non-base, non-gap chars ... ok test_stripBadAndGaps (test_core.test_sequence.CodonSequenceTests) Sequence stripBadAndGaps should remove gaps and bad chars ... ok test_stripDegenerate (test_core.test_sequence.CodonSequenceTests) Sequence stripDegenerate should remove any degenerate bases ... ok test_toDna (test_core.test_sequence.CodonSequenceTests) Returns copy of self as DNA. ... ok test_toFasta (test_core.test_sequence.CodonSequenceTests) Sequence toFasta() should return Fasta-format string ... ok test_toKwords (test_core.test_sequence.CodonSequenceTests) Sequence toKwords should give expected counts ... ok test_toRna (test_core.test_sequence.CodonSequenceTests) Returns copy of self as RNA. ... ok test_withTerminiUnknown (test_core.test_sequence.CodonSequenceTests) withTerminiUnknown should reset termini to unknown char ... ok test_degap (test_core.test_sequence.DnaSequenceGapTests) Gapped sequence degap() should return correct array ... ok test_gaps (test_core.test_sequence.DnaSequenceGapTests) Gapped sequence gaps() should return correct array ... ok test_init (test_core.test_sequence.DnaSequenceGapTests) Gapped sequence should init ok ... ok test_nongaps (test_core.test_sequence.DnaSequenceGapTests) Gapped sequence nongaps() should return correct array ... ok test_regap (test_core.test_sequence.DnaSequenceGapTests) Gapped sequence regap() should return correct sequence ... ok test_init (test_core.test_sequence.DnaSequenceTests) Sequence should do round-trip from string ... ok test_toFasta (test_core.test_sequence.DnaSequenceTests) Sequence toFasta() should return Fasta-format string ... ok test_toKwords (test_core.test_sequence.DnaSequenceTests) Sequence toKwords should give expected counts ... ok test_toPhylip (test_core.test_sequence.DnaSequenceTests) Sequence toPhylip() should return one-line phylip string ... ok test_MW (test_core.test_sequence.ModelSequenceTests) Sequence MW should return correct molecular weight ... ok test_canMatch (test_core.test_sequence.ModelSequenceTests) Sequence canMatch should return True if all positions can match ... ok test_canMismatch (test_core.test_sequence.ModelSequenceTests) Sequence canMismatch should return True on any possible mismatch ... ok test_canMispair (test_core.test_sequence.ModelSequenceTests) Sequence canMispair should return True on any possible mispair ... ok test_canPair (test_core.test_sequence.ModelSequenceTests) Sequence canPair should return True if all positions can pair ... ok test_compare_to_string (test_core.test_sequence.ModelSequenceTests) Sequence should compare equal to same string. ... ok test_complement (test_core.test_sequence.ModelSequenceTests) Sequence complement should correctly complement sequence ... ok test_consistent_gap_degen_handling (test_core.test_sequence.ModelSequenceTests) gap degen character should be treated consistently ... ok test_contains (test_core.test_sequence.ModelSequenceTests) Sequence contains should return correct result ... ok test_conversion (test_core.test_sequence.ModelSequenceTests) Should convert t to u automatically ... ok test_countDegenerate (test_core.test_sequence.ModelSequenceTests) Sequence countDegenerate should return correct degen base count ... ok test_countGaps (test_core.test_sequence.ModelSequenceTests) Sequence countGaps should return correct gap count ... ok test_degap (test_core.test_sequence.ModelSequenceTests) Sequence degap should remove all gaps from sequence ... ok test_diff (test_core.test_sequence.ModelSequenceTests) Sequence diff should count 1 for each difference between sequences ... ok test_disambiguate (test_core.test_sequence.ModelSequenceTests) Sequence disambiguate should remove degenerate bases ... ok test_distance (test_core.test_sequence.ModelSequenceTests) Sequence distance should calculate correctly based on function ... ok test_distance_indices (test_core.test_sequence.ModelSequenceTests) ModelSequence distance should work with function of indices ... ok test_firstDegenerate (test_core.test_sequence.ModelSequenceTests) Sequence firstDegenerate should return index of first degen symbol ... ok test_firstGap (test_core.test_sequence.ModelSequenceTests) Sequence firstGap should return index of first gap symbol, or None ... ok test_firstNonStrict (test_core.test_sequence.ModelSequenceTests) Sequence firstNonStrict should return index of first non-strict symbol ... ok test_fracDiff (test_core.test_sequence.ModelSequenceTests) Sequence fracDiff should return difference between sequences ... ok test_fracDiffGaps (test_core.test_sequence.ModelSequenceTests) Sequence fracDiffGaps should return difference in gap positions ... ok test_fracDiffNonGaps (test_core.test_sequence.ModelSequenceTests) Sequence fracDiffNonGaps should return differences at non-gaps ... ok test_fracSame (test_core.test_sequence.ModelSequenceTests) Sequence fracSame should return similarity between sequences ... ok test_fracSameGaps (test_core.test_sequence.ModelSequenceTests) Sequence fracSameGaps should return similarity in gap positions ... ok test_fracSameNonGaps (test_core.test_sequence.ModelSequenceTests) Sequence fracSameNonGaps should return similarities at non-gaps ... ok test_fracSimilar (test_core.test_sequence.ModelSequenceTests) Sequence fracSimilar should return the fraction similarity ... ok test_gapArray (test_core.test_sequence.ModelSequenceTests) Sequence gapArray should return array of gaps ... ok test_gapIndices (test_core.test_sequence.ModelSequenceTests) Sequence gapIndices should return positions of gaps ... ok test_gapList (test_core.test_sequence.ModelSequenceTests) Sequence gapList should return correct gap positions ... ok test_gapMaps (test_core.test_sequence.ModelSequenceTests) Sequence gapMaps should return dicts mapping gapped/ungapped pos ... ok test_gapVector (test_core.test_sequence.ModelSequenceTests) Sequence gapVector should return correct gap positions ... ok test_init_data (test_core.test_sequence.ModelSequenceTests) Sequence init with data should set data in correct location ... ok test_init_empty (test_core.test_sequence.ModelSequenceTests) Sequence and subclasses should init correctly. ... ok test_init_other_seq (test_core.test_sequence.ModelSequenceTests) Sequence init with other seq should preserve name and info. ... ok test_isDegenerate (test_core.test_sequence.ModelSequenceTests) Sequence isDegenerate should return True if degen symbol in seq ... ok test_isGap (test_core.test_sequence.ModelSequenceTests) Sequence isGap should return True if char is a valid gap char ... ok test_isGapped (test_core.test_sequence.ModelSequenceTests) Sequence isGapped should return True if gaps in seq ... ok test_isStrict (test_core.test_sequence.ModelSequenceTests) Sequence isStrict should return True if all symbols in Monomers ... ok test_iter (test_core.test_sequence.ModelSequenceTests) Sequence iter should iterate over sequence ... ok test_matrixDistance (test_core.test_sequence.ModelSequenceTests) Sequence matrixDistance should look up distances from a matrix ... ok test_mustMatch (test_core.test_sequence.ModelSequenceTests) Sequence mustMatch should return True when no possible mismatches ... ok test_mustPair (test_core.test_sequence.ModelSequenceTests) Sequence mustPair should return True when no possible mispairs ... ok test_possibilites (test_core.test_sequence.ModelSequenceTests) Sequence possibilities should return correct # possible sequences ... ok test_rc (test_core.test_sequence.ModelSequenceTests) Sequence rc should correctly reverse-complement sequence ... ok test_serialize (test_core.test_sequence.ModelSequenceTests) Sequence should be serializable ... ok test_shuffle (test_core.test_sequence.ModelSequenceTests) Sequence shuffle should return new random sequence w/ same monomers ... ok test_slice (test_core.test_sequence.ModelSequenceTests) Sequence slicing should work as expected ... ok test_stripBad (test_core.test_sequence.ModelSequenceTests) Sequence stripBad should remove any non-base, non-gap chars ... ok test_stripBadAndGaps (test_core.test_sequence.ModelSequenceTests) Sequence stripBadAndGaps should remove gaps and bad chars ... ok test_stripDegenerate (test_core.test_sequence.ModelSequenceTests) Sequence stripDegenerate should remove any degenerate bases ... ok test_toDna (test_core.test_sequence.ModelSequenceTests) Returns copy of self as DNA. ... ok test_toFasta (test_core.test_sequence.ModelSequenceTests) Sequence toFasta() should return Fasta-format string ... ok test_toRna (test_core.test_sequence.ModelSequenceTests) Returns copy of self as RNA. ... ok test_withTerminiUnknown (test_core.test_sequence.ModelSequenceTests) withTerminiUnknown should reset termini to unknown char ... ok test_ModelDnaCodonSequence (test_core.test_sequence.SequenceIntegrationTests) ModelDnaCodonSequence should behave as expected ... ok test_ModelRnaCodonSequence (test_core.test_sequence.SequenceIntegrationTests) ModelRnaCodonSequence should behave as expected ... ok test_model_to_model (test_core.test_sequence.SequenceIntegrationTests) Model sequence should convert to model sequence ... ok test_model_to_regular (test_core.test_sequence.SequenceIntegrationTests) Model sequence should convert to regular sequence ... ok test_regular_to_model (test_core.test_sequence.SequenceIntegrationTests) Regular sequence should convert to model sequence ... ok test_regular_to_regular (test_core.test_sequence.SequenceIntegrationTests) Regular sequence should convert to regular sequence ... ok test_DnaSequence (test_core.test_sequence.SequenceSubclassTests) DnaSequence should behave as expected ... ok test_MW (test_core.test_sequence.SequenceTests) Sequence MW should return correct molecular weight ... ok test_canMatch (test_core.test_sequence.SequenceTests) Sequence canMatch should return True if all positions can match ... ok test_canMismatch (test_core.test_sequence.SequenceTests) Sequence canMismatch should return True on any possible mismatch ... ok test_canMispair (test_core.test_sequence.SequenceTests) Sequence canMispair should return True on any possible mispair ... ok test_canPair (test_core.test_sequence.SequenceTests) Sequence canPair should return True if all positions can pair ... ok test_compare_to_string (test_core.test_sequence.SequenceTests) Sequence should compare equal to same string. ... ok test_complement (test_core.test_sequence.SequenceTests) Sequence complement should correctly complement sequence ... ok test_consistent_gap_degen_handling (test_core.test_sequence.SequenceTests) gap degen character should be treated consistently ... ok test_contains (test_core.test_sequence.SequenceTests) Sequence contains should return correct result ... ok test_conversion (test_core.test_sequence.SequenceTests) Should convert t to u automatically ... ok test_countDegenerate (test_core.test_sequence.SequenceTests) Sequence countDegenerate should return correct degen base count ... ok test_countGaps (test_core.test_sequence.SequenceTests) Sequence countGaps should return correct gap count ... ok test_degap (test_core.test_sequence.SequenceTests) Sequence degap should remove all gaps from sequence ... ok test_diff (test_core.test_sequence.SequenceTests) Sequence diff should count 1 for each difference between sequences ... ok test_disambiguate (test_core.test_sequence.SequenceTests) Sequence disambiguate should remove degenerate bases ... ok test_distance (test_core.test_sequence.SequenceTests) Sequence distance should calculate correctly based on function ... ok test_firstDegenerate (test_core.test_sequence.SequenceTests) Sequence firstDegenerate should return index of first degen symbol ... ok test_firstGap (test_core.test_sequence.SequenceTests) Sequence firstGap should return index of first gap symbol, or None ... ok test_firstNonStrict (test_core.test_sequence.SequenceTests) Sequence firstNonStrict should return index of first non-strict symbol ... ok test_fracDiff (test_core.test_sequence.SequenceTests) Sequence fracDiff should return difference between sequences ... ok test_fracDiffGaps (test_core.test_sequence.SequenceTests) Sequence fracDiffGaps should return difference in gap positions ... ok test_fracDiffNonGaps (test_core.test_sequence.SequenceTests) Sequence fracDiffNonGaps should return differences at non-gaps ... ok test_fracSame (test_core.test_sequence.SequenceTests) Sequence fracSame should return similarity between sequences ... ok test_fracSameGaps (test_core.test_sequence.SequenceTests) Sequence fracSameGaps should return similarity in gap positions ... ok test_fracSameNonGaps (test_core.test_sequence.SequenceTests) Sequence fracSameNonGaps should return similarities at non-gaps ... ok test_fracSimilar (test_core.test_sequence.SequenceTests) Sequence fracSimilar should return the fraction similarity ... ok test_gapList (test_core.test_sequence.SequenceTests) Sequence gapList should return correct gap positions ... ok test_gapMaps (test_core.test_sequence.SequenceTests) Sequence gapMaps should return dicts mapping gapped/ungapped pos ... ok test_gapVector (test_core.test_sequence.SequenceTests) Sequence gapVector should return correct gap positions ... ok test_init_data (test_core.test_sequence.SequenceTests) Sequence init with data should set data in correct location ... ok test_init_empty (test_core.test_sequence.SequenceTests) Sequence and subclasses should init correctly. ... ok test_init_other_seq (test_core.test_sequence.SequenceTests) Sequence init with other seq should preserve name and info. ... ok test_isDegenerate (test_core.test_sequence.SequenceTests) Sequence isDegenerate should return True if degen symbol in seq ... ok test_isGap (test_core.test_sequence.SequenceTests) Sequence isGap should return True if char is a valid gap char ... ok test_isGapped (test_core.test_sequence.SequenceTests) Sequence isGapped should return True if gaps in seq ... ok test_isStrict (test_core.test_sequence.SequenceTests) Sequence isStrict should return True if all symbols in Monomers ... ok test_iter (test_core.test_sequence.SequenceTests) Sequence iter should iterate over sequence ... ok test_matrixDistance (test_core.test_sequence.SequenceTests) Sequence matrixDistance should look up distances from a matrix ... ok test_mustMatch (test_core.test_sequence.SequenceTests) Sequence mustMatch should return True when no possible mismatches ... ok test_mustPair (test_core.test_sequence.SequenceTests) Sequence mustPair should return True when no possible mispairs ... ok test_possibilites (test_core.test_sequence.SequenceTests) Sequence possibilities should return correct # possible sequences ... ok test_rc (test_core.test_sequence.SequenceTests) Sequence rc should correctly reverse-complement sequence ... ok test_serialize (test_core.test_sequence.SequenceTests) Sequence should be serializable ... ok test_shuffle (test_core.test_sequence.SequenceTests) Sequence shuffle should return new random sequence w/ same monomers ... ok test_slice (test_core.test_sequence.SequenceTests) Sequence slicing should work as expected ... ok test_stripBad (test_core.test_sequence.SequenceTests) Sequence stripBad should remove any non-base, non-gap chars ... ok test_stripBadAndGaps (test_core.test_sequence.SequenceTests) Sequence stripBadAndGaps should remove gaps and bad chars ... ok test_stripDegenerate (test_core.test_sequence.SequenceTests) Sequence stripDegenerate should remove any degenerate bases ... ok test_toDna (test_core.test_sequence.SequenceTests) Returns copy of self as DNA. ... ok test_toFasta (test_core.test_sequence.SequenceTests) Sequence toFasta() should return Fasta-format string ... ok test_toRna (test_core.test_sequence.SequenceTests) Returns copy of self as RNA. ... ok test_withTerminiUnknown (test_core.test_sequence.SequenceTests) withTerminiUnknown should reset termini to unknown char ... ok test_ascii (test_core.test_tree.BigTreeSingleTests) ... ok test_getEdgeNames (test_core.test_tree.BigTreeSingleTests) testing (well, exercising at least), getedgenames ... ok test_getTipNames (test_core.test_tree.BigTreeSingleTests) testing (well, exercising at least), getTipNames ... ok test_getsubtree (test_core.test_tree.BigTreeSingleTests) testing getting a subtree ... ok test_getsubtree_2 (test_core.test_tree.BigTreeSingleTests) tree.getSubTree() has same pairwise tip dists as tree (len0 node) ... ok test_getsubtree_3 (test_core.test_tree.BigTreeSingleTests) tree.getSubTree() has same pairwise tip dists as tree ... ok test_getsubtree_4 (test_core.test_tree.BigTreeSingleTests) tree.getSubTree() handles keep_root correctly ... ok test_sorttree (test_core.test_tree.BigTreeSingleTests) testing (well, exercising at least) treesort ... ok test__find_midpoint_nodes (test_core.test_tree.PhyloNodeTests) _find_midpoint_nodes should return nodes surrounding the midpoint ... ok test_compareByTipDistances (test_core.test_tree.PhyloNodeTests) ... ok test_compareByTipDistances_sample (test_core.test_tree.PhyloNodeTests) ... ok test_distance (test_core.test_tree.PhyloNodeTests) PhyloNode Distance should report correct distance between nodes ... ok test_getMaxTipTipDistance (test_core.test_tree.PhyloNodeTests) getMaxTipTipDistance should get max tip distance across tree ... ok test_init (test_core.test_tree.PhyloNodeTests) Check PhyloNode constructor ... ok test_maxTipTipDistance (test_core.test_tree.PhyloNodeTests) maxTipTipDistance returns the max dist between any pair of tips ... ok test_prune (test_core.test_tree.PhyloNodeTests) prune should reconstruct correct topology and Lengths of tree. ... ok test_rootAtMidpoint (test_core.test_tree.PhyloNodeTests) rootAtMidpoint performs midpoint rooting ... ok test_rootAtMidpoint2 (test_core.test_tree.PhyloNodeTests) rootAtMidpoint works when midpoint is on both sides of root ... ok test_rootAtMidpoint3 (test_core.test_tree.PhyloNodeTests) midpoint between nodes should behave correctly ... ok test_rootAtMidpoint4 (test_core.test_tree.PhyloNodeTests) midpoint should be selected correctly when it is an internal node ... ok test_rootAtMidpoint5 (test_core.test_tree.PhyloNodeTests) midpoint should be selected correctly when on an even 2tip tree ... ok test_scaleBranchLengths (test_core.test_tree.PhyloNodeTests) scaleBranchLengths should correclty scale branch lengths. ... ok test_setMaxTipTipDistance (test_core.test_tree.PhyloNodeTests) setMaxTipTipDistance sets MaxDistTips across tree ... ok test_setTipDistances (test_core.test_tree.PhyloNodeTests) setTipDistances should correctly set tip distances. ... ok test_str (test_core.test_tree.PhyloNodeTests) PhyloNode str should give expected results ... ok test_tipToTipDistances_endpoints (test_core.test_tree.PhyloNodeTests) Test getting specifc tip distances with tipToTipDistances ... ok test_tipsWithinDistance (test_core.test_tree.PhyloNodeTests) tipsWithinDistance returns tips that are within distance from self ... ok test_tipsWithinDistance_nodistances (test_core.test_tree.PhyloNodeTests) tipsWithinDistance returns tips that are within distance from self ... ok test_totalDescendingBranchLength (test_core.test_tree.PhyloNodeTests) totalDescendingBranchLength returns total branchlength below self ... ok test_unrooted (test_core.test_tree.PhyloNodeTests) unrooted should preserve tips, drop a node ... ok test_reroot (test_core.test_tree.SmallTreeReshapeTestClass) ... ok test_rootswaps (test_core.test_tree.SmallTreeReshapeTestClass) testing (well, exercising at least), unrooted ... ok test_sameShape (test_core.test_tree.SmallTreeReshapeTestClass) test topology assessment ... ok test_ascii (test_core.test_tree.TestTree) ... ok test_getsubtree (test_core.test_tree.TestTree) testing getting a subtree ... ok test_getsubtree_2 (test_core.test_tree.TestTree) tree.getSubTree() has same pairwise tip dists as tree (len0 node) ... ok test_getsubtree_3 (test_core.test_tree.TestTree) tree.getSubTree() has same pairwise tip dists as tree ... ok test_getsubtree_4 (test_core.test_tree.TestTree) tree.getSubTree() handles keep_root correctly ... ok test_sorttree (test_core.test_tree.TestTree) testing (well, exercising at least) treesort ... ok test_one_child (test_core.test_tree.Test_tip_tip_distances_array) tip_to_tip should work for tree with a single child ... ok test_one_level (test_core.test_tree.Test_tip_tip_distances_array) tip_to_tip should work for one-level multifurcating tree ... ok test_std (test_core.test_tree.Test_tip_tip_distances_array) tip_to_tip should work for small but complex tree ... ok test_two_level (test_core.test_tree.Test_tip_tip_distances_array) tip_to_tip should work for two-level tree ... ok test_XML (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_balanced (test_core.test_tree.TreeInterfaceForLikelihoodFunction) balancing an unrooted tree ... ok test_eq (test_core.test_tree.TreeInterfaceForLikelihoodFunction) testing (well, exercising at least), __eq__ ... ok test_getConnectingNode (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getEdgeNames (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getEdgeNamesUseOutgroup (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getEdgeVector (test_core.test_tree.TreeInterfaceForLikelihoodFunction) correctly return vector of edges from a tree ... ok test_getNewick (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getNewickRecursive (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getNodeMatchingName (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_getsetParamValue (test_core.test_tree.TreeInterfaceForLikelihoodFunction) test getting, setting of param values ... ok test_making_from_list (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_params_merge (test_core.test_tree.TreeInterfaceForLikelihoodFunction) ... ok test_parser (test_core.test_tree.TreeInterfaceForLikelihoodFunction) nasty newick ... ok test_repr (test_core.test_tree.TreeInterfaceForLikelihoodFunction) testing (well, exercising at least), __repr__ ... ok test_str (test_core.test_tree.TreeInterfaceForLikelihoodFunction) testing (well, exercising at least), __str__ ... ok test_Parent (test_core.test_tree.TreeNodeTests) TreeNode Parent should hold correct data and be mutable ... ok test_ancestors (test_core.test_tree.TreeNodeTests) TreeNode ancestors should provide list of ancestors, deepest first ... ok test_append (test_core.test_tree.TreeNodeTests) TreeNode append should add item to end of self ... ok test_bifurcating (test_core.test_tree.TreeNodeTests) Coerces nodes to have <= 2 children ... ok test_childGroups (test_core.test_tree.TreeNodeTests) TreeNode childGroups should divide children by grandchild presence ... ok test_children (test_core.test_tree.TreeNodeTests) TreeNode Children should allow getting/setting children ... ok test_cmp (test_core.test_tree.TreeNodeTests) TreeNode cmp should compare using id ... ok test_compareByNames (test_core.test_tree.TreeNodeTests) Compare names between trees ... ok test_compareBySubsets (test_core.test_tree.TreeNodeTests) compareBySubsets should return the fraction of shared subsets ... ok test_compareName (test_core.test_tree.TreeNodeTests) Compare names between TreeNodes ... ok test_copy (test_core.test_tree.TreeNodeTests) TreeNode.copy() should work on deep trees ... ok test_copyRecursive (test_core.test_tree.TreeNodeTests) TreeNode.copyRecursive() should produce deep copy ... ok test_copyTopology (test_core.test_tree.TreeNodeTests) TreeNode.copyTopology() should produce deep copy ignoring attrs ... ok test_deepcopy (test_core.test_tree.TreeNodeTests) copy.deepcopy should work on TreeNode ... ok test_delitem (test_core.test_tree.TreeNodeTests) TreeNode __delitem__ should delete item and set parent to None ... ok test_delslice (test_core.test_tree.TreeNodeTests) TreeNode __delslice__ should delete items from start to end ... ok test_eq (test_core.test_tree.TreeNodeTests) TreeNode should compare equal if same id ... ok test_extend (test_core.test_tree.TreeNodeTests) TreeNode extend should add many items to end of self ... ok test_getNewick (test_core.test_tree.TreeNodeTests) Should return Newick-style representation ... ok test_getNodeMatchingName (test_core.test_tree.TreeNodeTests) TreeNode getNodeMatchingName should return node that matches name ... ok test_getNodesDict (test_core.test_tree.TreeNodeTests) getNodesDict returns a dict keyed by name, value is node ... ok test_getNodesDict_nonunique_names (test_core.test_tree.TreeNodeTests) getNodesDict raises if non unique names are in tree ... ok test_getitem (test_core.test_tree.TreeNodeTests) TreeNode getitem should return item or slice ... ok test_indexInParent (test_core.test_tree.TreeNodeTests) TreeNode indexInParent should hold correct data ... ok test_init_empty (test_core.test_tree.TreeNodeTests) Empty TreeNode should init OK ... ok test_init_full (test_core.test_tree.TreeNodeTests) TreeNode should init OK with parent, data, and children ... ok test_insert (test_core.test_tree.TreeNodeTests) TreeNode insert should insert item at specified index ... ok test_isRoot (test_core.test_tree.TreeNodeTests) TreeNode isRoot should return True if parent is None ... ok test_isTip (test_core.test_tree.TreeNodeTests) TreeNode isTip should return True if node is a tip ... ok test_iter (test_core.test_tree.TreeNodeTests) TreeNode iter should iterate over children ... ok test_iterNonTips (test_core.test_tree.TreeNodeTests) TreeNode iterNontips should iterate over non-terminal descendants ... ok test_itertips (test_core.test_tree.TreeNodeTests) TreeNode itertips should iterate over terminal descendants ... ok test_lastCommonAncestor (test_core.test_tree.TreeNodeTests) TreeNode LastCommonAncestor should provide last common ancestor ... ok test_len (test_core.test_tree.TreeNodeTests) TreeNode len should return number of children ... ok test_levelorder (test_core.test_tree.TreeNodeTests) ... ok test_lowestCommonAncestor (test_core.test_tree.TreeNodeTests) TreeNode lowestCommonAncestor should return LCA for set of tips ... ok test_makeTreeArray (test_core.test_tree.TreeNodeTests) makeTreeArray maps nodes to the descendants in them ... ok test_multifurcating (test_core.test_tree.TreeNodeTests) Coerces nodes to have <= n children ... ok test_multifurcating_nameunnamed (test_core.test_tree.TreeNodeTests) Coerces nodes to have <= n children ... ok test_nameUnnamedNodes (test_core.test_tree.TreeNodeTests) nameUnnamedNodes assigns an arbitrary value when Name == None ... ok test_ne (test_core.test_tree.TreeNodeTests) TreeNode should compare ne by id or data ... ok test_nonTipChildren (test_core.test_tree.TreeNodeTests) TreeNode nonTipChildren should return all non-terminal children ... ok test_nontips (test_core.test_tree.TreeNodeTests) TreeNode nontips should return all non-terminal descendants ... ok test_pop (test_core.test_tree.TreeNodeTests) TreeNode pop should remove and return child at specified index ... ok test_prune (test_core.test_tree.TreeNodeTests) prune should reconstruct correct topology of tree. ... ok test_reassignNames (test_core.test_tree.TreeNodeTests) reassignNames should rename node names based on dict mapping ... ok test_reassignNames_specific_nodes (test_core.test_tree.TreeNodeTests) reassignNames should rename nodes based on dict mapping ... ok test_remove (test_core.test_tree.TreeNodeTests) TreeNode remove should remove first match by value, not id ... ok test_removeDeleted (test_core.test_tree.TreeNodeTests) removeDeleted should remove all nodes where is_deleted tests true. ... ok test_removeNode (test_core.test_tree.TreeNodeTests) TreeNode removeNode should delete node by id, not value ... ok test_root (test_core.test_tree.TreeNodeTests) TreeNode root() should find root of tree ... ok test_separation (test_core.test_tree.TreeNodeTests) TreeNode separation should return correct number of edges ... ok test_setitem (test_core.test_tree.TreeNodeTests) TreeNode setitem should set item or extended slice of nodes ... ok test_setslice (test_core.test_tree.TreeNodeTests) TreeNode setslice should set old-style slice of nodes ... ok test_siblings (test_core.test_tree.TreeNodeTests) TreeNode siblings() should return all siblings, not self ... ok test_slice (test_core.test_tree.TreeNodeTests) TreeNode slicing should return list, not TreeNode ... ok test_str (test_core.test_tree.TreeNodeTests) TreeNode str should give Newick-style representation ... ok test_subset (test_core.test_tree.TreeNodeTests) subset should return set of leaves that descends from node ... ok test_subsets (test_core.test_tree.TreeNodeTests) subsets should return all subsets descending from a set ... ok test_tipChildren (test_core.test_tree.TreeNodeTests) TreeNode tipChildren should return all terminal children ... ok test_tips (test_core.test_tree.TreeNodeTests) TreeNode tips should return all terminal descendants ... ok test_traverse (test_core.test_tree.TreeNodeTests) TreeNode traverse should iterate over nodes in tree. ... ok test_LoadTree (test_core.test_tree.TreeTests) LoadTree should load a tree from a file or a string ... ok test_aminoAcids (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage aminoAcids should return same object ... ok test_bases (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage bases should return most likely base freqs ... ok test_codons (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage codons should return most likely codon freqs ... ok test_init_data (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage should init with data ... ok test_init_empty (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage should init with empty freqs ... ok test_positionalBases (test_core.test_usage.AminoAcidUsageTests) AminoAcidUsage positionalBases should return best positional bases ... ok test_add (test_core.test_usage.BaseUsageTests) BaseUsage add should sum two base usages ... ok test_aminoAcids (test_core.test_usage.BaseUsageTests) BaseUsage aminoAcids should give the same results as the codons ... ok test_bases (test_core.test_usage.BaseUsageTests) BaseUsage bases() should return same object ... ok test_codons (test_core.test_usage.BaseUsageTests) BaseUsage codons should return most likely codon freqs ... ok test_content (test_core.test_usage.BaseUsageTests) BaseUsage content should return sum of specified bases. ... ok test_copy (test_core.test_usage.BaseUsageTests) BaseUsage copy should work correctly ... ok test_distance (test_core.test_usage.BaseUsageTests) BaseUsage distance() should return dist between two BUs ... ok test_fromCartesian (test_core.test_usage.BaseUsageTests) BaseUsage fromCartesian should init instance from x,y,z ... ok test_getitem (test_core.test_usage.BaseUsageTests) BaseUsage should map key on getitem ... ok test_getitem_multi (test_core.test_usage.BaseUsageTests) BaseUsage should get total frequency on getitem with 2-letter key ... ok test_init_data (test_core.test_usage.BaseUsageTests) BaseUsage should init with arbitrary data ... ok test_init_empty (test_core.test_usage.BaseUsageTests) BaseUsage should init with empty freqs ... ok test_normalize (test_core.test_usage.BaseUsageTests) BaseUsage normalize should work when empty ... ok test_positionalBases (test_core.test_usage.BaseUsageTests) BaseUsage positionalBases should have copy of self at each position ... ok test_setitem (test_core.test_usage.BaseUsageTests) BaseUsage should map keys on setitem ... ok test_toCartesian (test_core.test_usage.BaseUsageTests) BaseUsage toCartesian should return x, y, z from instance ... ok test_add (test_core.test_usage.CodonUsageTests) CodonUsage add should sum two base usages ... ok test_aminoAcids (test_core.test_usage.CodonUsageTests) CodonUsage aminoAcids should correctly count amino acids ... ok test_bases (test_core.test_usage.CodonUsageTests) CodonUsage bases should count bases correctly ... ok test_codons (test_core.test_usage.CodonUsageTests) CodonUsage codons should return same object ... ok test_fingerprint (test_core.test_usage.CodonUsageTests) CodonUsage fingerprint should give correct ratios. ... ok test_getitem (test_core.test_usage.CodonUsageTests) CodonUsage should allow lookup as RNA or DNA, case-insensitive ... ok test_init_empty (test_core.test_usage.CodonUsageTests) Empty CodonUsage init should have 64 codons, all 0 ... ok test_init_string (test_core.test_usage.CodonUsageTests) CodonUsage should count codons in string ... ok test_positionalBases (test_core.test_usage.CodonUsageTests) CodonUsage bases should count bases at each position correctly ... ok test_positionalGC (test_core.test_usage.CodonUsageTests) CodonUsage positionalGC should give correct GC contents. ... ok test_pr2bias (test_core.test_usage.CodonUsageTests) CodonUsage pr2bias should give correct ratios. ... ok test_rscu (test_core.test_usage.CodonUsageTests) CodonUsage rscu should calculate synonymous usage correctly ... ok test_distance (test_core.test_usage.DinucUsageTests) Dinuc distance should calculate Euclidean dist. correctly ... ok test_init_from_seq (test_core.test_usage.DinucUsageTests) DinucUsage should init correctly from string. ... ok test_info (test_core.test_usage.InfoFreqsTests) InfoFreqs info changes should work as expected. ... ok test_init_data (test_core.test_usage.InfoFreqsTests) InfoFreqs init with data should count freqs ... ok test_init_empty (test_core.test_usage.InfoFreqsTests) InfoFreqs empty init should include only required items ... ok test_init_info (test_core.test_usage.InfoFreqsTests) InfoFreqs init from object with Info should get ref to Info ... ok test_normalize (test_core.test_usage.InfoFreqsTests) InfoFreqs normalize should delete non-required keys, if any required ... ok test_aminoAcids (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage aminoAcids should return correct amino acids ... ok test_bases (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage bases should sum bases at each position ... ok test_codons (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage codons should give expected codon freqs ... ok test_getitem (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage getitem should return 1st, 2nd, 3rd in order ... ok test_info (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage info should work as expected ... ok test_init_empty (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage init when empty should set all freqs to 0 ... ok test_normalize (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage normalize should normalize each position ... ok test_positionalBases (test_core.test_usage.PositionalBaseUsageTests) PositionalBaseUsage positionalBases should return same object ... ok test_init (test_core.test_usage.UnsafeBaseUsageTests) UnsafeFreqs uses dict init, so must use += after creation for others ... ok test_normalize (test_core.test_usage.UnsafeBaseUsageTests) UnsafeFreqs should normalize based on the uppercase RNA alphabet ... ok test_call (test_data.test_molecular_weight.WeightCalculatorTests) WeightCalculator should return correct molecular weight ... ok test_BestLogLikelihood (test_evolve.test_best_likelihood.TestGoldman93) ... ok test__take (test_evolve.test_best_likelihood.TestGoldman93) test taking selected rows from an array ... ok test__transpose (test_evolve.test_best_likelihood.TestGoldman93) test transposing an array ... ok test_aligned_columns_to_rows (test_evolve.test_best_likelihood.TestGoldman93) ... ok test_count_column_freqs (test_evolve.test_best_likelihood.TestGoldman93) ... ok test_get_G93_lnL_from_array (test_evolve.test_best_likelihood.TestGoldman93) ... ok test_get_ML_probs (test_evolve.test_best_likelihood.TestGoldman93) ... ok test_conf_int (test_evolve.test_bootstrap.BootstrapTests) testing estimation of confidence intervals. ... ok test_prob (test_evolve.test_bootstrap.BootstrapTests) testing estimation of probability. ... ok test_ancestral_state_alignment_aln_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: difference aln -> different result ... ok test_ancestral_state_alignment_ancestor_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: different ancestor -> different result ... ok test_ancestral_state_alignment_bifurcating_tree (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: handles bifurcating tree correctly ... ok test_ancestral_state_alignment_handles_ancestral_state_calc (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: functions when calc'ing ancestral states ... ok test_ancestral_state_alignment_no_error_on_gap (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: return w/o error with gapped seqs ... ok test_ancestral_state_alignment_non_bifurcating_tree (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: handles non-bifurcating tree correctly ... ok test_ancestral_state_alignment_tree_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_alignment: different result on different tree ... ok test_ancestral_state_methods_handle_bad_ancestor_aln (test_evolve.test_coevolution.AncestorCoevolve) ancestral state methods raise error on bad ancestor alignment ... ok test_ancestral_state_pair_aln_difference (test_evolve.test_coevolution.AncestorCoevolve) acestral_state_pair: different aln -> different result ... ok test_ancestral_state_pair_ancestor_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_pair: difference_ancestor -> different result ... ok test_ancestral_state_pair_handles_ancestral_state_calc (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_position: functions when calc'ing ancestral states ... ok test_ancestral_state_pair_symmetry (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_pair: value[i,j] == value[j,i] ... ok test_ancestral_state_pair_tree_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_pair: different result on different tree ... ok test_ancestral_state_position_aln_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_position: difference aln -> different result ... ok test_ancestral_state_position_ancestor_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_position: difference_ancestor -> different result ... ok test_ancestral_state_position_handles_ancestral_state_calc (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_position: functions when calc'ing ancestral states ... ok test_ancestral_state_position_tree_difference (test_evolve.test_coevolution.AncestorCoevolve) ancestral_state_position: different result on different tree ... ok test_ancestral_states_input_validation (test_evolve.test_coevolution.AncestorCoevolve) ancestral_states_input_validation: all validation steps performed ... ok test_ancestral_states_methods_handle_bad_position_numbers (test_evolve.test_coevolution.AncestorCoevolve) coevolve_* w/ ancestral_states raise ValueError on bad position ... ok test_get_ancestral_seqs (test_evolve.test_coevolution.AncestorCoevolve) get_ancestral_seqs: returns valid collection of ancestral seqs ... ok test_get_ancestral_seqs_handles_ambiguous_residues (test_evolve.test_coevolution.AncestorCoevolve) get_ancestral_seqs: handles ambiguous residues ... ok test_get_ancestral_seqs_handles_gaps (test_evolve.test_coevolution.AncestorCoevolve) get_ancestral_seqs: handles gaps ... ok test_validate_ancestral_seqs_invalid (test_evolve.test_coevolution.AncestorCoevolve) validate_ancestral_seqs: ValueError on incompatible anc. seqs & tree ... ok test_validate_ancestral_seqs_valid (test_evolve.test_coevolution.AncestorCoevolve) validate_ancestral_seqs: does nothing on compatible anc. seqs & tree ... ok test_validate_tree_invalid (test_evolve.test_coevolution.AncestorCoevolve) validate_tree: raises ValueError on incompatible tree and aln ... ok test_validate_tree_valid (test_evolve.test_coevolution.AncestorCoevolve) validate_tree: does nothing on compatible tree and aln ... ok test_alignment_analyses_moltype_dna (test_evolve.test_coevolution.CoevolutionTests) alignment methods work with moltype = DNA ... ok test_alignment_analyses_moltype_protein (test_evolve.test_coevolution.CoevolutionTests) alignment methods work with moltype = PROTEIN ... ok test_alignment_analyses_moltype_rna (test_evolve.test_coevolution.CoevolutionTests) alignment methods work with moltype = RNA ... ok test_aln_position_pairs_cmp_threshold_intramolecular (test_evolve.test_coevolution.CoevolutionTests) aln_position_pairs_ge_threshold: intramolecular matrix ... ok test_aln_position_pairs_ge_threshold_intermolecular (test_evolve.test_coevolution.CoevolutionTests) aln_position_pairs_ge_threshold: intermolecular matrix ... ok test_build_coevolution_matrix_filepath (test_evolve.test_coevolution.CoevolutionTests) build_coevolution_matrix_filepath functions w/ varied input ... ok test_coevolve_alignment (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignment functions as expected with varied input ... ok test_coevolve_alignments (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments: returns correct len(aln1) x len(aln2) matrix ... ok test_coevolve_alignments_different_MolType (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments: different MolTypes supported ... ok test_coevolve_alignments_validation_idenifiers (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments_validation: seq/tree validation functions ... ok test_coevolve_alignments_validation_max_num_seqs (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments_validation: min_num_seqs <= max_num_seqs ... ok test_coevolve_alignments_validation_min_num_seqs (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments_validation: ValueError on fewer than min_num_seqs ... ok test_coevolve_alignments_validation_moltypes (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments_validation: valid for acceptable MolTypes ... ok test_coevolve_alignments_watches_max_num_seqs (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments: filtering or error on too many sequences ... ok test_coevolve_alignments_watches_min_num_seqs (test_evolve.test_coevolution.CoevolutionTests) coevolve_alignments: error on too few sequences ... ok test_coevolve_functions_validate_alignment (test_evolve.test_coevolution.CoevolutionTests) coevolve_*: functions run validate alignment ... ok test_coevolve_pair (test_evolve.test_coevolution.CoevolutionTests) coevolve_pair: returns same as pair methods called directly ... ok test_coevolve_position (test_evolve.test_coevolution.CoevolutionTests) coevolve_position: returns same as position methods called directly ... ok test_count_ge_threshold (test_evolve.test_coevolution.CoevolutionTests) count_ge_threshold works as expected ... ok test_count_ge_threshold_symmetric_ignore_diagonal (test_evolve.test_coevolution.CoevolutionTests) count_ge_threshold works with symmetric and/or ignoring diag = True ... ok test_count_le_threshold (test_evolve.test_coevolution.CoevolutionTests) count_le_threshold works as expected ... ok test_count_le_threshold_symmetric_ignore_diagonal (test_evolve.test_coevolution.CoevolutionTests) count_le_threshold works with symmetric and/or ignoring diag = True ... ok test_csv_and_uncsv (test_evolve.test_coevolution.CoevolutionTests) converting to/from csv matrix results in correct coevolution matrix ... ok test_csv_coevolution_result_error (test_evolve.test_coevolution.CoevolutionTests) matrix -> csv: IOError handled correctly ... ok test_filter_exclude_positions_intermolecular (test_evolve.test_coevolution.CoevolutionTests) filter_exclude_positions: functions for intermolecular data ... ok test_filter_exclude_positions_intramolecular (test_evolve.test_coevolution.CoevolutionTests) filter_exclude_positions: functions for intramolecular data ... ok test_filter_non_parsimony_informative_intermolecular (test_evolve.test_coevolution.CoevolutionTests) non-parsimony informative sites in intermolecular matrix -> null ... ok test_filter_non_parsimony_informative_intramolecular (test_evolve.test_coevolution.CoevolutionTests) non-parsimony informative sites in intramolecular matrix -> null ... ok test_filter_threshold_based_multiple_interdependency_intermolecular (test_evolve.test_coevolution.CoevolutionTests) multiple interdependency filter functions with intermolecular data ... ok test_filter_threshold_based_multiple_interdependency_intramolecular (test_evolve.test_coevolution.CoevolutionTests) multiple interdependency filter functions with intramolecular data ... ok test_freqs_from_aln (test_evolve.test_coevolution.CoevolutionTests) freqs_from_aln: freqs of alphabet chars in aln is calc'ed correctly ... ok test_freqs_to_array (test_evolve.test_coevolution.CoevolutionTests) freqs_to_array: should convert Freqs object to array ... ok test_get_allowed_perturbations (test_evolve.test_coevolution.CoevolutionTests) get_allowed_perturbations: should work for different cutoff values ... ok test_get_dg (test_evolve.test_coevolution.CoevolutionTests) get_dg: returns delta_g vector ... ok test_get_dgg (test_evolve.test_coevolution.CoevolutionTests) get_dgg: returns delta_delta_g value given two delta_g vectors ... ok test_get_positional_frequencies (test_evolve.test_coevolution.CoevolutionTests) get_positional_frequencies: works with non-default scaled_aln_size ... ok test_get_positional_frequencies_w_scale (test_evolve.test_coevolution.CoevolutionTests) get_positional_frequencies: works with default scaled_aln_size ... ok test_get_positional_probabilities_w_def_num_seqs (test_evolve.test_coevolution.CoevolutionTests) get_positional_probabilities: works w/ num_seqs scaled to 100 (def) ... ok test_get_positional_probabilities_w_non_def_num_seqs (test_evolve.test_coevolution.CoevolutionTests) get_positional_probabilities: works w/ non-def num_seqs ... ok test_get_positional_probs_handles_rounding_error_in_freqs (test_evolve.test_coevolution.CoevolutionTests) get_positional_probabilities: works w/ rounding error in freqs ... ok test_get_subalignments (test_evolve.test_coevolution.CoevolutionTests) get_subalignments: works with different alignment sizes and cutoffs ... ok test_identify_aln_positions_above_threshold (test_evolve.test_coevolution.CoevolutionTests) Extracting scores above threshold works as expected ... ok test_is_parsimony_informative_non_default (test_evolve.test_coevolution.CoevolutionTests) is_parsimony_informative functions w non default paramters ... ok test_is_parsimony_informative_non_strict (test_evolve.test_coevolution.CoevolutionTests) is_parsimony_informative functions as expected with strict=False ... ok test_is_parsimony_informative_strict (test_evolve.test_coevolution.CoevolutionTests) is_parsimony_informative functions as expected with strict=True ... ok test_join_positions (test_evolve.test_coevolution.CoevolutionTests) join_positions functions as expected ... ok test_ltm_to_symmetric (test_evolve.test_coevolution.CoevolutionTests) ltm_to_symmetric: making ltm matrices symmetric functions ... ok test_merge_alignments (test_evolve.test_coevolution.CoevolutionTests) merging alignments of same moltype functions as expected ... ok test_merge_alignments_different_moltype (test_evolve.test_coevolution.CoevolutionTests) merging alignments of different moltype functions as expected ... ok test_merge_alignments_ignores_id_following_plus (test_evolve.test_coevolution.CoevolutionTests) merge_alignments ignores all seq id characters after '+' ... ok test_mi (test_evolve.test_coevolution.CoevolutionTests) mi calculations function as expected with valid data ... ok test_mi_alignment_excludes (test_evolve.test_coevolution.CoevolutionTests) mi_alignment handles excludes properly ... ok test_mi_alignment_high (test_evolve.test_coevolution.CoevolutionTests) mi_alignment detected perfectly correlated columns ... ok test_mi_alignment_low (test_evolve.test_coevolution.CoevolutionTests) mi_alignment detected in perfectly uncorrelated columns ... ok test_mi_pair (test_evolve.test_coevolution.CoevolutionTests) mi_pair calculates mi from a pair of columns ... ok test_mi_pair_alt_calculator (test_evolve.test_coevolution.CoevolutionTests) mi_pair uses alternate mi_calculator when provided ... ok test_mi_pair_cols_and_entropies (test_evolve.test_coevolution.CoevolutionTests) mi_pair calculates mi from a pair of columns and precalc entropies ... ok test_mi_pair_cols_default_exclude_handling (test_evolve.test_coevolution.CoevolutionTests) mi_pair returns null_value on excluded by default ... ok test_mi_pair_cols_non_default_exclude_handling (test_evolve.test_coevolution.CoevolutionTests) mi_pair uses non-default exclude_handler when provided ... ok test_mi_position_from_alignment_default_exclude_handling (test_evolve.test_coevolution.CoevolutionTests) mi_position handles excludes by setting to null_value ... ok test_mi_position_from_alignment_nmi (test_evolve.test_coevolution.CoevolutionTests) mi_position functions w/ alternate mi_calculator ... ok test_mi_position_from_alignment_non_default_exclude_handling (test_evolve.test_coevolution.CoevolutionTests) mi_position handles excludes w/ non-default method ... ok test_mi_position_valid_input (test_evolve.test_coevolution.CoevolutionTests) mi_position functions with varied valid input ... ok test_n_random_seqs (test_evolve.test_coevolution.CoevolutionTests) n_random_seqs: functions as expected ... ok test_normalized_mi (test_evolve.test_coevolution.CoevolutionTests) normalized mi calculations function as expected with valid data ... ok test_parse_coevolution_matrix_filepath (test_evolve.test_coevolution.CoevolutionTests) Parsing matrix filepaths works as expected. ... ok test_parse_coevolution_matrix_filepath_error (test_evolve.test_coevolution.CoevolutionTests) Parsing matrix file paths handles invalid filepaths ... ok test_pickle_and_unpickle (test_evolve.test_coevolution.CoevolutionTests) unpickle(pickle(matrix)) == matrix ... ok test_pickle_coevolution_result_error (test_evolve.test_coevolution.CoevolutionTests) pickle matrix: IOError handled correctly ... ok test_probs_from_dict (test_evolve.test_coevolution.CoevolutionTests) probs_from_dict: dict of probs -> list of probs in alphabet's order ... ok test_resampled_mi_alignment (test_evolve.test_coevolution.CoevolutionTests) resampled_mi_alignment returns without error ... ok test_sca_alignment_error (test_evolve.test_coevolution.CoevolutionTests) sca_alignment: returns w/ error when appropriate ... ok test_sca_alignment_no_error (test_evolve.test_coevolution.CoevolutionTests) sca_alignment: returns w/o error ... ok test_sca_alignment_returns_same_as_sca_position (test_evolve.test_coevolution.CoevolutionTests) sca_alignment: returns same as sca_position on every position ... ok test_sca_input_validation (test_evolve.test_coevolution.CoevolutionTests) sca_input_validation: handles sca-specific validation steps ... ok test_sca_pair_error (test_evolve.test_coevolution.CoevolutionTests) sca_pair:returns w/ error when appropriate ... ok test_sca_pair_gpcr (test_evolve.test_coevolution.CoevolutionTests) sca_pair: reproduces several GPCR data from Suel et al., 2003 ... ok test_sca_pair_no_error (test_evolve.test_coevolution.CoevolutionTests) sca_pair: returns w/o error ... ok test_sca_pair_return_all (test_evolve.test_coevolution.CoevolutionTests) sca_pair: handles return_all by returning lists of proper length ... ok test_sca_position_error (test_evolve.test_coevolution.CoevolutionTests) sca_position: returns w/ error when appropriate ... ok test_sca_position_gpcr (test_evolve.test_coevolution.CoevolutionTests) sca_position: reproduces several GPCR data from Suel et al., 2003 ... ok test_sca_position_no_error (test_evolve.test_coevolution.CoevolutionTests) sca_position: returns w/o error ... ok test_sca_position_returns_same_as_sca_pair (test_evolve.test_coevolution.CoevolutionTests) sca_position: returns same as sca_pair called on each pos ... ok test_uncsv_coevolution_result_error (test_evolve.test_coevolution.CoevolutionTests) csv -> matrix: IOError handled correctly ... ok test_unpickle_coevolution_result_error (test_evolve.test_coevolution.CoevolutionTests) unpickle matrix: IOError handled correctly ... ok test_validate_alignment (test_evolve.test_coevolution.CoevolutionTests) validate_alignment: ValueError on bad alignment characters ... ok test_validate_alphabet_invalid (test_evolve.test_coevolution.CoevolutionTests) validate_alphabet: raises error on incompatible alpabet and freqs ... ok test_validate_alphabet_valid (test_evolve.test_coevolution.CoevolutionTests) validate_alphabet: does nothing on compatible alpabet and freqs ... ok test_validate_position_invalid (test_evolve.test_coevolution.CoevolutionTests) validate_position: raises error on invalid position ... ok test_validate_position_valid (test_evolve.test_coevolution.CoevolutionTests) validate_position: does nothing on valid position ... ok test_wrapper_functions_handle_invalid_parameters (test_evolve.test_coevolution.CoevolutionTests) coevolve_*: functions error on missing parameters ... ok test_build_q_ignores_zero_counts (test_evolve.test_coevolution.GctmpcaTests) build_rate_matrix: recoded counts (i.e., w/ many 0s) yeilds right Q ... ok test_build_q_yields_roughly_gctmpca_default (test_evolve.test_coevolution.GctmpcaTests) build_rate_matrix: from DSO78 data yields Yeang's default Q ... ok test_create_gctmpca_input (test_evolve.test_coevolution.GctmpcaTests) Gctmpca: create_gctmpca_input generates proper data ... ok test_gctmpca_alignment (test_evolve.test_coevolution.GctmpcaTests) Gctmpca: alignment method works on trivial data ... ok test_gctmpca_pair (test_evolve.test_coevolution.GctmpcaTests) Gctmpca: pair method works on trivial data ... ok test_parse_gctmpca_result (test_evolve.test_coevolution.GctmpcaTests) Gctmpca: result (as list) yeilds correctly matrix ... ok test_parse_gctmpca_result_line (test_evolve.test_coevolution.GctmpcaTests) Gctmpca: result line parsing functions as expected ... ok test_calc_weights (test_evolve.test_coevolution.ResampledMiTests) resampled mi weights should be correctly computed ... ok test_resampled_mi_interface (test_evolve.test_coevolution.ResampledMiTests) resampled_mi_alignment should correctly compute statistic from ... ok test_scaled_mi (test_evolve.test_coevolution.ResampledMiTests) resampled mi should match hand calc ... ok test_aa_models (test_evolve.test_models.CannedModelsTest) excercising aa model construction ... ok test_bin_options (test_evolve.test_models.CannedModelsTest) ... ok test_codon_models (test_evolve.test_models.CannedModelsTest) excercising codon model construction ... ok test_empirical_values_roundtrip (test_evolve.test_models.CannedModelsTest) ... ok test_nuc_models (test_evolve.test_models.CannedModelsTest) excercising nucleotide model construction ... ok test_solved_models (test_evolve.test_models.CannedModelsTest) ... ok test_impossible_change (test_evolve.test_motifchange.TestPredicates) ... ok test_indels (test_evolve.test_motifchange.TestPredicates) ... ok test_isC (test_evolve.test_motifchange.TestPredicates) ... ok test_isCCC (test_evolve.test_motifchange.TestPredicates) ... ok test_isCGtoCA (test_evolve.test_motifchange.TestPredicates) ... ok test_isCpT_T_only (test_evolve.test_motifchange.TestPredicates) ... ok test_isCtoT (test_evolve.test_motifchange.TestPredicates) ... ok test_isFromCpA_C_only (test_evolve.test_motifchange.TestPredicates) ... ok test_isFromToCpA_C_only (test_evolve.test_motifchange.TestPredicates) ... ok test_isfromcpg (test_evolve.test_motifchange.TestPredicates) ... ok test_isfromtocpg (test_evolve.test_motifchange.TestPredicates) ... ok test_wildcards (test_evolve.test_motifchange.TestPredicates) ... ok test_isIndel (test_evolve.test_substitution_model.CodonSubstModelTests) test isIndel for codon model ... ok test_isReplacement (test_evolve.test_substitution_model.CodonSubstModelTests) test isReplacement for the two major genetic codes ... ok test_isSilent (test_evolve.test_substitution_model.CodonSubstModelTests) testing isSilent for the two major genetic codes ... ok test_isTransition (test_evolve.test_substitution_model.CodonSubstModelTests) testing codon isTransition ... ok test_str_ (test_evolve.test_substitution_model.CodonSubstModelTests) str() and repr() of a substitution model ... ok test_excludeinggaps (test_evolve.test_substitution_model.ModelDataInteractionTestMethods) testing excluding gaps from model ... ok test_getMotifs (test_evolve.test_substitution_model.ModelDataInteractionTestMethods) testing return of motifs ... ok test_getParamList (test_evolve.test_substitution_model.ModelDataInteractionTestMethods) testing getting the parameter list ... ok test_includinggaps (test_evolve.test_substitution_model.ModelDataInteractionTestMethods) testing excluding gaps from model ... ok test_asciiArt (test_evolve.test_substitution_model.MultiLetterMotifSubstModelTests) ... ok test_isIndel (test_evolve.test_substitution_model.MultiLetterMotifSubstModelTests) testing indel comparison for dinucleotide model ... ok test_PredicateChecks (test_evolve.test_substitution_model.NucleotideModelTestMethods) ... ok test_isIndel (test_evolve.test_substitution_model.NucleotideModelTestMethods) testing indel comparison nucleotide model ... ok test_isTransition (test_evolve.test_substitution_model.NucleotideModelTestMethods) testing isTransition ... ok test_isTransversion (test_evolve.test_substitution_model.NucleotideModelTestMethods) testing isTransversion ... ok test_isIndel (test_evolve.test_substitution_model.ThreeLetterMotifSubstModelTests) testing indel comparison for trinucleotide model ... ok test_binned (test_evolve.test_scale_rules.ScaleRuleTests) ... ok test_scaled (test_evolve.test_scale_rules.ScaleRuleTests) Scale rule requiring matrix entries to have all pars specified ... ok test_scaled_or (test_evolve.test_scale_rules.ScaleRuleTests) Scale rule where matrix entries can have any of the pars specified ... ok test_scaling (test_evolve.test_scale_rules.ScaleRuleTests) Testing scaling calculations using Dn and Ds as an example. ... ok test_unscaled (test_evolve.test_scale_rules.ScaleRuleTests) Scale rule on a model which has scaling performed after calculation ... ok test_binned_gamma (test_evolve.test_likelihood_function.LikelihoodCalcs) just rate is gamma distributed ... ok test_binned_gamma_ordered_param (test_evolve.test_likelihood_function.LikelihoodCalcs) rate is gamma distributed omega follows ... ok test_binned_partition (test_evolve.test_likelihood_function.LikelihoodCalcs) ... ok test_codon (test_evolve.test_likelihood_function.LikelihoodCalcs) test a three taxa codon model. ... ok test_complex_binned_partition (test_evolve.test_likelihood_function.LikelihoodCalcs) ... ok test_dinucleotide (test_evolve.test_likelihood_function.LikelihoodCalcs) test a dinucleotide model. ... ok test_discrete_nucleotide (test_evolve.test_likelihood_function.LikelihoodCalcs) test that partially discrete nucleotide model can be constructed, ... ok test_no_seq_named_root (test_evolve.test_likelihood_function.LikelihoodCalcs) root is a reserved name ... ok test_nucleotide (test_evolve.test_likelihood_function.LikelihoodCalcs) test a nucleotide model. ... ok test_protein (test_evolve.test_likelihood_function.LikelihoodCalcs) test a protein model. ... ok test_ancestralsequences (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_calclikelihood (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_constant_to_free (test_evolve.test_likelihood_function.LikelihoodFunctionTests) excercise setting a constant param rule, then freeing it ... ok test_g_statistic (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_getAnnotatedTree (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_getMotifProbs (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_get_psub_rate_matrix (test_evolve.test_likelihood_function.LikelihoodFunctionTests) lf should return consistent rate matrix and psub ... ok test_get_statistics_from_empirical_model (test_evolve.test_likelihood_function.LikelihoodFunctionTests) should return valid dict from an empirical substitution model ... ok test_getparamsasdict (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_information_criteria (test_evolve.test_likelihood_function.LikelihoodFunctionTests) test get information criteria from a model. ... ok test_likely_ancestral (test_evolve.test_likelihood_function.LikelihoodFunctionTests) excercising the most likely ancestral sequences ... ok test_make_discrete_markov (test_evolve.test_likelihood_function.LikelihoodFunctionTests) lf ignores tree lengths if a discrete Markov model ... ok test_pc_initial_parameters (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Default parameter values from original annotated tree ... ok test_result_str (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_set_par_all (test_evolve.test_likelihood_function.LikelihoodFunctionTests) ... ok test_simulateAlignment (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Simulate DNA alignment ... ok test_simulateAlignment2 (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Simulate alignment with dinucleotide model ... ok test_simulateAlignment3 (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Simulated alignment with gap-induced ambiguous positions ... ok test_simulateAlignment_root_sequence (test_evolve.test_likelihood_function.LikelihoodFunctionTests) provide a root sequence for simulating an alignment ... ok test_simulateHetergeneousAlignment (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Simulate substitution-heterogeneous DNA alignment ... ok test_simulatePatchyHetergeneousAlignment (test_evolve.test_likelihood_function.LikelihoodFunctionTests) Simulate patchy substitution-heterogeneous DNA alignment ... ok test_compute_conditional_mprobs (test_evolve.test_newq.NewQ) equal likelihood from position specific and conditional mprobs ... ok test_cond_pos_differ (test_evolve.test_newq.NewQ) lnL should differ when motif probs are not multiplicative ... ok test_get_statistics (test_evolve.test_newq.NewQ) get statistics should correctly apply arguments ... ok test_getting_node_mprobs (test_evolve.test_newq.NewQ) return correct motif probability vector for tree nodes ... ok test_lf_display (test_evolve.test_newq.NewQ) str of likelihood functions should not fail ... ok test_newQ_is_nuc_process (test_evolve.test_newq.NewQ) newQ is an extension of an independent nucleotide process ... ok test_position_specific_mprobs (test_evolve.test_newq.NewQ) correctly compute likelihood when positions have distinct ... ok test_reconstruct_ancestor (test_evolve.test_newq.NewQ) should be able to reconstruct ancestral sequences under all ... ok test_results_different (test_evolve.test_newq.NewQ) ... ok test_sim_alignment (test_evolve.test_newq.NewQ) should be able to simulate an alignment under all models ... ok test_char_to_index (test_evolve.test_pairwise_distance.TestPair) should correctly recode a DNA & RNA seqs into indices ... ok test_distance_pair (test_evolve.test_pairwise_distance.TestPair) get distances dict ... ok test_fill_diversity_matrix_all (test_evolve.test_pairwise_distance.TestPair) make correct diversity matrix when all chars valid ... ok test_fill_diversity_matrix_some (test_evolve.test_pairwise_distance.TestPair) make correct diversity matrix when not all chars valid ... ok test_jc69_from_alignment (test_evolve.test_pairwise_distance.TestPair) compute JC69 dists from an alignment ... ok test_jc69_from_matrix (test_evolve.test_pairwise_distance.TestPair) compute JC69 from diversity matrix ... ok test_logdet_for_determinant_lte_zero (test_evolve.test_pairwise_distance.TestPair) returns distance of None if the determinant is <= 0 ... ok test_logdet_missing_states (test_evolve.test_pairwise_distance.TestPair) should calculate logdet measurement with missing states ... ok test_logdet_pair_aa (test_evolve.test_pairwise_distance.TestPair) logdet shouldn't fail to produce distances for aa seqs ... ok test_logdet_pair_dna (test_evolve.test_pairwise_distance.TestPair) logdet should produce distances that match MEGA ... ok test_logdet_tk_adjustment (test_evolve.test_pairwise_distance.TestPair) logdet using tamura kumar differs from classic ... ok test_logdet_variance (test_evolve.test_pairwise_distance.TestPair) calculate logdet variance consistent with hand calculation ... ok test_paralinear_distance (test_evolve.test_pairwise_distance.TestPair) calculate paralinear variance consistent with hand calculation ... ok test_paralinear_for_determinant_lte_zero (test_evolve.test_pairwise_distance.TestPair) returns distance of None if the determinant is <= 0 ... ok test_paralinear_pair_aa (test_evolve.test_pairwise_distance.TestPair) paralinear shouldn't fail to produce distances for aa seqs ... ok test_paralinear_pair_dna (test_evolve.test_pairwise_distance.TestPair) calculate paralinear distance consistent with logdet distance ... ok test_paralinear_variance (test_evolve.test_pairwise_distance.TestPair) calculate paralinear variance consistent with hand calculation ... ok test_python_vs_cython_fill_matrix (test_evolve.test_pairwise_distance.TestPair) python & cython fill_diversity_matrix give same answer ... ok test_tn93_from_matrix (test_evolve.test_pairwise_distance.TestPair) compute TN93 distances ... ok test_bounds (test_evolve.test_parameter_controller.test_parameter_controller) Test setting upper and lower bounds for parameters ... ok test_complex_parameter_rules (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_local_clock (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_pairwise_clock (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_scoped_local (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_setConstantLengths (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_setLocalClock (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_setMotifProbs (test_evolve.test_parameter_controller.test_parameter_controller) Mprobs supplied to the parameter controller ... ok test_setMultiLocus (test_evolve.test_parameter_controller.test_parameter_controller) 2 loci each with own mprobs ... ok test_setParamRules (test_evolve.test_parameter_controller.test_parameter_controller) ... ok test_boolean_correctly_formatted (test_format.test_bedgraph.FormatBedgraph) boolean setting correctly formatted ... ok test_int_correctly_formatted (test_format.test_bedgraph.FormatBedgraph) int should be correctly formatted ... ok test_invalid_args_fail (test_format.test_bedgraph.FormatBedgraph) incorrect bedgraph args causes RuntimeError ... ok test_invalid_table_fails (test_format.test_bedgraph.FormatBedgraph) assertion error if table has > 4 columns ... ok test_merged_overlapping_spans (test_format.test_bedgraph.FormatBedgraph) bedgraph merged overlapping spans, one chrom ... ok test_merged_overlapping_spans_multichrom (test_format.test_bedgraph.FormatBedgraph) bedgraph merged overlapping spans, two crhoms ... ok test_only_required_columns (test_format.test_bedgraph.FormatBedgraph) generate bedgraph from minimal data ... ok test_raises_on_incorrect_format_val (test_format.test_bedgraph.FormatBedgraph) raise AssertionError when provide incorrect format value ... ok test_fastaFromSequence (test_format.test_fasta.FastaTests) should return correct fasta string. ... ok test_fasta_from_alignment (test_format.test_fasta.FastaTests) should return correct fasta string. ... ok test_fromCartesian (test_format.test_mage.KinemageTests) Kinemage fromCartesian should return Kinemage with A,C,G(,U) coords ... ok test_init (test_format.test_mage.KinemageTests) Kinemage should init with any of its usual fields ... ok test_init_empty (test_format.test_mage.KinemageTests) Kinemage empty init should work, but refuse to print ... ok test_iterGroupAndLists (test_format.test_mage.KinemageTests) Kinemage iterGroupsAndLists should behave as expected ... ok test_iterGroups (test_format.test_mage.KinemageTests) Kinemage iterGroups should behave as expected ... ok test_iterLists (test_format.test_mage.KinemageTests) Kinemage iterLists should behave as expected ... ok test_iterPoints (test_format.test_mage.KinemageTests) Kinemage iterPoints should behave as expected ... ok test_toCartesian (test_format.test_mage.KinemageTests) Kinemage toCartesian should return new Kinemage with UC,UG,UA coords ... ok test_fromCartesian (test_format.test_mage.MageGroupTests) MageGroup fromCartesian should return a new MageGroup ... ok test_init (test_format.test_mage.MageGroupTests) Nested MageGroups should set subgroup and cascades correctly. ... ok test_iterGroups (test_format.test_mage.MageGroupTests) MageGroup iterGroups should behave as expected ... ok test_iterGroupsAndLists (test_format.test_mage.MageGroupTests) MageGroup iterGroupsAndLists should behave as expected ... ok test_iterLists (test_format.test_mage.MageGroupTests) MageGroup iterLists should behave as expected ... ok test_iterPoints (test_format.test_mage.MageGroupTests) MageGroup iterPoints should behave as expected ... ok test_str (test_format.test_mage.MageGroupTests) MageGroup str should print correctly ... ok test_toCartesian (test_format.test_mage.MageGroupTests) MageGroup toCartesian should return a new MageGroup ... ok test_init (test_format.test_mage.MageHeaderTests) MageHeader should keep the string it was initialized with. ... ok test_fromCartesian (test_format.test_mage.MageListTests) MageList fromCartesian() should return new list with ACG coordinates ... ok test_init (test_format.test_mage.MageListTests) MageList should init correctly with data ... ok test_init_empty (test_format.test_mage.MageListTests) MageList should init correctly with no data ... ok test_iterPoints (test_format.test_mage.MageListTests) MageList iterPoints should yield all points in self ... ok test_toArray_coords_only (test_format.test_mage.MageListTests) MageList toArray should return the correct array ... ok test_toArray_radii (test_format.test_mage.MageListTests) MageList toArray should return the correct array ... ok test_toCartesian (test_format.test_mage.MageListTests) MageList toCartesian should return new list ... ok test_MagePointFromBaseFreqs (test_format.test_mage.MagePointFromBaseFreqsTests) MagePoint should fill itself from base freqs correctly ... ok test_MagePointFromBaseFreqs_functions (test_format.test_mage.MagePointFromBaseFreqsTests) MagePointFromBaseFreqs should apply functions correctly ... ok test_MagePointFromBaseFreqs_usage (test_format.test_mage.MagePointFromBaseFreqsTests) MagePoint should init correctly from base freqs ... ok test_cmp (test_format.test_mage.MagePointTests) MagePoint cmp should compare all fields ... ok test_fromCartesian (test_format.test_mage.MagePointTests) MagePoint fromCartesian should transform coordinates correctly ... ok test_get_coord (test_format.test_mage.MagePointTests) MagePoint _get_coord should return coordinate that is asked for ... ok test_init (test_format.test_mage.MagePointTests) MagePoint should init correctly with normal cases ... ok test_init_empty (test_format.test_mage.MagePointTests) MagePoint should init correctly with no data ... ok test_set_coord (test_format.test_mage.MagePointTests) MagePoint _get_coord should return coordinate that is asked for ... ok test_toCartesian (test_format.test_mage.MagePointTests) MagePoint toCartesian() should transform coordinates correctly ... ok test_align_subject_to_pdb (test_format.test_pdb_color.PdbColorTests) Tests for align_subject_to_pdb function. ... ok test_chains_to_seqs_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for chains_to_seqs function using nucleotide pdb chains. ... ok test_chains_to_seqs_protein (test_format.test_pdb_color.PdbColorTests) Tests for chains_to_seqs function using protein pdb chains. ... ok test_get_aligned_muscle (test_format.test_pdb_color.PdbColorTests) Tests for get_aligned_muscle function. ... ok test_get_best_muscle_hits (test_format.test_pdb_color.PdbColorTests) Tests for get_best_muscle_hits function. ... ok test_get_chains_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for get_chains function using nucleotide pdb lines. ... ok test_get_chains_protein (test_format.test_pdb_color.PdbColorTests) Tests for get_chains function using protein pdb lines. ... ok test_get_matching_chains (test_format.test_pdb_color.PdbColorTests) Tests for get_matching_chains function. ... ok test_make_color_list (test_format.test_pdb_color.PdbColorTests) Tests for make_color_list function. ... ok test_ungapped_to_pdb_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for ungapped_to_pdb function using nucleotide pdb chains. ... ok test_ungapped_to_pdb_protein (test_format.test_pdb_color.PdbColorTests) Tests for ungapped_to_pdb function using protein pdb chains. ... ok test_write_atom (test_format.test_xyzrn.XyzrnTest) ... ok test_constant (test_maths.test_fit_function.fit_function_test) test constant approximation ... ok test_exponential (test_maths.test_fit_function.fit_function_test) test exponential approximation ... ok test_linear (test_maths.test_fit_function.fit_function_test) test linear approximation ... ok test_CoM_one_array_wrong (test_maths.test_geometry.CenterOfMassTests) center_of_mass_one_array should fail on wrong input ... ok test_CoM_two_array_wrong (test_maths.test_geometry.CenterOfMassTests) center_of_mass_two_array should fail on wrong input ... ok test_center_of_mass (test_maths.test_geometry.CenterOfMassTests) center_of_mass should make right choice between functional methods ... ok test_center_of_mass_one_array (test_maths.test_geometry.CenterOfMassTests) center_of_mass_one_array should behave correctly ... ok test_center_of_mass_two_array (test_maths.test_geometry.CenterOfMassTests) center_of_mass_two_array should behave correctly ... ok test_distance (test_maths.test_geometry.CenterOfMassTests) distance should return Euclidean distance correctly. ... ok test_sphere_points (test_maths.test_geometry.CenterOfMassTests) tests sphere points ... ok test_is_generator_unique (test_maths.test_matrix_logarithm.logarithm_tests) is_generator_unique should identify non-unique primary roots or ... ok test_logm (test_maths.test_matrix_logarithm.logarithm_tests) logm results should match scipy's ... ok test_logm_taylor (test_maths.test_matrix_logarithm.logarithm_tests) logm_taylor should return same result as logm ... ok test_van_loan_integrating_exponentiator (test_maths.test_matrix_exponential_integration.TestIntegratingExponentiator) VanLoanIntegratingExponentiator should reproduce Felsenstein ... ok test_von_bing_integrating_exponentiator (test_maths.test_matrix_exponential_integration.TestIntegratingExponentiator) VonBingIntegratingExponentiator should reproduce Felsenstein ... ok test_autocorr (test_maths.test_period.TestPeriod) correctly compute autocorrelation ... ok test_dft (test_maths.test_period.TestPeriod) correctly compute discrete fourier transform ... ok test_goertzel (test_maths.test_period.TestPeriod) goertzel and ipdft should be the same ... ok test_hybrid (test_maths.test_period.TestPeriod) correctly compute hybrid statistic ... ok test_hybrid_returns_all (test_maths.test_period.TestPeriod) correctly returns hybrid, ipdft and autocorr statistics ... ok test_inner_funcs (test_maths.test_period.TestPeriod) python and pyrexed implementation should be the same ... ok test_ipdft (test_maths.test_period.TestPeriod) correctly compute integer discrete fourier transform ... ok test_Order_defaults (test_maths.test_matrix.test_distance.DistanceMatrixTests) RowOrder and ColOrder are set to default as expected ... ok test_Order_parameters (test_maths.test_matrix.test_distance.DistanceMatrixTests) RowOrder and ColOrder are set to paramters as expected ... ok test_all_init_parameters (test_maths.test_matrix.test_distance.DistanceMatrixTests) All parameters to init are handled correctly ... ok test_attribute_forwarder_integrity (test_maths.test_matrix.test_distance.DistanceMatrixTests) Integrity of attribute forwarding ... ok test_attribute_forwarder_integrity_after_copy (test_maths.test_matrix.test_distance.DistanceMatrixTests) Integrity of attribute forwarding following a copy() ... ok test_attribute_init (test_maths.test_matrix.test_distance.DistanceMatrixTests) Proper initialization of all attributes ... ok test_colKeys (test_maths.test_matrix.test_distance.DistanceMatrixTests) colKeys functions properly ... ok test_copy (test_maths.test_matrix.test_distance.DistanceMatrixTests) Copy functions as expected ... ok test_default_padding (test_maths.test_matrix.test_distance.DistanceMatrixTests) Default padding functions as expected ... ok test_dict_integrity (test_maths.test_matrix.test_distance.DistanceMatrixTests) Integrity of key -> value pairs ... ok test_elementPow_error_on_invalid (test_maths.test_matrix.test_distance.DistanceMatrixTests) elementPow correctly raises error on invalid data ... ok test_elementPow_ignore_invalid (test_maths.test_matrix.test_distance.DistanceMatrixTests) elementPow correctly detects and ignores invalid data ... ok test_elementPow_invalid_pow (test_maths.test_matrix.test_distance.DistanceMatrixTests) elementPow correctly raises error on invalid power ... ok test_elementPow_valid (test_maths.test_matrix.test_distance.DistanceMatrixTests) elementPow correctly scales all elements and updates self.Power ... ok test_init_data_types (test_maths.test_matrix.test_distance.DistanceMatrixTests) Correct init from varying data types ... ok test_reflect (test_maths.test_matrix.test_distance.DistanceMatrixTests) reflect functions as expected ... ok test_rowKeys (test_maths.test_matrix.test_distance.DistanceMatrixTests) rowKeys functions properly ... ok test_scale (test_maths.test_matrix.test_distance.DistanceMatrixTests) Scale correctly applies function to all elements ... ok test_setDiag (test_maths.test_matrix.test_distance.DistanceMatrixTests) setDiag works as expected ... ok test_sharedColKeys (test_maths.test_matrix.test_distance.DistanceMatrixTests) sharedColKeys functions properly ... ok test_sparse_init (test_maths.test_matrix.test_distance.DistanceMatrixTests) Init correctly from a sparse dict ... ok test_toDelimited (test_maths.test_matrix.test_distance.DistanceMatrixTests) DistanceMatrix toDelimited functions as expected ... ok test_transpose (test_maths.test_matrix.test_distance.DistanceMatrixTests) transpose functions as expected ... ok test_0import (test_maths.test_spatial.test_ckd3.KDTreeTest) tests if can import ckd3 cython extension. ... ok test_instance (test_maths.test_spatial.test_ckd3.KDTreeTest) check if KDTree instance behaves correctly. ... ok test_knn (test_maths.test_spatial.test_ckd3.KDTreeTest) testing k-nearest neighbors. ... ok test_rn (test_maths.test_spatial.test_ckd3.KDTreeTest) testing neighbors within radius. ... ok test_ACE (test_maths.test_stats.test_alpha_diversity.diversity_tests) ACE should match values calculated by hand ... ok test_berger_parker_d (test_maths.test_stats.test_alpha_diversity.diversity_tests) berger-parker_d should match hand-calculated values ... ok test_brillouin_d (test_maths.test_stats.test_alpha_diversity.diversity_tests) brillouin_d should match hand-calculated values ... ok test_chao1 (test_maths.test_stats.test_alpha_diversity.diversity_tests) chao1 should use right decision rules ... ok test_chao1_bias_corrected (test_maths.test_stats.test_alpha_diversity.diversity_tests) chao1_bias_corrected should return same result as EstimateS ... ok test_chao1_confidence (test_maths.test_stats.test_alpha_diversity.diversity_tests) chao1_confidence should match observed results from EstimateS ... ok test_chao1_uncorrected (test_maths.test_stats.test_alpha_diversity.diversity_tests) chao1_uncorrected should return same result as EstimateS ... ok test_chao1_var (test_maths.test_stats.test_alpha_diversity.diversity_tests) chao1_var should match observed results from EstimateS ... ok test_counts (test_maths.test_stats.test_alpha_diversity.diversity_tests) counts should return correct array ... ok test_dominance (test_maths.test_stats.test_alpha_diversity.diversity_tests) dominance should match hand-calculated values ... ok test_doubles (test_maths.test_stats.test_alpha_diversity.diversity_tests) doubles should return correct # of doubles ... ok test_equitability (test_maths.test_stats.test_alpha_diversity.diversity_tests) equitability should match hand-calculated values ... ok test_expand_counts (test_maths.test_stats.test_alpha_diversity.diversity_tests) expand_counts should return correct expanded array ... ok test_fisher_alpha (test_maths.test_stats.test_alpha_diversity.diversity_tests) fisher alpha should match hand-calculated value. ... ok test_heip_e (test_maths.test_stats.test_alpha_diversity.diversity_tests) heip e should match hand-calculated value ... ok test_kempton_taylor_q (test_maths.test_stats.test_alpha_diversity.diversity_tests) kempton_taylor_q should approximate Magurran 1998 calculation p143 ... ok test_margalef (test_maths.test_stats.test_alpha_diversity.diversity_tests) margalef should match hand-calculated values ... ok test_mcintosh_d (test_maths.test_stats.test_alpha_diversity.diversity_tests) mcintosh_d should match hand-calculated values ... ok test_mcintosh_e (test_maths.test_stats.test_alpha_diversity.diversity_tests) mcintosh e should match hand-calculated value. ... ok test_menhinick (test_maths.test_stats.test_alpha_diversity.diversity_tests) menhinick should match hand-calculated values ... ok test_michaelis_menten_fit (test_maths.test_stats.test_alpha_diversity.diversity_tests) michaelis_menten_fit should match hand values in limiting cases ... ok test_observed_species (test_maths.test_stats.test_alpha_diversity.diversity_tests) observed_species should return # observed species ... ok test_osd (test_maths.test_stats.test_alpha_diversity.diversity_tests) osd should return correct # of observeds, singles, doubles ... ok test_reciprocal_simpson (test_maths.test_stats.test_alpha_diversity.diversity_tests) reciprocal_simpson should match hand-calculated results ... ok test_robbins (test_maths.test_stats.test_alpha_diversity.diversity_tests) robbins metric should match hand-calculated value ... ok test_robbins_confidence (test_maths.test_stats.test_alpha_diversity.diversity_tests) robbins CI should match hand-calculated value ... ok test_shannon (test_maths.test_stats.test_alpha_diversity.diversity_tests) shannon should match hand-calculated values ... ok test_simpson (test_maths.test_stats.test_alpha_diversity.diversity_tests) simpson should match hand-calculated values ... ok test_simpson_e (test_maths.test_stats.test_alpha_diversity.diversity_tests) simpson e should match hand-calculated value ... ok test_simpson_reciprocal (test_maths.test_stats.test_alpha_diversity.diversity_tests) simpson_reciprocal should match 1/D results ... ok test_singles (test_maths.test_stats.test_alpha_diversity.diversity_tests) singles should return correct # of singles ... ok test_strong (test_maths.test_stats.test_alpha_diversity.diversity_tests) strong's dominance index should match hand-calculated values ... ok test_bdtr (test_maths.test_stats.test_distribution.DistributionsTests) bdtr should match cephes results ... ok test_bdtrc (test_maths.test_stats.test_distribution.DistributionsTests) bdtrc should give same results as cephes ... ok test_bdtri (test_maths.test_stats.test_distribution.DistributionsTests) bdtri should match cephes results ... ok test_binomial_exact (test_maths.test_stats.test_distribution.DistributionsTests) binomial_exact should match values from R for integer successes ... ok test_binomial_exact_errors (test_maths.test_stats.test_distribution.DistributionsTests) binomial_exact should raise errors on invalid input ... ok test_binomial_exact_floats (test_maths.test_stats.test_distribution.DistributionsTests) binomial_exact should be within limits for floating point numbers ... ok test_binomial_high (test_maths.test_stats.test_distribution.DistributionsTests) Binomial high should match values from R for integer successes ... ok test_binomial_low (test_maths.test_stats.test_distribution.DistributionsTests) Binomial low should match values from R for integer successes ... ok test_binomial_series (test_maths.test_stats.test_distribution.DistributionsTests) binomial_exact should match values from R on a whole series ... ok test_chdtri (test_maths.test_stats.test_distribution.DistributionsTests) chdtri should match cephes results ... ok test_chi_high (test_maths.test_stats.test_distribution.DistributionsTests) chi_high should match R's pchisq(lower.tail=FALSE) function ... ok test_chi_low (test_maths.test_stats.test_distribution.DistributionsTests) chi_low should match R's pchisq() function ... ok test_f_high (test_maths.test_stats.test_distribution.DistributionsTests) F high should match values from R for integer successes ... ok test_f_low (test_maths.test_stats.test_distribution.DistributionsTests) F low should match values from R for integer successes ... ok test_fdtr (test_maths.test_stats.test_distribution.DistributionsTests) fdtr should match cephes results ... ok test_fdtrc (test_maths.test_stats.test_distribution.DistributionsTests) fdtrc should match cephes results ... ok test_fdtri (test_maths.test_stats.test_distribution.DistributionsTests) fdtri should match cephes results ... ok test_fprob (test_maths.test_stats.test_distribution.DistributionsTests) fprob should return twice the tail on a particular side ... ok test_gdtr (test_maths.test_stats.test_distribution.DistributionsTests) gdtr should match cephes results ... ok test_gdtrc (test_maths.test_stats.test_distribution.DistributionsTests) gdtrc should match cephes results ... ok test_gdtri (test_maths.test_stats.test_distribution.DistributionsTests) gdtri should match cephes results ... ok test_pdtr (test_maths.test_stats.test_distribution.DistributionsTests) pdtr should match cephes results ... ok test_pdtrc (test_maths.test_stats.test_distribution.DistributionsTests) pdtrc should match cephes results ... ok test_pdtri (test_maths.test_stats.test_distribution.DistributionsTests) pdtri should match cephes results ... ok test_poisson_exact (test_maths.test_stats.test_distribution.DistributionsTests) Poisson exact should match expected values from R ... ok test_poisson_high (test_maths.test_stats.test_distribution.DistributionsTests) Upper tail of poisson should match R for integer successes ... ok test_poisson_low (test_maths.test_stats.test_distribution.DistributionsTests) Lower tail of poisson should match R for integer successes ... ok test_stdtr (test_maths.test_stats.test_distribution.DistributionsTests) stdtr should match cephes results ... ok test_stdtri (test_maths.test_stats.test_distribution.DistributionsTests) stdtri should match cephes results ... ok test_t_high (test_maths.test_stats.test_distribution.DistributionsTests) t_high should match R's pt(lower.tail=FALSE) function ... ok test_t_low (test_maths.test_stats.test_distribution.DistributionsTests) t_low should match R's pt() function ... ok test_tprob (test_maths.test_stats.test_distribution.DistributionsTests) tprob should match twice the t_high probability for abs(t) ... ok test_z_high (test_maths.test_stats.test_distribution.DistributionsTests) z_high should match R's pnorm(lower.tail=FALSE) function ... ok test_z_low (test_maths.test_stats.test_distribution.DistributionsTests) z_low should match R's pnorm() function ... ok test_zprob (test_maths.test_stats.test_distribution.DistributionsTests) zprob should match twice the z_high probability for abs(z) ... ok test_call (test_maths.test_stats.test_histogram.HistogramTests) Histogram __call__ should update with new data ... ok test_clear (test_maths.test_stats.test_histogram.HistogramTests) Histogram clear should reset all data ... ok test_init_bins (test_maths.test_stats.test_histogram.HistogramTests) Histogram should set _bins property correctly ... ok test_init_bins_data (test_maths.test_stats.test_histogram.HistogramTests) Histogram should fill bins with data if supplied ... ok test_init_no_bins (test_maths.test_stats.test_histogram.HistogramTests) Histogram should raise error if initialized without bins ... ok test_mapping (test_maths.test_stats.test_histogram.HistogramTests) Histogram Mapping should apply correct function to values ... ok test_multi (test_maths.test_stats.test_histogram.HistogramTests) Histogram Multi should allow values to match multiple bins ... ok test_toFreqs (test_maths.test_stats.test_histogram.HistogramTests) Histogram toFreqs() should return a Freqs object ... ok test_aic (test_maths.test_stats.test_information_criteria.InformationCriteria) correctly compute AIC from Burnham & Anderson 2002, p102 ... ok test_aic_corrected (test_maths.test_stats.test_information_criteria.InformationCriteria) correctly compute AIC corrected for small sample size ... ok test_bic (test_maths.test_stats.test_information_criteria.InformationCriteria) correctly compute BIC ... ok test_chi_square (test_maths.test_stats.test_period.TestPeriodStat) ... ok test_circular_indices (test_maths.test_stats.test_period.TestPeriodStat) ... ok test_factorial (test_maths.test_stats.test_period.TestPeriodStat) ... ok test_g_statitic (test_maths.test_stats.test_period.TestPeriodStat) calc g-stat correctly ... ok test_get_num_stats (test_maths.test_stats.test_period.TestPeriodStat) calculators should return correct num stats ... ok test_permutation (test_maths.test_stats.test_period.TestPeriodStat) ... ok test_permutation_all (test_maths.test_stats.test_period.TestPeriodStat) performs permutation test of Hybrid, but considers all stats ... ok test_permutation_skips (test_maths.test_stats.test_period.TestPeriodStat) permutation test correctly handles data without symbols ... ok test_seq_to_symbol (test_maths.test_stats.test_period.TestPeriodStat) both py and pyx seq_to_symbol versions correctly convert a sequence ... ok test_seq_to_symbol_factory (test_maths.test_stats.test_period.TestPeriodStat) checks factory function for conversion works ... ok test_combinations (test_maths.test_stats.test_special.SpecialTests) combinations should return expected results when int as input ... ok test_combinations_errors (test_maths.test_stats.test_special.SpecialTests) combinations should raise errors on invalid input ... ok test_combinations_exact (test_maths.test_stats.test_special.SpecialTests) combinations_exact should return expected results ... ok test_combinations_float (test_maths.test_stats.test_special.SpecialTests) combinations should use gamma function when floats as input ... ok test_combinations_range (test_maths.test_stats.test_special.SpecialTests) combinations should decrease gradually with increasing k ... ok test_igami (test_maths.test_stats.test_special.SpecialTests) igami should give same result as cephes implementation ... ok test_incbi (test_maths.test_stats.test_special.SpecialTests) incbi results should match cephes libraries ... ok test_ln_binomial_floats (test_maths.test_stats.test_special.SpecialTests) Binomial exact should match values from R for integer successes ... ok test_ln_binomial_integer (test_maths.test_stats.test_special.SpecialTests) ln_binomial should match R results for integer values ... ok test_ln_binomial_range (test_maths.test_stats.test_special.SpecialTests) ln_binomial should increase in a monotonically increasing region. ... ok test_ln_combinations (test_maths.test_stats.test_special.SpecialTests) ln_combinations should return expected results ... ok test_ln_permutations (test_maths.test_stats.test_special.SpecialTests) ln_permutations should return expected results ... ok test_log1p (test_maths.test_stats.test_special.SpecialTests) log1p should give same results as cephes ... ok test_log_one_minus_large (test_maths.test_stats.test_special.SpecialTests) log_one_minus_x should return math.log(1-x) if x is large ... ok test_log_one_minus_small (test_maths.test_stats.test_special.SpecialTests) log_one_minus_x should return -x if x is small ... ok test_ndtri (test_maths.test_stats.test_special.SpecialTests) ndtri should give same result as implementation in cephes ... ok test_one_minus_exp_large (test_maths.test_stats.test_special.SpecialTests) one_minus_exp_x should return 1 - math.exp(x) if x is large ... ok test_one_minus_exp_small (test_maths.test_stats.test_special.SpecialTests) one_minus_exp_x should return -x if x is small ... ok test_permutations (test_maths.test_stats.test_special.SpecialTests) permutations should return expected results ... ok test_permutations_errors (test_maths.test_stats.test_special.SpecialTests) permutations should raise errors on invalid input ... ok test_permutations_exact (test_maths.test_stats.test_special.SpecialTests) permutations_exact should return expected results ... ok test_permutations_float (test_maths.test_stats.test_special.SpecialTests) permutations should use gamma function when floats as input ... ok test_permutations_range (test_maths.test_stats.test_special.SpecialTests) permutations should increase gradually with increasing k ... ok test_ks2x (test_maths.test_stats.test_ks.KSTests) KS two-sample, 2-sided should match answers from R ... ok test_ks_boot (test_maths.test_stats.test_ks.KSTests) excercising the bootstrapped version of KS ... ok test_pk1x (test_maths.test_stats.test_ks.KSTests) 1 sample 1-sided should match answers from R ... ok test_pk2x (test_maths.test_stats.test_ks.KSTests) 1 sample 2-sided should match answers from R ... ok test_pkstwo (test_maths.test_stats.test_ks.KSTests) kolmogorov asymptotic should match answers from R ... ok test_ps2x (test_maths.test_stats.test_ks.KSTests) 2 sample 2-sided smirnov should match answers from R ... ok test_naive_histogram (test_maths.test_stats.test_rarefaction.TopLevelTests) naive_histogram should produce expected result ... ok test_rarefaction (test_maths.test_stats.test_rarefaction.TopLevelTests) rarefaction should produce expected curve ... ok test_subsample (test_maths.test_stats.test_rarefaction.TopLevelTests) subsample should return a random subsample of a vector ... ok test_subsample_freq_dist_nonzero (test_maths.test_stats.test_rarefaction.TopLevelTests) subsample_freq_dist_nonzero should return a random subsample of a vector ... ok test_subsample_multinomial (test_maths.test_stats.test_rarefaction.TopLevelTests) subsample_multinomial should return a random subsample of a vector ... ok test_subsample_random (test_maths.test_stats.test_rarefaction.TopLevelTests) subsample_random should return a random subsample of a vector ... ok test_wrap_numpy_histogram (test_maths.test_stats.test_rarefaction.TopLevelTests) wrap_numpy_histogram should provide expected result ... ok test_Count (test_maths.test_stats.test_util.FreqsStaticTests) Freqs Count should return correct count (number of categories) ... ok test_Mean (test_maths.test_stats.test_util.FreqsStaticTests) Freqs Mean should return mean of counts in categories ... ok test_StandardDeviation (test_maths.test_stats.test_util.FreqsStaticTests) Freqs StandardDeviation should return stdev of counts in categories ... ok test_Sum (test_maths.test_stats.test_util.FreqsStaticTests) Freqs Sum should return sum of item counts in all categories ... ok test_SumSquares (test_maths.test_stats.test_util.FreqsStaticTests) Freqs SumSquared should return sum of squared freq of each category ... ok test_Uncertainty (test_maths.test_stats.test_util.FreqsStaticTests) Freqs Shannon uncertainty values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.FreqsStaticTests) Freqs Variance should return variance of counts in categories ... ok test_add (test_maths.test_stats.test_util.FreqsStaticTests) Freqs + should make new object, adding from any known data type ... ok test_choice (test_maths.test_stats.test_util.FreqsStaticTests) Freqs choice should work as expected ... ok test_copy (test_maths.test_stats.test_util.FreqsStaticTests) Freqs copy should preserve class of original ... ok test_delitem (test_maths.test_stats.test_util.FreqsStaticTests) Freqs delitem is implementation-dependent ... ok test_expand (test_maths.test_stats.test_util.FreqsStaticTests) Freqs expand should give expected results ... ok test_find_conversion_function (test_maths.test_stats.test_util.FreqsStaticTests) Freqs _find_conversion_function should return correct value. ... ok test_fromDict (test_maths.test_stats.test_util.FreqsStaticTests) Freqs fromDict should add from dict of {key:count} ... ok test_fromDicts (test_maths.test_stats.test_util.FreqsStaticTests) Freqs fromDicts should add from list of dicts of {key:count} ... ok test_fromSeq (test_maths.test_stats.test_util.FreqsStaticTests) Freqs fromSeq should add items from sequence, according to weight ... ok test_fromSeqs (test_maths.test_stats.test_util.FreqsStaticTests) Freqs fromSeqs should add items from sequences, according to weight ... ok test_fromTuples (test_maths.test_stats.test_util.FreqsStaticTests) Freqs fromTuples should add from key, count pairs w/ repeated keys ... ok test_getSortedList (test_maths.test_stats.test_util.FreqsStaticTests) Freqs getSortedList should return sorted list of key, val tuples ... ok test_iadd (test_maths.test_stats.test_util.FreqsStaticTests) Freqs += should add in place from any known data type ... ok test_isValid (test_maths.test_stats.test_util.FreqsStaticTests) Freqs isValid should return True if valid ... ok test_isub (test_maths.test_stats.test_util.FreqsStaticTests) Freqs -= should subtract in place using any known data type ... ok test_mode (test_maths.test_stats.test_util.FreqsStaticTests) Freqs mode should return most frequent item ... ok test_newFromDict (test_maths.test_stats.test_util.FreqsStaticTests) Freqs newFromDict should work as expected. ... ok test_newFromDicts (test_maths.test_stats.test_util.FreqsStaticTests) Freqs newFromDicts should work as expected. ... ok test_newFromSeq (test_maths.test_stats.test_util.FreqsStaticTests) Freqs newFromSeq should work as expected. ... ok test_newFromSeqs (test_maths.test_stats.test_util.FreqsStaticTests) Freqs newFromSeqs should work as expected. ... ok test_newFromTuples (test_maths.test_stats.test_util.FreqsStaticTests) Freqs newFromTuples should work as expected. ... ok test_normalize (test_maths.test_stats.test_util.FreqsStaticTests) Freqs should allow normalization ... ok test_purge (test_maths.test_stats.test_util.FreqsStaticTests) Freqs purge should have no effect if keys are fixed ... ok test_randomSequence_bad (test_maths.test_stats.test_util.FreqsStaticTests) Empty Freqs should raise error on randomSequence ... ok test_randomSequence_good (test_maths.test_stats.test_util.FreqsStaticTests) Freqs randomSequence should give correct counts ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.FreqsStaticTests) Freqs randomSequence should work with one key ... ok test_rekey (test_maths.test_stats.test_util.FreqsStaticTests) Freqs rekey should map the results onto new keys ... ok test_round (test_maths.test_stats.test_util.FreqsStaticTests) Freqs round should round all frequencies to integers ... ok test_scale (test_maths.test_stats.test_util.FreqsStaticTests) Freqs scale should multiply all values with the given scale ... ok test_setdefault_good (test_maths.test_stats.test_util.FreqsStaticTests) Freqs setdefault should work with positive values if key present ... ok test_setitem_good (test_maths.test_stats.test_util.FreqsStaticTests) Freqs should allow non-negative values to be set ... ok test_str (test_maths.test_stats.test_util.FreqsStaticTests) Freqs abstract interface doesn't specify string result ... ok test_sub (test_maths.test_stats.test_util.FreqsStaticTests) Freqs - should make new object, subtracting using any known data type ... ok test_subset_preserve (test_maths.test_stats.test_util.FreqsStaticTests) Freqs subset should preserve wanted items ... ok test_subset_remove (test_maths.test_stats.test_util.FreqsStaticTests) Freqs subset should delete unwanted items if asked ... ok test_summarize (test_maths.test_stats.test_util.FreqsStaticTests) Freqs summarize should return Summary: Count, Sum, SumSquares, Var ... ok test_delitem (test_maths.test_stats.test_util.FreqsSubclassTests) Freqs subclass delitem shouldn't allow deletion of RequiredKeys ... ok test_init (test_maths.test_stats.test_util.FreqsSubclassTests) Freqs subclass init should add RequiredKeys ... ok test_normalize (test_maths.test_stats.test_util.FreqsSubclassTests) Freqs subclass normalize should optionally elminate non-required keys ... ok test_purge (test_maths.test_stats.test_util.FreqsSubclassTests) Freqs subclass purge should eliminate anything not in RequiredKeys ... ok test_Count (test_maths.test_stats.test_util.FreqsTests) Freqs Count should return correct count (number of categories) ... ok test_Mean (test_maths.test_stats.test_util.FreqsTests) Freqs Mean should return mean of counts in categories ... ok test_StandardDeviation (test_maths.test_stats.test_util.FreqsTests) Freqs StandardDeviation should return stdev of counts in categories ... ok test_Sum (test_maths.test_stats.test_util.FreqsTests) Freqs Sum should return sum of item counts in all categories ... ok test_SumSquares (test_maths.test_stats.test_util.FreqsTests) Freqs SumSquared should return sum of squared freq of each category ... ok test_Uncertainty (test_maths.test_stats.test_util.FreqsTests) Freqs Shannon uncertainty values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.FreqsTests) Freqs Variance should return variance of counts in categories ... ok test_add (test_maths.test_stats.test_util.FreqsTests) Freqs + should make new object, adding from any known data type ... ok test_choice (test_maths.test_stats.test_util.FreqsTests) Freqs choice should work as expected ... ok test_copy (test_maths.test_stats.test_util.FreqsTests) Freqs copy should preserve class of original ... ok test_delitem (test_maths.test_stats.test_util.FreqsTests) Freqs delitem should refuse to delete a required key ... ok test_expand (test_maths.test_stats.test_util.FreqsTests) Freqs expand should give expected results ... ok test_find_conversion_function (test_maths.test_stats.test_util.FreqsTests) Freqs _find_conversion_function should return correct value. ... ok test_fromDict (test_maths.test_stats.test_util.FreqsTests) Freqs fromDict should add from dict of {key:count} ... ok test_fromDicts (test_maths.test_stats.test_util.FreqsTests) Freqs fromDicts should add from list of dicts of {key:count} ... ok test_fromSeq (test_maths.test_stats.test_util.FreqsTests) Freqs fromSeq should add items from sequence, according to weight ... ok test_fromSeqs (test_maths.test_stats.test_util.FreqsTests) Freqs fromSeqs should add items from sequences, according to weight ... ok test_fromTuples (test_maths.test_stats.test_util.FreqsTests) Freqs fromTuples should add from key, count pairs w/ repeated keys ... ok test_getSortedList (test_maths.test_stats.test_util.FreqsTests) Freqs getSortedList should return sorted list of key, val tuples ... ok test_iadd (test_maths.test_stats.test_util.FreqsTests) Freqs += should add in place from any known data type ... ok test_init_alphabet_failure (test_maths.test_stats.test_util.FreqsTests) Freqs should fail if keys don't match alphabet ... ok test_init_alphabet_success (test_maths.test_stats.test_util.FreqsTests) Freqs should init ok with keys matching alphabet ... ok test_init_empty (test_maths.test_stats.test_util.FreqsTests) Freqs should initialize OK with empty list ... ok test_init_fails_negative (test_maths.test_stats.test_util.FreqsTests) Freqs init should fail on negative frequencies ... ok test_init_from_dict (test_maths.test_stats.test_util.FreqsTests) Freqs should init OK from dictionary ... ok test_init_from_dicts (test_maths.test_stats.test_util.FreqsTests) Freqs should init OK from list of dicts ... ok test_init_from_strings (test_maths.test_stats.test_util.FreqsTests) Freqs should init OK from list of strings ... ok test_init_from_tuples (test_maths.test_stats.test_util.FreqsTests) Freqs should init OK from list of key-value pairs ... ok test_init_same_key (test_maths.test_stats.test_util.FreqsTests) Freqs should initialize OK with duplicate items ... ok test_init_single (test_maths.test_stats.test_util.FreqsTests) Freqs should initialize OK with single item ... ok test_init_strings (test_maths.test_stats.test_util.FreqsTests) Freqs should initialize OK with characters in string ... ok test_init_two_keys (test_maths.test_stats.test_util.FreqsTests) Freqs should initialize OK with distinct items ... ok test_isValid (test_maths.test_stats.test_util.FreqsTests) Freqs isValid should return True if valid ... ok test_isValid_bad (test_maths.test_stats.test_util.FreqsTests) Freqs should reject invalid data, so isValid() always True ... ok test_isub (test_maths.test_stats.test_util.FreqsTests) Freqs -= should subtract in place using any known data type ... ok test_mode (test_maths.test_stats.test_util.FreqsTests) Freqs mode should return most frequent item ... ok test_normalize (test_maths.test_stats.test_util.FreqsTests) Freqs should allow normalization on any type ... ok test_purge (test_maths.test_stats.test_util.FreqsTests) Freqs purge should have no effect unless RequiredKeys set. ... ok test_randomSequence_bad (test_maths.test_stats.test_util.FreqsTests) Empty Freqs should raise error on randomSequence ... ok test_randomSequence_good (test_maths.test_stats.test_util.FreqsTests) Freqs randomSequence should give correct counts ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.FreqsTests) Freqs randomSequence should work with one key ... ok test_rekey (test_maths.test_stats.test_util.FreqsTests) Freqs rekey should map the results onto new keys. ... ok test_round (test_maths.test_stats.test_util.FreqsTests) Freqs round should round all frequencies to integers ... ok test_scale (test_maths.test_stats.test_util.FreqsTests) Freqs scale should multiply all values with the given scale ... ok test_setdefault_bad (test_maths.test_stats.test_util.FreqsTests) Freqs setdefault should fail if default < 0 ... ok test_setdefault_good (test_maths.test_stats.test_util.FreqsTests) Freqs setdefault should work with positive values ... ok test_setitem_bad (test_maths.test_stats.test_util.FreqsTests) Freqs should not allow negative values ... ok test_setitem_good (test_maths.test_stats.test_util.FreqsTests) Freqs should allow non-negative values to be set ... ok test_str (test_maths.test_stats.test_util.FreqsTests) Freqs should print as tab-delimited table, or 'Empty' ... ok test_sub (test_maths.test_stats.test_util.FreqsTests) Freqs - should make new object, subtracting using any known data type ... ok test_subset_preserve (test_maths.test_stats.test_util.FreqsTests) Freqs subset should preserve unwanted items ... ok test_subset_remove (test_maths.test_stats.test_util.FreqsTests) Freqs subset should delete unwanted items if asked ... ok test_summarize (test_maths.test_stats.test_util.FreqsTests) Freqs summarize should return Summary: Count, Sum, SumSquares, Var ... ok test_Count (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs counts should match hand-calculated values ... ok test_Mean (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs means should match hand-calculated values ... ok test_Mode (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs mode should return most frequent item ... ok test_NumberFreqsQuantiles (test_maths.test_stats.test_util.NumberFreqsTests) quantiles should match Numbers, including Median ... ok test_Stdev (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs stdev should match spreadsheet ... ok test_Sum (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs sums should match hand-calculated values ... ok test_Sumsq (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs sum of squares should match spreadsheet ... ok test_Uncertainty (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs Shannon entropy values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs variance should match values from R. ... ok test_add_bad (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs add should fail if key not numeric ... ok test_add_good (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs should allow addition of counts or items ... ok test_normalize (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs should allow normalization on any type ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs randomSequence should work with one key ... ok test_setitem_bad (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs should not allow non-numeric values ... ok test_setitem_good (test_maths.test_stats.test_util.NumberFreqsTests) NumberFreqs should allow non-negative values to be set ... ok test_Count (test_maths.test_stats.test_util.NumbersTests) Numbers Count should be the same as len() ... ok test_Mean (test_maths.test_stats.test_util.NumbersTests) Numbers Mean should be mean of individual numbers ... ok test_Mode (test_maths.test_stats.test_util.NumbersTests) Numbers Mode should return most common element ... ok test_NumberQuantiles (test_maths.test_stats.test_util.NumbersTests) quantiles should be correct ... ok test_StandardDeviation (test_maths.test_stats.test_util.NumbersTests) Numbers StandardDeviation should be sd of individual numbers ... ok test_Sum (test_maths.test_stats.test_util.NumbersTests) Numbers Sum should be the same as sum() ... ok test_SumSquares (test_maths.test_stats.test_util.NumbersTests) Numbers SumSquares should be sum of squares ... ok test_Uncertainty (test_maths.test_stats.test_util.NumbersTests) Numbers Uncertainty should act via Freqs ... ok test_Variance (test_maths.test_stats.test_util.NumbersTests) Numbers Variance should be variance of individual numbers ... ok test_accumulate (test_maths.test_stats.test_util.NumbersTests) Numbers accumulate should do cumulative sum in place ... ok test_add_empty (test_maths.test_stats.test_util.NumbersTests) Numbers should be unchanged on addition of empty list ... ok test_add_nonempty (test_maths.test_stats.test_util.NumbersTests) Numbers should allow addition of two nonempty Numbers ... ok test_add_repeated (test_maths.test_stats.test_util.NumbersTests) Numbers should support repeated addition, a+b+c ... ok test_append_bad (test_maths.test_stats.test_util.NumbersTests) Numbers should reject append of a non-number ... ok test_append_good (test_maths.test_stats.test_util.NumbersTests) Numbers should support append of a number ... ok test_choice (test_maths.test_stats.test_util.NumbersTests) Numbers choice should return random element from self ... ok test_copy (test_maths.test_stats.test_util.NumbersTests) Numbers copy should leave class intact (unlike slice) ... ok test_extend (test_maths.test_stats.test_util.NumbersTests) Numbers should support extend with a sequence ... ok test_firstIndexGreaterThan (test_maths.test_stats.test_util.NumbersTests) Numbers firstIndexGreaterThan should return first index less than val ... ok test_firstIndexLessThan (test_maths.test_stats.test_util.NumbersTests) Numbers firstIndexLessThan should return first index less than val ... ok test_iadd (test_maths.test_stats.test_util.NumbersTests) Numbers should support in-place addition ... ok test_init_bad_string (test_maths.test_stats.test_util.NumbersTests) Numbers should raise ValueError if float() can't convert string ... ok test_init_bad_type (test_maths.test_stats.test_util.NumbersTests) Numbers should fail with TypeError if input not iterable ... ok test_init_empty (test_maths.test_stats.test_util.NumbersTests) Numbers should initialize OK with empty list ... ok test_init_list (test_maths.test_stats.test_util.NumbersTests) Numbers should initialize OK with list of numbers ... ok test_init_single (test_maths.test_stats.test_util.NumbersTests) Numbers should initialize OK with single number ... ok test_init_string (test_maths.test_stats.test_util.NumbersTests) Numbers should initialize by treating string as list of digits ... ok test_isValid (test_maths.test_stats.test_util.NumbersTests) Numbers isValid should return True if all items numbers ... ok test_items (test_maths.test_stats.test_util.NumbersTests) Numbers should support items() method ... ok test_lastIndexGreaterThan (test_maths.test_stats.test_util.NumbersTests) Numbers lastIndexGreaterThan should return last index > val ... ok test_lastIndexLessThan (test_maths.test_stats.test_util.NumbersTests) Numbers lastIndexLessThan should return last index < val ... ok test_normalize (test_maths.test_stats.test_util.NumbersTests) Numbers normalize should return items summing to 1 by default ... ok test_normalize_parameter (test_maths.test_stats.test_util.NumbersTests) Numbers normalize(x) should divide items by x ... ok test_randomSequence (test_maths.test_stats.test_util.NumbersTests) Numbers randomSequence should return random sequence from self ... ok test_round (test_maths.test_stats.test_util.NumbersTests) Numbers round should round numbers in-place ... ok test_setitem (test_maths.test_stats.test_util.NumbersTests) Numbers should support assignment to positive index ... ok test_setitem_negative_index (test_maths.test_stats.test_util.NumbersTests) Numbers should support assignment to negative index ... ok test_setslice (test_maths.test_stats.test_util.NumbersTests) Numbers should support slice assignment ... ok test_subset (test_maths.test_stats.test_util.NumbersTests) Numbers subset should delete (or keep) selected items ... ok test_summarize (test_maths.test_stats.test_util.NumbersTests) Numbers summarize should return SummaryStatistics object ... ok test_toFixedWidth (test_maths.test_stats.test_util.NumbersTests) Numbers should be able to convert items to fixed-width string ... ok test_toFixedWidth_empty (test_maths.test_stats.test_util.NumbersTests) Numbers should return empty string when converting no items ... ok test_toFixedWidth_mixed (test_maths.test_stats.test_util.NumbersTests) Numbers should convert all kinds of floats to fixed precision ... ok test_toFixedWidth_specified_precision (test_maths.test_stats.test_util.NumbersTests) Numbers should convert all kinds of floats to specified precision ... ok test_Count (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics Count should work if Count or Sum and Mean ok ... ok test_Mean (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics Mean should work if Mean or Count and Sum ok ... ok test_StandardDeviation (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics StandardDeviation should work if it or variance ok ... ok test_Sum (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics Sum should work if Sum or Count and Mean ok ... ok test_SumSquares (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics SumSquares should work if set ... ok test_Variance (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics Variance should work if it or std dev ok ... ok test_cmp (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics should sort by count, then sum, then variance ... ok test_init (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics should initialize correctly. ... ok test_str (test_maths.test_stats.test_util.SummaryStatisticsTests) SummaryStatistics str should print known fields. ... ok test_Count (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs Count should return correct count (number of categories) ... ok test_Mean (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs Mean should return mean of counts in categories ... ok test_StandardDeviation (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs StandardDeviation should return stdev of counts in categories ... ok test_Sum (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs Sum should return sum of item counts in all categories ... ok test_SumSquares (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs SumSquared should return sum of squared freq of each category ... ok test_Uncertainty (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs Shannon uncertainty values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs Variance should return variance of counts in categories ... ok test_add (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs + should make new object, adding from any known data type ... ok test_choice (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs choice should work as expected ... ok test_copy (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs copy should preserve class of original ... ok test_delitem (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs delitem is implementation-dependent ... ok test_expand (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs expand should give expected results ... ok test_find_conversion_function (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs _find_conversion_function should return correct value. ... ok test_fromDict (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs fromDict should add from dict of {key:count} ... ok test_fromDicts (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs fromDicts should add from list of dicts of {key:count} ... ok test_fromSeq (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs fromSeq should add items from sequence, according to weight ... ok test_fromSeqs (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs fromSeqs should add items from sequences, according to weight ... ok test_fromTuples (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs fromTuples should add from key, count pairs w/ repeated keys ... ok test_getSortedList (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs getSortedList should return sorted list of key, val tuples ... ok test_iadd (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs += should add in place from any known data type ... ok test_isValid (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs isValid should return True if valid ... ok test_isub (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs -= should subtract in place using any known data type ... ok test_mode (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs mode should return most frequent item ... ok test_newFromDict (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs newFromDict should work as expected. ... ok test_newFromDicts (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs newFromDicts should work as expected. ... ok test_newFromSeq (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs newFromSeq should work as expected. ... ok test_newFromSeqs (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs newFromSeqs should work as expected. ... ok test_newFromTuples (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs newFromTuples should work as expected. ... ok test_normalize (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs should allow normalization ... ok test_purge (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs purge should have no effect if keys are fixed ... ok test_randomSequence_bad (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Empty Freqs should raise error on randomSequence ... ok test_randomSequence_good (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs randomSequence should give correct counts ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs randomSequence should work with one key ... ok test_rekey (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs rekey should map the results onto new keys ... ok test_round (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs round should round all frequencies to integers ... ok test_scale (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs scale should multiply all values with the given scale ... ok test_setdefault_good (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs setdefault should work with positive values if key present ... ok test_setitem_good (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs should allow non-negative values to be set ... ok test_str (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs abstract interface doesn't specify string result ... ok test_sub (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs - should make new object, subtracting using any known data type ... ok test_subset_preserve (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs subset should preserve wanted items ... ok test_subset_remove (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs subset should delete unwanted items if asked ... ok test_summarize (test_maths.test_stats.test_util.UnsafeFreqsStaticTests) Freqs summarize should return Summary: Count, Sum, SumSquares, Var ... ok test_Count (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs Count should return correct count (number of categories) ... ok test_Mean (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs Mean should return mean of counts in categories ... ok test_StandardDeviation (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs StandardDeviation should return stdev of counts in categories ... ok test_Sum (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs Sum should return sum of item counts in all categories ... ok test_SumSquares (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs SumSquared should return sum of squared freq of each category ... ok test_Uncertainty (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs Shannon uncertainty values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs Variance should return variance of counts in categories ... ok test_add (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs + should make new object, adding from any known data type ... ok test_choice (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs choice should work as expected ... ok test_copy (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs copy should preserve class of original ... ok test_delitem (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs delitem should refuse to delete a required key ... ok test_expand (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs expand should give expected results ... ok test_find_conversion_function (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs _find_conversion_function should return correct value. ... ok test_fromDict (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs fromDict should add from dict of {key:count} ... ok test_fromDicts (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs fromDicts should add from list of dicts of {key:count} ... ok test_fromSeq (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs fromSeq should add items from sequence, according to weight ... ok test_fromSeqs (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs fromSeqs should add items from sequences, according to weight ... ok test_fromTuples (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs fromTuples should add from key, count pairs w/ repeated keys ... ok test_getSortedList (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs getSortedList should return sorted list of key, val tuples ... ok test_iadd (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs += should add in place from any known data type ... ok test_init_empty (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs should initialize OK with empty list ... ok test_init_from_dict (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs should init OK from dictionary ... ok test_init_from_dicts (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init should init LIKE A DICT from list of dicts ... ok test_init_from_strings (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init should FAIL from list of strings ... ok test_init_from_tuples (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs should init LIKE A DICT from list of key-value pairs ... ok test_init_negative (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init should SUCCEED on negative frequencies ... ok test_init_same_key (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init FAILS with list of items ... ok test_init_single (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init FAILS with single item ... ok test_init_strings (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs init FAILS with string ... ok test_isValid (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs isValid should return True if valid ... ok test_isValid_bad (test_maths.test_stats.test_util.UnsafeFreqsTests) UnsafeFreqs should allow invalid data, returning False for isValid ... ok test_isub (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs -= should subtract in place using any known data type ... ok test_mode (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs mode should return most frequent item ... ok test_normalize (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs should allow normalization on any type ... ok test_purge (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs purge should have no effect unless RequiredKeys set. ... ok test_randomSequence_bad (test_maths.test_stats.test_util.UnsafeFreqsTests) Empty Freqs should raise error on randomSequence ... ok test_randomSequence_good (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs randomSequence should give correct counts ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs randomSequence should work with one key ... ok test_rekey (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs rekey should map the results onto new keys. ... ok test_round (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs round should round all frequencies to integers ... ok test_scale (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs scale should multiply all values with the given scale ... ok test_setdefault_good (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs setdefault should work with positive values ... ok test_setitem_good (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs should allow non-negative values to be set ... ok test_str (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs should print as tab-delimited table, or 'Empty' ... ok test_sub (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs - should make new object, subtracting using any known data type ... ok test_subset_preserve (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs subset should preserve unwanted items ... ok test_subset_remove (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs subset should delete unwanted items if asked ... ok test_summarize (test_maths.test_stats.test_util.UnsafeFreqsTests) Freqs summarize should return Summary: Count, Sum, SumSquares, Var ... ok test_Count (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs counts should match hand-calculated values ... ok test_Mean (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs means should match hand-calculated values ... ok test_Mode (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs mode should return most frequent item ... ok test_NumberFreqsQuantiles (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) quantiles should match Numbers, including Median ... ok test_Stdev (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs stdev should match spreadsheet ... ok test_Sum (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs sums should match hand-calculated values ... ok test_Sumsq (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs sum of squares should match spreadsheet ... ok test_Uncertainty (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs Shannon entropy values should match spreadsheet ... ok test_Variance (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs variance should match values from R. ... ok test_add_good (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs should allow addition of counts or items ... ok test_normalize (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs should allow normalization on any type ... ok test_randomSequence_one_item (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs randomSequence should work with one key ... ok test_setitem_good (test_maths.test_stats.test_util.UnsafeNumberFreqsTests) NumberFreqs should allow non-negative values to be set ... ok test_Count (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Count should be the same as len() ... ok test_Mean (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Mean should be mean of individual numbers ... ok test_Mode (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Mode should return most common element ... ok test_NumberQuantiles (test_maths.test_stats.test_util.UnsafeNumbersTests) quantiles should be correct ... ok test_StandardDeviation (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers StandardDeviation should be sd of individual numbers ... ok test_Sum (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Sum should be the same as sum() ... ok test_SumSquares (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers SumSquares should be sum of squares ... ok test_Uncertainty (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Uncertainty should act via Freqs ... ok test_Variance (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers Variance should be variance of individual numbers ... ok test_accumulate (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers accumulate should do cumulative sum in place ... ok test_add_empty (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should be unchanged on addition of empty list ... ok test_add_nonempty (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should allow addition of two nonempty Numbers ... ok test_add_repeated (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support repeated addition, a+b+c ... ok test_append_bad (test_maths.test_stats.test_util.UnsafeNumbersTests) UnsafeNumbers should allow append of a non-number ... ok test_append_good (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support append of a number ... ok test_choice (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers choice should return random element from self ... ok test_copy (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers copy should leave class intact (unlike slice) ... ok test_extend (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support extend with a sequence ... ok test_firstIndexGreaterThan (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers firstIndexGreaterThan should return first index less than val ... ok test_firstIndexLessThan (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers firstIndexLessThan should return first index less than val ... ok test_iadd (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support in-place addition ... ok test_init_bad_string (test_maths.test_stats.test_util.UnsafeNumbersTests) UnsafeNumbers should silently incorporate unfloatable string ... ok test_init_bad_type (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should fail with TypeError if input not iterable ... ok test_init_empty (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should initialize OK with empty list ... ok test_init_list (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should initialize OK with list of numbers ... ok test_init_single (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should initialize OK with single number ... ok test_init_string (test_maths.test_stats.test_util.UnsafeNumbersTests) UnsafeNumbers should treat string as list of chars ... ok test_isValid (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers isValid should return True if all items numbers ... ok test_isValid_bad (test_maths.test_stats.test_util.UnsafeNumbersTests) UnsafeNumbers should return False if invalid ... ok test_items (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support items() method ... ok test_lastIndexGreaterThan (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers lastIndexGreaterThan should return last index > val ... ok test_lastIndexLessThan (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers lastIndexLessThan should return last index < val ... ok test_normalize (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers normalize should return items summing to 1 by default ... ok test_normalize_parameter (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers normalize(x) should divide items by x ... ok test_randomSequence (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers randomSequence should return random sequence from self ... ok test_round (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers round should round numbers in-place ... ok test_setitem (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support assignment to positive index ... ok test_setitem_negative_index (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support assignment to negative index ... ok test_setslice (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should support slice assignment ... ok test_subset (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers subset should delete (or keep) selected items ... ok test_summarize (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers summarize should return SummaryStatistics object ... ok test_toFixedWidth (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should be able to convert items to fixed-width string ... ok test_toFixedWidth_empty (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should return empty string when converting no items ... ok test_toFixedWidth_mixed (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should convert all kinds of floats to fixed precision ... ok test_toFixedWidth_specified_precision (test_maths.test_stats.test_util.UnsafeNumbersTests) Numbers should convert all kinds of floats to specified precision ... ok test_arithmetic_mean (test_maths.test_stats.test_cai.test_util.cai_tests) arithmetic_mean should average a list of means with freqs ... ok test_as_rna (test_maths.test_stats.test_cai.test_util.cai_tests) as_rna should do correct conversion to RNA ... ok test_cai_1 (test_maths.test_stats.test_cai.test_util.cai_tests) cai_1 should produce expected results ... ok test_cai_2 (test_maths.test_stats.test_cai.test_util.cai_tests) cai_2 should produce expected results ... ok test_cai_3 (test_maths.test_stats.test_cai.test_util.cai_tests) cai_3 should produce expected results ... ok test_codon_adaptiveness_all (test_maths.test_stats.test_cai.test_util.cai_tests) codon_adaptiveness_all should normalize all codons relative to the best one. ... ok test_codon_adaptiveness_blocks (test_maths.test_stats.test_cai.test_util.cai_tests) codon_adaptiveness_blocks should normalize codons by the best in each block ... ok test_geometric_mean (test_maths.test_stats.test_cai.test_util.cai_tests) geometric_mean should average a list of means with freqs ... ok test_norm_to_max (test_maths.test_stats.test_cai.test_util.cai_tests) norm_to_max should normalize vals in list to best val ... ok test_set_min (test_maths.test_stats.test_cai.test_util.cai_tests) set_min should set minimum value to specified threshold. ... ok test_sum_codon_freqs (test_maths.test_stats.test_cai.test_util.cai_tests) sum_codon_freqs should add list of codon freqs together, incl, missing keys ... ok test_synonyms (test_maths.test_stats.test_cai.test_util.cai_tests) synonyms should produce correct results for standard genetic code. ... ok test_synonyms_to_rna (test_maths.test_stats.test_cai.test_util.cai_tests) synonyms_to_rna should convert as expected ... ok test_valid_codons (test_maths.test_stats.test_cai.test_util.cai_tests) valid_codons should extract all valid codons from blocks ... ok test_bounded (test_maths.test_optimisers.OptimiserTestCase) ... ok test_checkpointing (test_maths.test_optimisers.OptimiserTestCase) ... ok test_global (test_maths.test_optimisers.OptimiserTestCase) ... ok test_limited (test_maths.test_optimisers.OptimiserTestCase) ... ok test_local (test_maths.test_optimisers.OptimiserTestCase) ... ok test_binary_dist_chisq (test_maths.test_distance_transform.functionTests) tests binary_dist_chisq ... ok test_binary_dist_chord (test_maths.test_distance_transform.functionTests) tests binary_dist_chord ... ok test_binary_dist_euclidean (test_maths.test_distance_transform.functionTests) tests binary_dist_euclidean ... ok test_binary_dist_hamming (test_maths.test_distance_transform.functionTests) tests binary_dist_hamming ... ok test_binary_dist_jaccard (test_maths.test_distance_transform.functionTests) tests binary_dist_jaccard ... ok test_binary_dist_lennon (test_maths.test_distance_transform.functionTests) tests binary_dist_lennon ... ok test_binary_dist_ochiai (test_maths.test_distance_transform.functionTests) tests binary_dist_ochiai ... ok test_binary_dist_otu_gain (test_maths.test_distance_transform.functionTests) binary OTU gain functions as expected ... ok test_binary_dist_pearson (test_maths.test_distance_transform.functionTests) tests binary_dist_pearson ... ok test_binary_dist_sorensen_dice (test_maths.test_distance_transform.functionTests) tests binary_dist_sorensen_dice ... ok test_chisq_distance (test_maths.test_distance_transform.functionTests) dist_chisq should return the exp result. ... ok test_chisq_transform (test_maths.test_distance_transform.functionTests) trans_chisq should return the exp result in the ref paper. ... ok test_chord_dist (test_maths.test_distance_transform.functionTests) dist_chord should return the exp result. ... ok test_chord_transform (test_maths.test_distance_transform.functionTests) trans_chord should return the exp result in the ref paper. ... ok test_dist_abund_jaccard (test_maths.test_distance_transform.functionTests) dist_abund_jaccard should compute distances for dense1 and mtx1 ... ok test_dist_bray_curtis (test_maths.test_distance_transform.functionTests) tests dist_bray_curtis ... ok test_dist_bray_curtis_faith (test_maths.test_distance_transform.functionTests) tests dist_bray_curtis_faith ... ok test_dist_bray_curtis_magurran1 (test_maths.test_distance_transform.functionTests) zero values should return zero dist, or 1 with nonzero samples ... ok test_dist_bray_curtis_magurran2 (test_maths.test_distance_transform.functionTests) should match hand-calculated values ... ok test_dist_canberra (test_maths.test_distance_transform.functionTests) tests dist_canberra ... ok test_dist_euclidean (test_maths.test_distance_transform.functionTests) tests dist_euclidean ... ok test_dist_gower (test_maths.test_distance_transform.functionTests) tests dist_gower ... ok test_dist_kulczynski (test_maths.test_distance_transform.functionTests) tests dist_kulczynski ... ok test_dist_manhattan (test_maths.test_distance_transform.functionTests) tests dist_manhattan ... ok test_dist_morisita_horn (test_maths.test_distance_transform.functionTests) tests dist_morisita_horn ... ok test_dist_pearson (test_maths.test_distance_transform.functionTests) tests dist_pearson ... ok test_dist_soergel (test_maths.test_distance_transform.functionTests) tests dist_soergel ... ok test_dist_spearman_approx (test_maths.test_distance_transform.functionTests) tests dist_spearman_approx ... ok test_hellinger_distance (test_maths.test_distance_transform.functionTests) dist_hellinger should return the exp result. ... ok test_hellinger_transform (test_maths.test_distance_transform.functionTests) dist_hellinger should return the exp result in the ref paper. ... ok test_species_profile_distance (test_maths.test_distance_transform.functionTests) dist_specprof should return the exp result. ... ok test_species_profile_transform (test_maths.test_distance_transform.functionTests) trans_specprof should return the exp result. ... ok test_cmp (test_motif.test_util.LocationTests) Location object should sort properly with __cmp__ overwritten. ... ok test_init_complete (test_motif.test_util.LocationTests) __init__ should properly initialize Location object ... ok test_init_no_end (test_motif.test_util.LocationTests) __init__ should properly initialize Location object ... ok test_cmp (test_motif.test_util.ModuleInstanceTests) ModuleInstances should sort properly with __cmp__ overwritten. ... ok test_init_no_e_values (test_motif.test_util.ModuleInstanceTests) Init should properly initialize ModuleInstance objects. ... ok test_init_no_p_e_values (test_motif.test_util.ModuleInstanceTests) Init should properly initialize ModuleInstance objects. ... ok test_len (test_motif.test_util.ModuleInstanceTests) len() should return correct length of the ModuleInstance sequence. ... ok test_str (test_motif.test_util.ModuleInstanceTests) str() should return the correct string for each ModuleInstance. ... ok test_LocationDict (test_motif.test_util.ModuleTests) LocationDict should return correct dictionary of locations. ... ok test_cmp (test_motif.test_util.ModuleTests) Module objects should sort properly with __cmp__ overwritten. ... ok test_init (test_motif.test_util.ModuleTests) Init should properly initialize Module object. ... ok test_getColorMap (test_motif.test_util.MotifFormatterTests) tests for getColorMap ... ok test_getColorMapRgb (test_motif.test_util.MotifFormatterTests) tests for getColorMapRgb ... ok test_getColorMapS0 (test_motif.test_util.MotifFormatterTests) tests for getColorMapS0 ... ok test_init (test_motif.test_util.MotifResultsTests) Init should properly initialize MotifResults object. ... ok test_init (test_motif.test_util.MotifTests) Init should properly initialize Motif object. ... ok test_html_color_to_rgb (test_motif.test_util.UtilTests) Tests for html_to_color_rgb. ... ok test_make_remap_dict (test_motif.test_util.UtilTests) Tests for make_remap_dict. ... ok test_general_init_data (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests init correctly initializes data ... ok test_init (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests init method returns with no errors ... ok test_toDistanceMatrix (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that toDistanceMatrix functions as expected ... ok test_toDistanceMatrix_w_stops (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that toDistanceMatrix works right w/ stops ... ok test_toSquareDistanceMatrix (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that _toSquareDistanceMatrix runs without returning an error ... ok test_toSquareDistanceMatrix_data_integrity (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that _toSquareDistanceMatrix works right w/o stops ... ok test_toSquareDistanceMatrix_data_integrity_diagonal (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that diag = 0 when square matrix is built ... ok test_toSquareDistanceMatrix_data_integrity_w_stops (test_parse.test_aaindex.AAIndex1RecordTests) AAIR1: Tests that _toSquareDistanceMatrix works right w/ stops ... ok test_Square_Matrix_values_row_by_col (test_parse.test_aaindex.AAIndex2RecordTests) AAIR2: Tests that key -> value pair integrity in Square matrix ... ok test_init (test_parse.test_aaindex.AAIndex2RecordTests) AAIR2: Tests init method returns with no errors ... ok test_init_data (test_parse.test_aaindex.AAIndex2RecordTests) AAIR2: Tests init correctly initializes data ... ok test_toSquareDistanceMatrix_data_integrity (test_parse.test_aaindex.AAIndex2RecordTests) AAIR2: Tests that _toSquareDistanceMatrix works right w/o stops ... ok test_toSquareDistanceMatrix_data_integrity_w_stops (test_parse.test_aaindex.AAIndex2RecordTests) AAIR2: Tests that _toSquareDistanceMatrix works right with stops ... ok test_Authors_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Authors Entries ... ok test_Citation_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Citation Entries ... ok test_Comments_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Comments Entries ... ok test_Data_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Data Entries ... ok test_ID_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test ID Entries ... ok test_LITDB_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test LITDB Entries ... ok test_correct_num_of_records (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test that one object is created per record ... ok test_empty_Correlating_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test empty Correlating Entries ... ok test_init (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test that init run w/o error ... ok test_mult_line_Title_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Multi Line Title Entries ... ok test_multi_line_Correlating_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test multi line Correlating Entries ... ok test_multi_line_Description_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Multi Line Description Entries ... ok test_read_file_as_list (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test that a file is correctly opened as a list ... ok test_sing_line_Title_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Single Line Title Entries ... ok test_single_line_Correlating_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test single line Correlating Entries ... ok test_single_line_Description_entries (test_parse.test_aaindex.test_aaindex1_parser) AAI1: Test Single Line Description Entries ... ok test_Authors_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test Atuthor Entries ... ok test_Citation_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test citation entries ... ok test_Comments_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Tests null, single line, multi line comments ... ok test_Data_entries_20x20_LTM (test_parse.test_aaindex.test_aaindex2_parser) AAI2: correct data entries when 20x20 LTM ... ok test_Data_entries_20x20_Square (test_parse.test_aaindex.test_aaindex2_parser) AAI2: correct data entries when 20x20 squ matrix ... ok test_Data_entries_21x21_LTM (test_parse.test_aaindex.test_aaindex2_parser) AAI2: correct data entries when 21x21 LTM ... ok test_Data_entries_22x21_square (test_parse.test_aaindex.test_aaindex2_parser) AAI2: correct data entries when 22x21 square matrix ... ok test_Data_entries_with_abnormal_fields (test_parse.test_aaindex.test_aaindex2_parser) AAI2: test correct data entries when more than std fields present ... ok test_Description_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test Description Entries ... ok test_ID_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test ID Entries ... ok test_LITDB_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test LITDB Entries ... ok test_Title_entries (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test Title Entries ... ok test_correct_num_of_records (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test that one object is created per record ... ok test_init (test_parse.test_aaindex.test_aaindex2_parser) AAI2: Test that init run w/o error ... ok test_read_file_as_list (test_parse.test_aaindex.test_aaindex2_parser) AAI1: Test that a file is correctly opened as a list ... ok test_MicroarrayParser (test_parse.test_agilent_microarray.MicroarrayParserTests) ... ok test_MicroarrayParser_empty_list (test_parse.test_agilent_microarray.MicroarrayParserTests) ... ok test_base36_decode (test_parse.test_binary_sff.Base36Tests) ... ok test_base36_encode (test_parse.test_binary_sff.Base36Tests) ... ok test_decode_accession (test_parse.test_binary_sff.Base36Tests) ... ok test_decode_location (test_parse.test_binary_sff.Base36Tests) ... ok test_decode_sff_filename (test_parse.test_binary_sff.Base36Tests) ... ok test_decode_timestamp (test_parse.test_binary_sff.Base36Tests) ... ok test_format_binary_sff (test_parse.test_binary_sff.FormattingFunctionTests) ... ok test_format_common_header (test_parse.test_binary_sff.FormattingFunctionTests) ... ok test_format_read_header (test_parse.test_binary_sff.FormattingFunctionTests) ... ok test_parse_common_header (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_parse_read (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_parse_read_data (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_parse_read_header (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_parse_sff (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_seek_pad (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_validate_common_header (test_parse.test_binary_sff.ParsingFunctionTests) ... ok test_write_binary_sff (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_write_common_header (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_write_pad (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_write_read (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_write_read_data (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_write_read_header (test_parse.test_binary_sff.WritingFunctionTests) ... ok test_FastaCmdTaxonomyParser (test_parse.test_blast.BlastTests) FastaCmdTaxonomyParser should parse taxonomy record to dict ... ok test_GenericBlastParser9 (test_parse.test_blast.BlastTests) GenericBlastParser9 should read blast's tabular format (#9). ... ok test_LastProteinIds9 (test_parse.test_blast.BlastTests) LastProteinIds9 should give last protein ids in iter ... ok test_PsiBlastParser9 (test_parse.test_blast.BlastTests) PsiBlastParser9 should provide convenient results for format #9. ... ok test_PsiBlastTableParser (test_parse.test_blast.BlastTests) PsiBlastTableParser should wrap values in table. ... ok test_QMEBlast9 (test_parse.test_blast.BlastTests) QMEBlast9 should return expected lines from all iterations ... ok test_QMEPsiBlast9 (test_parse.test_blast.BlastTests) QMEPsiBlast9 should only return items from last iterations ... ok test_TableToValues (test_parse.test_blast.BlastTests) TableToValues should convert itself into the correct type. ... ok test_fastacmd_taxonomy_splitter (test_parse.test_blast.BlastTests) fastacmd_taxonomy_splitter should split records into groups ... ok test_is_junk (test_parse.test_blast.BlastTests) is_junk should reject an assortment of invalid lines ... ok test_iter_finder (test_parse.test_blast.BlastTests) iter_finder should split on lines starting with '# Iteration:' ... ok test_iteration_set_finder (test_parse.test_blast.BlastTests) iter_finder should split on lines starting with '# Iteration:' ... ok test_make_label (test_parse.test_blast.BlastTests) make_label should turn comment lines into (key, val) pairs ... ok test_query_finder (test_parse.test_blast.BlastTests) query_finder should split on lines starting with '# Query:' ... ok test_getting_seq_coords (test_parse.test_bowtie.BowtieOutputTest) get correct information from the table ... ok test_no_row_converter (test_parse.test_bowtie.BowtieOutputTest) setting row_converter=None returns strings ... ok test_parsing (test_parse.test_bowtie.BowtieOutputTest) make sure that the bowtie output file is parsed properly ... ok test_psl_to_table (test_parse.test_bowtie.BowtieOutputTest) make sure that the table is built without any errors ... ok test_BpseqParser (test_parse.test_bpseq.BpseqParserTests) BpseqParser: should work on valid data, returning Vienna or Pairs ... ok test_BpseqParser_errors (test_parse.test_bpseq.BpseqParserTests) BpseqParser: should skip lines in unknown format ... ok test_MinimalBpseqParser (test_parse.test_bpseq.BpseqParserTests) MinimalBpseqParser: should separate lines correctly ... ok test_construct_sequence (test_parse.test_bpseq.BpseqParserTests) construct_sequence: should return correct sequence or raise error ... ok test_parse_header (test_parse.test_bpseq.BpseqParserTests) parse_header: should work on standard header ... ok test_parse_residues (test_parse.test_bpseq.BpseqParserTests) parse_residues: should work on valid data ... ok test_parse_residues_diff_base (test_parse.test_bpseq.BpseqParserTests) parse_residues: should work with diff base and unpaired_symbol ... ok test_parse_residues_errors (test_parse.test_bpseq.BpseqParserTests) parse_residues: should raise BpseqParseErrors in several cases ... ok test_bpseq_specify_output (test_parse.test_bpseq.ConvenienceFunctionTests) bpseq_specify_output: different return values ... ok test_CigarParser (test_parse.test_cigar.TestCigar) test without slice ... ok test_aligned_from_cigar (test_parse.test_cigar.TestCigar) test generating aligned seq from cigar ... ok test_cigar_to_map (test_parse.test_cigar.TestCigar) test generating a Map from cigar ... ok test_map_to_cigar (test_parse.test_cigar.TestCigar) convert a Map to cigar string ... ok test_slice_cigar (test_parse.test_cigar.TestCigar) test slicing cigars ... ok test_bad (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should reject bad data if strict ... ok test_minimal (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should handle single-line input correctly ... ok test_null (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should return empty dict and list on null input ... ok test_real (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should handle real Clustal output ... ok test_space_labels (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should tolerate spaces in labels ... ok test_two (test_parse.test_clustal.MinimalClustalParserTests) MinimalClustalParser should handle two-sequence input correctly ... ok test_delete_trailing_number (test_parse.test_clustal.clustalTests) delete_trailing_number should delete the trailing number if present ... ok test_is_clustal_seq_line (test_parse.test_clustal.clustalTests) is_clustal_seq_line should reject blanks and 'CLUSTAL' ... ok test_last_space (test_parse.test_clustal.clustalTests) last_space should split on last whitespace ... ok test_foldalign_find_struct (test_parse.test_column.ColumnParserTest) Test for foldalign parser find struct function ... ok test_foldalign_output (test_parse.test_column.ColumnParserTest) Test for column_parser for foldalign format ... ok test_pfold_output (test_parse.test_column.ColumnParserTest) Test for column_parser for pfold format ... ok test_common_func (test_parse.test_comrna.ComrnaParserTest) Test common function in comrna parser ... ok test_comrna_output (test_parse.test_comrna.ComrnaParserTest) Test for comrna format parser ... ok test_consan_output (test_parse.test_consan.ConsanParserTest) Test for consan format parser ... ok test_cove_output (test_parse.test_cove.CovesParserTest) Test coves format parser ... ok test_carnac_output (test_parse.test_ct.CtParserTest) Test for ct_parser for carnac format ... ok test_dynalign_output (test_parse.test_ct.CtParserTest) Test for ct_parser for dynalign format ... ok test_knetfold_output (test_parse.test_ct.CtParserTest) Test for ct_parser for knetfold format ... ok test_mfold_output (test_parse.test_ct.CtParserTest) Test for ct_parser for mfold format ... ok test_sfold_output (test_parse.test_ct.CtParserTest) Test for ct_parser for sfold format ... ok test_unafold_output (test_parse.test_ct.CtParserTest) Test for ct_parser for unafold format ... ok test_cut_parser (test_parse.test_cut.CutParserTest) cut_parser should work on first few lines of supplied file ... ok test_init (test_parse.test_cutg.CutgParserTests) CutgParser should read records one at a time from lines ... ok test_init (test_parse.test_cutg.CutgSpeciesParserTests) CutgSpeciesParser should read records one at a time from lines ... ok test_init (test_parse.test_cutg.InfoFromLabelTests) InfoFromLabel should handle a typical label line ... ok test_init_unknown_db (test_parse.test_cutg.InfoFromLabelTests) InfoFromLabel should handle a line whose database is unknown ... ok test_aligned_from_dialign (test_parse.test_dialign.TestDialign) test getting aligned seqs ... ok test_line_split (test_parse.test_dialign.TestDialign) test splitting of sequence record lines ... ok test_quality_scores (test_parse.test_dialign.TestDialign) test quality scores correctly returned ... ok test_cc_alternative_products_parser (test_parse.test_ebi.CC_Tests) cc_alternative_products_parser: know values ... ok test_cc_basic_itemparser (test_parse.test_ebi.CC_Tests) cc_basic_itemparser: known results or FieldError ... ok test_cc_biophysicochemical_properties_parser (test_parse.test_ebi.CC_Tests) cc_biophysicochemical_properties_parser: known values ... ok test_cc_interaction_parser (test_parse.test_ebi.CC_Tests) cc_interaction_parser: known values ... ok test_cc_itemfinder_raise (test_parse.test_ebi.CC_Tests) cc_itemfinder: raise RecordError if license block bad. ... ok test_cc_itemfinder_valid (test_parse.test_ebi.CC_Tests) cc_itemfinder: yield each expected block. ... ok test_cc_parser (test_parse.test_ebi.CC_Tests) cc_parser: known values and raise when strict ... ok test_EbiFinder (test_parse.test_ebi.EbiTests) EbiFinder should return expected list ... ok test_EbiParser (test_parse.test_ebi.EbiTests) EbiParser: ... ok test_MinimalEbiParser_valid (test_parse.test_ebi.EbiTests) MinimalEbiParser: integrity of output ... ok test_hanging_paragraph_finder (test_parse.test_ebi.EbiTests) hanging_paragraph_finder should give expected results ... ok test_item_empty_filter (test_parse.test_ebi.EbiTests) item_empty_filter: known values ... ok test_join_parser (test_parse.test_ebi.EbiTests) join parser should return expected str. ... ok test_join_split_dict_parser (test_parse.test_ebi.EbiTests) join_split_dict_parser: should return expected ... ok test_join_split_parser (test_parse.test_ebi.EbiTests) join_split_parser: should return expected ... ok test_labeloff (test_parse.test_ebi.EbiTests) labeloff: should return expected lines ... ok test_linecode_maker (test_parse.test_ebi.EbiTests) linecode_maker: should return expected tuple ... ok test_linecode_merging_maker (test_parse.test_ebi.EbiTests) linecode_merging_maker: ... ok test_mapping_parser (test_parse.test_ebi.EbiTests) mapping_parser: should return expected dict ... ok test_pairs_to_dict (test_parse.test_ebi.EbiTests) pairs_to_dict should return the expected dict ... ok test_parse_header (test_parse.test_ebi.EbiTests) ... ok test_period_tail_finder (test_parse.test_ebi.EbiTests) period_tail_finder should yield each group of expected lines. ... ok test_rstrip_ (test_parse.test_ebi.EbiTests) rstrip_ should generate the expected function ... ok test_ft_basic_itemparser (test_parse.test_ebi.FT_Tests) ft_basic_itemparser: known values ... ok test_ft_id_mutation_parser (test_parse.test_ebi.FT_Tests) ft_id_mutation_parser: known values ... ok test_ft_id_parser (test_parse.test_ebi.FT_Tests) ft_id_parser: known values ... ok test_ft_mutagen_parser (test_parse.test_ebi.FT_Tests) ft_mutagen_parser: known values ... ok test_ft_mutation_parser (test_parse.test_ebi.FT_Tests) ft_mutation_parser: known values ... ok test_ft_mutation_parser_raise (test_parse.test_ebi.FT_Tests) ft_mutation_parser: raise ValueError ... ok test_ft_parser (test_parse.test_ebi.FT_Tests) ft_parser should return expected dict ... ok test_try_int (test_parse.test_ebi.FT_Tests) try_int: known values ... ok test_ra_parser (test_parse.test_ebi.ReferenceTests) ra_parser should return expected list ... ok test_rc_parser (test_parse.test_ebi.ReferenceTests) rc_parser should return expected dict ... ok test_ref_finder (test_parse.test_ebi.ReferenceTests) ref_finder: should return a list of ref blocks ... ok test_refs_parser (test_parse.test_ebi.ReferenceTests) refs_parser: should return a dict of {RN: ref_dict} ... ok test_rg_parser (test_parse.test_ebi.ReferenceTests) rg_parser should return expected str ... ok test_rl_parser (test_parse.test_ebi.ReferenceTests) rl_parser should return expected str ... ok test_rn_parser (test_parse.test_ebi.ReferenceTests) rn_parser should return expected str ... ok test_rp_parser (test_parse.test_ebi.ReferenceTests) rp_parser should return expected str ... ok test_rt_parser (test_parse.test_ebi.ReferenceTests) rt_parser should return expected str ... ok test_rx_parser (test_parse.test_ebi.ReferenceTests) rx_parser should return expected dict ... ok test_single_ref_parser (test_parse.test_ebi.ReferenceTests) single_ref_parser: should return the expected dict ... ok test_ac_parser (test_parse.test_ebi.RootParsersKnownValues) ac_parser should return expected list ... ok test_de_itemparser (test_parse.test_ebi.RootParsersKnownValues) de_itemparser: known values ... ok test_de_parser (test_parse.test_ebi.RootParsersKnownValues) de_parser should return expected list ... ok test_dr_parser (test_parse.test_ebi.RootParsersKnownValues) dr_parser should return expected dict ... ok test_dt_parser (test_parse.test_ebi.RootParsersKnownValues) dt_parser should return expected list of list ... ok test_gn_parser (test_parse.test_ebi.RootParsersKnownValues) gn_parser should return expected list of dict ... ok test_id_parser (test_parse.test_ebi.RootParsersKnownValues) id_parser should return expected dict ... ok test_oc_parser (test_parse.test_ebi.RootParsersKnownValues) oc_parser should return expected list ... ok test_og_parser (test_parse.test_ebi.RootParsersKnownValues) og_parser should return expected list ... ok test_os_parser (test_parse.test_ebi.RootParsersKnownValues) os_parser should return expected list ... ok test_ox_parser (test_parse.test_ebi.RootParsersKnownValues) ox_parser should return expected dict ... ok test_pr_parser (test_parse.test_ebi.RootParsersKnownValues) pr_parser should return expected list ... ok test_sq_parser (test_parse.test_ebi.RootParsersKnownValues) sq_parser should return expected dict ... ok test_empty (test_parse.test_fasta.FastaParserTests) FastaParser should return empty list from 'file' w/o labels ... ok test_multiple (test_parse.test_fasta.FastaParserTests) FastaParser should read multiline records correctly ... ok test_multiple_bad (test_parse.test_fasta.FastaParserTests) Parser should complain or skip bad records ... ok test_multiple_constructor_bad (test_parse.test_fasta.FastaParserTests) Parser should complain or skip bad records w/ constructor ... ok test_no_labels (test_parse.test_fasta.FastaParserTests) FastaParser should return empty list from file w/o seqs ... ok test_single (test_parse.test_fasta.FastaParserTests) FastaParser should read single record as seq object ... ok test_single_constructor (test_parse.test_fasta.FastaParserTests) FastaParser should use constructors if supplied ... ok test_groups (test_parse.test_fasta.GroupFastaParsingTest) correctly yield grouped sequences from fasta formatted data ... ok test_label_parser (test_parse.test_fasta.LabelParsingTest) label parser factory function cope with mixed structure labels ... ok test_rich_label (test_parse.test_fasta.LabelParsingTest) rich label correctly constructs label strings ... ok test_empty (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser should return empty list from 'file' w/o labels ... ok test_gt_bracket_in_seq (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser handles alternate finder function ... ok test_multiple (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser should read multiline records correctly ... ok test_multiple_bad (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser should complain or skip bad records ... ok test_no_labels (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser should return empty list from file w/o seqs ... ok test_single (test_parse.test_fasta.MinimalFastaParserTests) MinimalFastaParser should read single record as (label, seq) tuple ... ok test_init (test_parse.test_fasta.NcbiFastaLabelParserTests) Labels from genpept.fsa should work as expected ... ok test_bad (test_parse.test_fasta.NcbiFastaParserTests) NcbiFastaParser should raise error on bad records if strict ... ok test_empty (test_parse.test_fasta.NcbiFastaParserTests) NcbiFastaParser should accept empty input ... ok test_normal (test_parse.test_fasta.NcbiFastaParserTests) NcbiFastaParser should accept normal record if loose or strict ... ok test_parse (test_parse.test_fastq.ParseFastq) sequence and info objects should correctly match ... ok test_parse (test_parse.test_gbseq.ParseGBseq) ... ok test_build_module_objects (test_parse.test_gibbs.GibbsTests) build_module_objects tests. ... ok test_get_motif_blocks (test_parse.test_gibbs.GibbsTests) get_motif_blocks tests. ... ok test_get_motif_p_value (test_parse.test_gibbs.GibbsTests) get_motif_p_value tests. ... ok test_get_motif_sequences (test_parse.test_gibbs.GibbsTests) get_motif_sequences tests. ... ok test_get_sequence_and_motif_blocks (test_parse.test_gibbs.GibbsTests) get_sequence_and_motif_blocks tests. ... ok test_get_sequence_map (test_parse.test_gibbs.GibbsTests) get_sequence_map tests. ... ok test_guess_alphabet (test_parse.test_gibbs.GibbsTests) guess_alphabet tests. ... ok test_module_ids_to_int (test_parse.test_gibbs.GibbsTests) module_ids_to_int tests. ... ok test_block_consolidator (test_parse.test_genbank.GenBankTests) block_consolidator should join the block together. ... ok test_indent_splitter (test_parse.test_genbank.GenBankTests) indent_splitter should split lines at correct locations ... ok test_location_line_tokenizer (test_parse.test_genbank.GenBankTests) location_line_tokenizer should tokenize location lines ... ok test_parse_feature (test_parse.test_genbank.GenBankTests) parse_feature should return dict containing annotations of feature ... ok test_parse_location_line (test_parse.test_genbank.GenBankTests) parse_location_line should give correct list of location objects ... ok test_parse_locus (test_parse.test_genbank.GenBankTests) parse_locus should give correct results on specimen locus lines ... ok test_parse_organism (test_parse.test_genbank.GenBankTests) parse_organism should return species, taxonomy (up to genus) ... ok test_parse_reference (test_parse.test_genbank.GenBankTests) parse_reference should give correct fields ... ok test_parse_sequence (test_parse.test_genbank.GenBankTests) parse_sequence should strip bad chars out of sequence lines ... ok test_parse_simple_location_segment (test_parse.test_genbank.GenBankTests) parse_simple_location_segment should parse simple segments ... ok test_parse_single_line (test_parse.test_genbank.GenBankTests) parse_single_line should split off the label and return the rest ... ok test_parse_source (test_parse.test_genbank.GenBankTests) parse_source should split into source and organism ... ok test_rich_parser (test_parse.test_genbank.GenBankTests) correctly constructs +/- strand features ... ok test_extract (test_parse.test_genbank.LocationListTests) LocationList extract should return correct sequence ... ok test_init (test_parse.test_genbank.LocationTests) Location should init with 1 or 2 values, plus params. ... ok testGffParserData (test_parse.test_gff.GffTest) Test GffParser with valid data lines ... ok testGffParserHeaders (test_parse.test_gff.GffTest) Test GffParser with valid data headers ... ok test_parse_attributes (test_parse.test_gff.GffTest) Test parse_attributes ... ok test_MinimalGreengenesParser_mock (test_parse.test_greengenes.ParseGreengenesRecordsTests) Test MinimalGreengenesParser against mock data ... ok test_MinimalGreengenesParser_real (test_parse.test_greengenes.ParseGreengenesRecordsTests) Test MinimalGreengenesParser against real data ... ok test_SpecificGreengenesParser_real (test_parse.test_greengenes.ParseGreengenesRecordsTests) Test SpecificGreengenesParser against real data ... ok test_make_ignore_f (test_parse.test_greengenes.ParseGreengenesRecordsTests) Properly ignore empty records and the start line ... ok test_ilm_output (test_parse.test_ilm.IlmParserTest) Test for ilm format ... ok test_MinimalIlluminaSequenceParser (test_parse.test_illumina_sequence.ParseIlluminaSequenceTests) MinimalIlluminaSequenceParser functions as expected ... ok test_MinimalIlluminaSequenceParser_handles_file_as_input (test_parse.test_illumina_sequence.ParseIlluminaSequenceTests) MinimalIlluminaSequenceParser functions with file handle as input ... ok test_MinimalIlluminaSequenceParser_handles_filepath_as_input (test_parse.test_illumina_sequence.ParseIlluminaSequenceTests) MinimalIlluminaSequenceParser functions with filepath as input ... ok test_LinesToLocusLink (test_parse.test_locuslink.locuslinkTests) LinesToLocusLink should give expected results on sample data ... ok test_read_accession (test_parse.test_locuslink.locuslinkTests) _read_accession should perform correct conversions ... ok test_read_accnum (test_parse.test_locuslink.locuslinkTests) _read_accnum should perform correct conversions ... ok test_read_cdd (test_parse.test_locuslink.locuslinkTests) _read_cdd should perform correct conversions ... ok test_read_comp (test_parse.test_locuslink.locuslinkTests) _read_comp should perform correct conversions ... ok test_read_contig (test_parse.test_locuslink.locuslinkTests) _read_contig should perform correct conversions ... ok test_read_extannot (test_parse.test_locuslink.locuslinkTests) _read_extannot should perform correct conversions ... ok test_read_go (test_parse.test_locuslink.locuslinkTests) _read_go should perform correct conversions ... ok test_read_grif (test_parse.test_locuslink.locuslinkTests) _read_grif should perform correct conversions ... ok test_read_map (test_parse.test_locuslink.locuslinkTests) _read_map should perform correct conversions ... ok test_read_pmid (test_parse.test_locuslink.locuslinkTests) _read_pmid should perform correct conversions ... ok test_read_rell (test_parse.test_locuslink.locuslinkTests) _read_rell should perform correct conversions ... ok test_read_sts (test_parse.test_locuslink.locuslinkTests) _read_sts should perform correct conversions ... ok test_MageGroupFromString (test_parse.test_mage.MageGroupFromStringTests) MageGroupFromString should fill itself from string correctly ... ok test_MageGroupFromString_wrong (test_parse.test_mage.MageGroupFromStringTests) MageGroupFromString should fail on wrong input ... ok test_MageListFromString (test_parse.test_mage.MageListFromStringTests) MageListFromString should fill itself from string correctly ... ok test_MageListFromString_wrong (test_parse.test_mage.MageListFromStringTests) MageListFromString should fail on wrong input ... ok test_MageParser (test_parse.test_mage.MageParserTests) MageParser should work on valid input ... ok test_MagePointFromString (test_parse.test_mage.MagePointFromStringTests) MagePoint should fill itself from string correctly ... ok test_dict_from_list (test_parse.test_meme.MemeTests) dictFromList should return a dict given a list. ... ok test_extract_command_line_data (test_parse.test_meme.MemeTests) extractCommandLineData should return a dict of command line data. ... ok test_extract_module_data (test_parse.test_meme.MemeTests) extractModuleData should return a Module object. ... ok test_extract_summary_data (test_parse.test_meme.MemeTests) extractSummaryData should return a dict of MEME summary data. ... ok test_get_alphabet (test_parse.test_meme.MemeTests) getMolType should return the correct alphabet. ... ok test_get_command_module_blocks (test_parse.test_meme.MemeTests) getCommandModuleBlocks should return the command and module blocks. ... ok test_get_consensus_sequence (test_parse.test_meme.MemeTests) getConsensusSequence should return Module's Consensus sequence. ... ok test_get_data_block (test_parse.test_meme.MemeTests) getDataBlock should return the main block and the alphabet. ... ok test_get_module_data_blocks (test_parse.test_meme.MemeTests) getModuleDataBlocks should return a list of blocks for each module. ... ok test_get_module_general_info (test_parse.test_meme.MemeTests) getModuleGeneralInfo should return a dict of Module info. ... ok test_get_summary_block (test_parse.test_meme.MemeTests) getSummaryBlock should return the MEME summary block. ... ok test_meme_parser (test_parse.test_meme.MemeTests) MemeParser should correctly return a MotifResults object. ... ok test_parseVertFile (test_parse.test_msms.MsmsTest) ... ok test_init (test_parse.test_ncbi_taxonomy.NcbiNameLookupTest) NcbiNameLookup should map taxon ids to scientific names ... ok test_bad_input (test_parse.test_ncbi_taxonomy.NcbiNameTests) NcbiName init should raise correct errors on bad data ... ok test_init (test_parse.test_ncbi_taxonomy.NcbiNameTests) NcbiName should init OK with well-formed name line ... ok test_str (test_parse.test_ncbi_taxonomy.NcbiNameTests) NcbiName str should return line in original format ... ok test_init (test_parse.test_ncbi_taxonomy.NcbiTaxonLookupTest) NcbiTaxonLookup should have correct fields for input NcbiTaxon ... ok test_getRankedDescendants (test_parse.test_ncbi_taxonomy.NcbiTaxonNodeTests) NcbiTaxonNode getRankedDescendants should return correct list ... ok test_bad_input (test_parse.test_ncbi_taxonomy.NcbiTaxonTests) NcbiTaxon init should raise ValueError if nodes missing ... ok test_init (test_parse.test_ncbi_taxonomy.NcbiTaxonTests) NcbiTaxon init should return object containing taxonomy data ... ok test_str (test_parse.test_ncbi_taxonomy.NcbiTaxonTests) NcbiTaxon str should write data in input format from nodes.dmp ... ok test_Ancestors (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should support Ancestors correctly, not incl. self ... ok test_Children (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should support Children correctly ... ok test_Names (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should fill in names correctly ... ok test_Parent (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should support Parent correctly ... ok test_Siblings (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should support Siblings correctly ... ok test_init_bad (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomyFromFiles should produce deadbeats by default ... ok test_init_good (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomyFromFiles should pass spot-checks of resulting objects ... ok test_init_strict (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomyFromFiles should fail if strict and deadbeats exist ... ok test_lastCommonAncestor (test_parse.test_ncbi_taxonomy.NcbiTaxonomyTests) NcbiTaxonomy should support lastCommonAncestor() ... ok test_find_fields (test_parse.test_nexus.NexusParserTests) find_fields takes BL table line and returns field names mapped to info ... ok test_get_BL_table (test_parse.test_nexus.NexusParserTests) get_BL_table returns the section of the log file w/ the BL table ... ok test_get_tree_info (test_parse.test_nexus.NexusParserTests) get_tree_info returns the Nexus file section that describes the tree ... ok test_parse_PAUP_log (test_parse.test_nexus.NexusParserTests) parse_PAUP_log extracts branch length info from a PAUP log file ... ok test_parse_dnd (test_parse.test_nexus.NexusParserTests) parse_dnd returns a dict with dnd indexed by tree name ... ok test_parse_nexus_tree (test_parse.test_nexus.NexusParserTests) parse_nexus_tree returns a dnd string and a translation table list ... ok test_parse_nexus_tree_sq (test_parse.test_nexus.NexusParserTests) remove single quotes from tree and translate tables ... ok test_parse_taxa (test_parse.test_nexus.NexusParserTests) parse_taxa should return the taxa # from a taxa_field from find_fields ... ok test_parse_trans_table (test_parse.test_nexus.NexusParserTests) parse_trans_table returns a dict with the taxa names indexed by number ... ok test_split_tree_info (test_parse.test_nexus.NexusParserTests) split_tree_info splits lines into header, Trans_table, and dnd ... ok test_nupack_output (test_parse.test_nupack.NupackParserTest) Test for nupack format ... ok test_PDBParser (test_parse.test_pdb.pdbTests) tests the UI parsing function. ... ok test_dict2pdb (test_parse.test_pdb.pdbTests) testing pdb dict round-trip. ... ok test_dict2ter (test_parse.test_pdb.pdbTests) ... ok test_get_coords_offset (test_parse.test_pdb.pdbTests) ... ok test_get_symmetry (test_parse.test_pdb.pdbTests) testing parsing of symmetry operators ... ok test_get_trailer_offset (test_parse.test_pdb.pdbTests) ... ok test_parse_coords (test_parse.test_pdb.pdbTests) testing minimal structure building and coords parsing. ... ok test_parse_header (test_parse.test_pdb.pdbTests) testing header parsing. ... ok test_parse_trailer (test_parse.test_pdb.pdbTests) testing trailer parsing dummy. ... ok test_getting_seq_coords (test_parse.test_psl.Test) get correct sequence coordinates to produce a trimmed sequence ... ok test_header (test_parse.test_psl.Test) should return correct header ... ok test_psl_to_table (test_parse.test_psl.Test) ... ok test_FromFileStructureParser (test_parse.test_structure.structuresTests) ... ok test_FromFilenameStructureParser (test_parse.test_structure.structuresTests) ... ok test_parse (test_parse.test_pamlmatrix.TestParsePamlMatrix) ... ok test_empty (test_parse.test_phylip.MinimalPhylipParserTests) MinimalFastaParser should return empty list from 'file' w/o labels ... ok test_get_align (test_parse.test_phylip.MinimalPhylipParserTests) get_align_for_phylip should return Aligment object for phylip files ... ok test_minimal_parser (test_parse.test_phylip.MinimalPhylipParserTests) MinimalFastaParser should read single record as (label, seq) tuple ... ok test_pknotsrg_output (test_parse.test_pknotsrg.PknotsrgParserTest) Test for pknotsrg format parser ... ok test_empty (test_parse.test_rdb.InfoMakerTests) InfoMaker: should return empty Info from empty header ... ok test_full (test_parse.test_rdb.InfoMakerTests) InfoMaker should return Info object with name, value pairs ... ok test_empty (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should return empty list from file w/o seqs ... ok test_multiple (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should read multiple record correctly ... ok test_multiple_bad (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should complain or skip bad records ... ok test_only_labels (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should return empty list from file w/o seqs ... ok test_only_sequences (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should return empty list form file w/o lables ... ok test_single (test_parse.test_rdb.MinimalRdbParserTests) MinimalRdbParser should read single record as (header,seq) tuple ... ok test_strange (test_parse.test_rdb.MinimalRdbParserTests) MRP: handle strange char. according to constr. and strip off '*' ... ok test_empty (test_parse.test_rdb.RdbParserTests) RdbParser should return empty list from 'file' w/o labels ... ok test_full (test_parse.test_rdb.RdbParserTests) RdbParser: full data, valid and invalid ... ok test_multiple_constructor_bad (test_parse.test_rdb.RdbParserTests) RdbParser should complain or skip bad records w/ constructor ... ok test_only_labels (test_parse.test_rdb.RdbParserTests) RdbParser should return empty list from file w/o seqs ... ok test_only_sequences (test_parse.test_rdb.RdbParserTests) RdbParser should return empty list form file w/o lables ... ok test_single (test_parse.test_rdb.RdbParserTests) RdbParser should read single record as (header,seq) tuple ... ok test_single_constructor (test_parse.test_rdb.RdbParserTests) RdbParser should use constructors if supplied ... ok test_create_acceptable_sequence (test_parse.test_rdb.RdbTests) create_acceptable_sequence: should handle 'o' and sec. struct ... ok test_is_seq_label (test_parse.test_rdb.RdbTests) is_seq_label should return True if a line starts with 'seq:' ... ok test_parsers (test_parse.test_record.DelimitedSplitterTests) DelimitedSplitter should return function with correct behavior ... ok test_altered_default (test_parse.test_record.FieldMorpherTests) FieldMorpher with default set should apply it ... ok test_default (test_parse.test_record.FieldMorpherTests) FieldMorpher default should use correct constructors ... ok test_default_error (test_parse.test_record.FieldMorpherTests) FieldMorpher default should raise FieldError on unknown fields ... ok test_constructor (test_parse.test_record.FieldWrapperTests) FieldWrapper with constructor should use that constructor ... ok test_default (test_parse.test_record.FieldWrapperTests) Default FieldWrapper should wrap fields and labels ... ok test_splitter (test_parse.test_record.FieldWrapperTests) FieldWrapper with splitter should use that splitter ... ok test_copy (test_parse.test_record.GenericRecordTests) GenericRecord copy should include attributes and set correct class ... ok test_delitem (test_parse.test_record.GenericRecordTests) GenericRecord delitem should fail if item required ... ok test_init (test_parse.test_record.GenericRecordTests) GenericRecord init should work OK empty or with data ... ok test_init_subclass (test_parse.test_record.GenericRecordTests) GenericRecord subclass init should include required data ... ok test_call (test_parse.test_record.GrouperTests) Grouper should return lists containing correct number of groups ... ok test_call_bad (test_parse.test_record.GrouperTests) Grouper call should raise ValueError if NumItems is not an int ... ok test_empty_LOC (test_parse.test_record.LineOrientedConstructorTests) LOC empty should fail if strict, fill fields if not strict ... ok test_full_LOC (test_parse.test_record.LineOrientedConstructorTests) LOC should behave as expected when initialized with rich data ... ok test_init_empty (test_parse.test_record.LineOrientedConstructorTests) LOC empty init should succeed with expected defaults ... ok test_DefaultValue (test_parse.test_record.MappedRecordTests) MappedRecord DefaultValue should give new copy when requested ... ok test_contains (test_parse.test_record.MappedRecordTests) MappedRecord contains should use aliases, but not apply to attrs ... ok test_copy (test_parse.test_record.MappedRecordTests) MappedRecord copy should return correct class ... ok test_delattr (test_parse.test_record.MappedRecordTests) MappedRecord delattr should work for 'normal' and other attributes ... ok test_delitem (test_parse.test_record.MappedRecordTests) MappedRecord delitem should only work for keys, not attributes ... ok test_get (test_parse.test_record.MappedRecordTests) MappedRecord get should be typesafe against unhashables ... ok test_getattr (test_parse.test_record.MappedRecordTests) MappedRecord getattr should look in dict after real attrs ... ok test_getitem (test_parse.test_record.MappedRecordTests) MappedRecord getitem should work only for keys, not attributes ... ok test_init_data (test_parse.test_record.MappedRecordTests) MappedRecord should work like normal dict init ... ok test_init_empty (test_parse.test_record.MappedRecordTests) MappedRecord empty init should work OK ... ok test_init_subclass (test_parse.test_record.MappedRecordTests) MappedRecord subclasses should behave as expected ... ok test_setattr (test_parse.test_record.MappedRecordTests) MappedRecord setattr should add to dict ... ok test_setdefault (test_parse.test_record.MappedRecordTests) MappedRecord setdefault should not be typesafe against unhashables ... ok test_setitem (test_parse.test_record.MappedRecordTests) MappedRecord setitem should work only for keys, not attributes ... ok test_subclass (test_parse.test_record.MappedRecordTests) MappedRecord subclassing should work correctly ... ok test_update (test_parse.test_record.MappedRecordTests) MappedRecord update should transparently convert keys ... ok test_constructor (test_parse.test_record.StrictFieldWrapperTests) StrictFieldWrapper with constructor should use that constructor ... ok test_default (test_parse.test_record.StrictFieldWrapperTests) Default StrictFieldWrapper should wrap fields if count correct ... ok test_splitter (test_parse.test_record.StrictFieldWrapperTests) StrictFieldWrapper with splitter should use that splitter ... ok test_dict_adder (test_parse.test_record.TypeSetterLikeTests) dict_adder should add items to dict, creating if necessary ... ok test_list_adder (test_parse.test_record.TypeSetterLikeTests) list_adder should add items to list, creating if necessary ... ok test_list_extender (test_parse.test_record.TypeSetterLikeTests) list_adder should add items to list, creating if necessary ... ok test_setter_empty (test_parse.test_record.TypeSetterTests) TypeSetter should set attrs to vals on empty init ... ok test_setter_typed (test_parse.test_record.TypeSetterTests) TypeSetter should set attrs to constructor(val) when specified ... ok test_raise_unknown_field (test_parse.test_record.recordsTests) raise_unknown_field should always raise FieldError ... ok test_string_and_strip (test_parse.test_record.recordsTests) string_and_strip should convert all items to strings and strip them ... ok test_parsers (test_parse.test_record_finder.DelimitedRecordFinderTests) DelimitedRecordFinder should split records into lines correctly ... ok test_parsers_empty (test_parse.test_record_finder.DelimitedRecordFinderTests) DelimitedRecordFinder should return empty list on empty lines ... ok test_parsers_error (test_parse.test_record_finder.DelimitedRecordFinderTests) DelimitedRecordFinder should raise RecordError if trailing data ... ok test_parsers_ignore (test_parse.test_record_finder.DelimitedRecordFinderTests) DelimitedRecordFinder should skip lines to ignore. ... ok test_parsers_strip (test_parse.test_record_finder.DelimitedRecordFinderTests) DelimitedRecordFinder should trim each line correctly ... ok test_parsers (test_parse.test_record_finder.LabeledRecordFinderTests) LabeledRecordFinder should split records into lines correctly ... ok test_parsers_empty (test_parse.test_record_finder.LabeledRecordFinderTests) LabeledRecordFinder should return empty list on empty lines ... ok test_parsers_ignore (test_parse.test_record_finder.LabeledRecordFinderTests) LabeledRecordFinder should skip lines to ignore. ... ok test_parsers_leftover (test_parse.test_record_finder.LabeledRecordFinderTests) LabeledRecordFinder should not raise RecordError if last line label ... ok test_parsers_strip (test_parse.test_record_finder.LabeledRecordFinderTests) LabeledRecordFinder should trim each line correctly ... ok test_parser (test_parse.test_record_finder.LineGrouperTests) LineGrouper should return n non-blank lines at a time ... ok test_parser_ignore (test_parse.test_record_finder.LineGrouperTests) LineGrouper should skip lines to ignore. ... ok test_parsers (test_parse.test_record_finder.TailedRecordFinderTests) TailedRecordFinder should split records into lines correctly ... ok test_parsers_empty (test_parse.test_record_finder.TailedRecordFinderTests) TailedRecordFinder should return empty list on empty lines ... ok test_parsers_ignore (test_parse.test_record_finder.TailedRecordFinderTests) TailedRecordFinder should skip lines to ignore. ... ok test_parsers_leftover (test_parse.test_record_finder.TailedRecordFinderTests) TailedRecordFinder should raise error or yield leftover ... ok test_parsers_strip (test_parse.test_record_finder.TailedRecordFinderTests) TailedRecordFinder should trim each line correctly ... ok test_ChangedSequence (test_parse.test_rfam.RfamParserTests) ChangedSequence: integrity of output ... ok test_HeaderToInfo (test_parse.test_rfam.RfamParserTests) HeaderToInfo: correctly builds info object from header information ... ok test_HeaderToInfo_invalid_data (test_parse.test_rfam.RfamParserTests) HeaderToInfo: correctly raises error when necessary ... ok test_MinimalRfamParser_strict_invalid_sequence (test_parse.test_rfam.RfamParserTests) MinimalRfamParser: toggle strict functions w/ invalid seq ... ok test_MinimalRfamParser_strict_invalid_structure (test_parse.test_rfam.RfamParserTests) MinimalRfamParser: toggle strict functions w/ invalid structure ... ok test_MinimalRfamParser_strict_missing_fields (test_parse.test_rfam.RfamParserTests) MinimalRfamParser: toggle strict functions w/ missing fields ... ok test_MinimalRfamParser_w_valid_data (test_parse.test_rfam.RfamParserTests) MinimalRfamParser: integrity of output ... ok test_NameToInfo (test_parse.test_rfam.RfamParserTests) NameToInfo: integrity of output ... ok test_NameToInfo_invalid_label (test_parse.test_rfam.RfamParserTests) NameToInfo: raises error on invalid label ... ok test_RFamParser_strict_invalid_headers (test_parse.test_rfam.RfamParserTests) RfamParser: functions when toggling strict w/ record w/ bad header ... ok test_RfamFinder (test_parse.test_rfam.RfamParserTests) RfamFinder: integrity of output ... ok test_RfamParser (test_parse.test_rfam.RfamParserTests) RfamParser: integrity of output ... ok test_RfamParser_single_family (test_parse.test_rfam.RfamParserTests) RfamParser: should work on a single family in stockholm format ... ok test_RfamParser_strict_invalid_sequences (test_parse.test_rfam.RfamParserTests) RfamParser: functions when toggling strict w/ record w/ bad seq ... ok test_RfamParser_strict_invalid_structure (test_parse.test_rfam.RfamParserTests) RfamParser: functions when toggling strict w/ record w/ bad struct ... ok test_RfamParser_strict_missing_fields (test_parse.test_rfam.RfamParserTests) RfamParser: toggle strict functions correctly ... ok test_is_empty_or_html (test_parse.test_rfam.RfamParserTests) is_empty_or_html: should ignore empty and HTML line ... ok test_is_header_line (test_parse.test_rfam.RfamParserTests) is_header_line: functions correctly w/ various lines ... ok test_is_seq_line (test_parse.test_rfam.RfamParserTests) is_seq_line: functions correctly w/ various lines ... ok test_is_structure_line (test_parse.test_rfam.RfamParserTests) is_structure_line: functions correctly w/ various lines ... ok test_rnaalifold_output (test_parse.test_rnaalifold.MinimalRnaalifoldParserTest) Test for rnaalifold format parser ... ok test_rnaalifold_output (test_parse.test_rnaalifold.RnaalifoldParserTest) Test for rnaalifold format parser ... ok test_RnaFoldParser (test_parse.test_rna_fold.RnaFoldParserTests) ... ok test_getIndices (test_parse.test_rna_fold.RnaFoldParserTests) ... ok test_getSequence (test_parse.test_rna_fold.RnaFoldParserTests) ... ok test_init (test_parse.test_rnaview.BaseMultipletTests) BaseMultiplet __init__: should work as expected ... ok test_str (test_parse.test_rnaview.BaseMultipletTests) BaseMultiplet __str__: should give expected string ... ok test_init (test_parse.test_rnaview.BaseMultipletsTests) BaseMultiplets __init__: from list and tuple ... ok test_str (test_parse.test_rnaview.BaseMultipletsTests) BaseMultiplets __str__: should give expected string ... ok test_eq (test_parse.test_rnaview.BasePairTests) BasePair ==: should function as expected ... ok test_init (test_parse.test_rnaview.BasePairTests) BasePair __init__: should initialize on standard data ... ok test_isWC (test_parse.test_rnaview.BasePairTests) BasePair isWC: should return True for GC or AU pair ... ok test_isWobble (test_parse.test_rnaview.BasePairTests) BasePair isWobble: should return True for GU pair ... ok test_ne (test_parse.test_rnaview.BasePairTests) BasePair !=: should function as expected ... ok test_str (test_parse.test_rnaview.BasePairTests) BasePair __str__: should return correct string ... ok test_PresentChains (test_parse.test_rnaview.BasePairsTests) BasePairs PresentChains: should work on single/multiple chain(s) ... ok test_cliques (test_parse.test_rnaview.BasePairsTests) BasePairs cliques: single/multiple chains and cliques ... ok test_hasConflicts (test_parse.test_rnaview.BasePairsTests) BasePairs hadConflicts: handle chains and residue IDs ... ok test_init (test_parse.test_rnaview.BasePairsTests) BasePairs __init__: should work with or without Model ... ok test_select (test_parse.test_rnaview.BasePairsTests) BasePairs select: should work with any good function ... ok test_str (test_parse.test_rnaview.BasePairsTests) BasePairs __str__: should produce expected string ... ok test_eq (test_parse.test_rnaview.BaseTests) Base ==: functions as expected ... ok test_init (test_parse.test_rnaview.BaseTests) Base __init__: should initialize on standard data ... ok test_ne (test_parse.test_rnaview.BaseTests) Base !=: functions as expected ... ok test_str (test_parse.test_rnaview.BaseTests) Base __str__: should return correct string ... ok test_MinimalRnaviewParser (test_parse.test_rnaview.RnaviewParserTests) MinimalRnaviewParser: should divide lines into right classes ... ok test_MinimalRnaviewParser_short (test_parse.test_rnaview.RnaviewParserTests) MinimalRnaviewparser: should leave lists empty if no lines found ... ok test_RnaviewParser (test_parse.test_rnaview.RnaviewParserTests) RnaviewParser: should work with/without model and/or verification ... ok test_RnaviewParser_error (test_parse.test_rnaview.RnaviewParserTests) RnaviewParser: strict or not ... ok test_is_edge (test_parse.test_rnaview.RnaviewParserTests) is_edge: should identify valid edges correctly ... ok test_is_orientation (test_parse.test_rnaview.RnaviewParserTests) is_orientation: should fail on anything but 'cis' or 'tran' ... ok test_is_roman_numeral (test_parse.test_rnaview.RnaviewParserTests) is_roman_numeral: should work for all, including comma ... ok test_parse_annotation (test_parse.test_rnaview.RnaviewParserTests) parse_annotation: should return correct tuple of 4 or raise error ... ok test_parse_base_multiplets_basic (test_parse.test_rnaview.RnaviewParserTests) parse_base_multiplets: basic input ... ok test_parse_base_multiplets_errors (test_parse.test_rnaview.RnaviewParserTests) parse_base_multiplets: error checking ... ok test_parse_base_pairs_basic (test_parse.test_rnaview.RnaviewParserTests) parse_base_pairs: basic input ... ok test_parse_filename (test_parse.test_rnaview.RnaviewParserTests) parse_filename: should return name of file ... ok test_parse_number_of_pairs (test_parse.test_rnaview.RnaviewParserTests) parse_number_of_pairs: good/bad input ... ok test_parse_pair_counts (test_parse.test_rnaview.RnaviewParserTests) parse_pair_counts: should work for even number of lines ... ok test_parse_uncommon_residues (test_parse.test_rnaview.RnaviewParserTests) parse_uncommon_residues: should fail on some missing residue info ... ok test_verify_bp_counts (test_parse.test_rnaview.RnaviewParserTests) verify_bp_count: should raise an error if bp counts are wrong ... ok test_in_chain (test_parse.test_rnaview.SelectionFunctionTests) ... ok test_is_canocical (test_parse.test_rnaview.SelectionFunctionTests) is_canonical: work on annotation, not base identity ... ok test_is_not_canocical (test_parse.test_rnaview.SelectionFunctionTests) is_not_canonical: opposite of is_canonical ... ok test_is_not_stacked (test_parse.test_rnaview.SelectionFunctionTests) is_not_stacked: opposite of is_stacked ... ok test_is_not_stacked_or_tertiary (test_parse.test_rnaview.SelectionFunctionTests) is_not_stacked_or_tertiary: checks annotation, not base identity ... ok test_is_stacked (test_parse.test_rnaview.SelectionFunctionTests) is_stacked: checks annotation, not base identity ... ok test_is_tertiary (test_parse.test_rnaview.SelectionFunctionTests) is_tertiary: checks annotation, not base identity ... ok test_is_tertiary_base_base (test_parse.test_rnaview.SelectionFunctionTests) is_tertiary_base_base: checks annotation, not base identity ... ok test_init (test_parse.test_rnaview.TestPairCounts) PairCounts __init__: should work as dict ... ok test_rnaforester_output (test_parse.test_rnaforester.RnaforesterParserTest) Test for rnaforester format ... ok test_fix_sequence (test_parse.test_sprinzl.FixSequenceTests) Fix sequence should properly replace terminal gaps with CCA ... ok test_multi (test_parse.test_sprinzl.GenomicSprinzlParserTests) GenomicSprinzlParser should work with multiple sequences ... ok test_single (test_parse.test_sprinzl.GenomicSprinzlParserTests) GenomicSprinzlParser should work with single sequence ... ok test_init (test_parse.test_sprinzl.OneLineSprinzlParserTests) OneLineSprinzlParser should read small file correctly ... ok test_minimal (test_parse.test_sprinzl.OneLineSprinzlParserTests) OneLineSprinzlParser should work on a minimal 'file' ... ok test_get_counts (test_parse.test_sprinzl.SprinzlToViennaTests) get_counts: should return list of lengths of paired regions ... ok test_get_pieces (test_parse.test_sprinzl.SprinzlToViennaTests) get_pieces: should return the correct pieces ... ok test_sprinzl_to_vienna (test_parse.test_sprinzl.SprinzlToViennaTests) sprinzl_to_vienna: should give expected output ... ok test_parse (test_parse.test_tinyseq.ParseTinyseq) ... ok test_DndParser (test_parse.test_tree.DndParserTests) DndParser tests ... ok test_data (test_parse.test_tree.DndParserTests) DndParser should work as expected on real data ... ok test_gbad (test_parse.test_tree.DndParserTests) DndParser should fail if parens unbalanced ... ok test_gdouble (test_parse.test_tree.DndParserTests) DndParser should produce a double-child PhyloNode from data ... ok test_gnodedata (test_parse.test_tree.DndParserTests) DndParser should assign Name to internal nodes correctly ... ok test_gonenest (test_parse.test_tree.DndParserTests) DndParser should work correctly with nested data ... ok test_gsingle (test_parse.test_tree.DndParserTests) DndParser should produce a single-child PhyloNode on minimal data ... ok test_minimal (test_parse.test_tree.DndParserTests) DndParser should produce the correct minimal tree ... ok test_missing_tip_name (test_parse.test_tree.DndParserTests) DndParser should produce the correct tree when missing a name ... ok test_nonames (test_parse.test_tree.DndParserTests) DndParser should produce the correct tree when there are no names ... ok test_gdata (test_parse.test_tree.DndTokenizerTests) DndTokenizer should work as expected on real data ... ok test_minimal (test_parse.test_tree.DndTokenizerTests) DndTokenizer should work as expected a minimal tree without names ... ok test_missing_tip_name (test_parse.test_tree.DndTokenizerTests) DndTokenizer should work as expected on trees with a missing name ... ok test_nonames (test_parse.test_tree.DndTokenizerTests) DndTokenizer should work as expected on trees with no names ... ok test_gops (test_parse.test_tree.PhyloNodeTests) Basic PhyloNode operations should work as expected ... ok test_LinesToUniGene (test_parse.test_unigene.unigeneTests) LinesToUniGene should give expected results on sample data ... ok test_read_expression (test_parse.test_unigene.unigeneTests) _read_expression should perform correct conversions ... ok test_read_seq (test_parse.test_unigene.unigeneTests) _read_seq should perform correct conversions ... ok test_read_sts (test_parse.test_unigene.unigeneTests) _read_sts should perform correct conversions ... ok test_call (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel call should produce hand-calculated trees ... ok test_call_exact (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel call should produce right # taxa when exact ... ok test_changed_values_step (test_seqsim.test_birth_death.BirthDeathModelTests) Tests if values changed at specified steps in step(). ... ok test_init_bad (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel should raise exceptions on init with bad data ... ok test_init_deafults (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel should init correctly w/ default params ... ok test_init_extras (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel should init OK with extra params ... ok test_prob_step_check (test_seqsim.test_birth_death.BirthDeathModelTests) prob_check and step_check should return error when out of bounds. ... ok test_step (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel step should match hand-calculated results ... ok test_taxaOk (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel TaxaOk should return True if taxa not exceeded ... ok test_timeOk (test_seqsim.test_birth_death.BirthDeathModelTests) BirthDeathModel TimeOk should return True if time not exceeded ... ok test_double_birth_death (test_seqsim.test_birth_death.DoubleBirthDeathTests) double_birth_death should run without errors ... ok test_entropy (test_seqsim.test_markov.MarkovGeneratorTests) MarkovGenerator._entropy() should correctly calculate average H ... ok test_evaluateArrayProbability (test_seqsim.test_markov.MarkovGeneratorTests) evaluateArrayProbability should calc prob from array indices ... ok test_evaluateProbability (test_seqsim.test_markov.MarkovGeneratorTests) Should calculate proper P value for seq ... ok test_init (test_seqsim.test_markov.MarkovGeneratorTests) MarkovGenerator init should give right frequency distributions. ... ok test_next (test_seqsim.test_markov.MarkovGeneratorTests) MarkovGenerator.next should generate text with expected properties ... ok test_replaceDegenerateBases (test_seqsim.test_markov.MarkovGeneratorTests) strips degenerate bases.... ... ok test_wordToUniqueKey (test_seqsim.test_markov.MarkovGeneratorTests) wordToUniqueKey should generate proper integers ... ok test_init (test_seqsim.test_microarray.MicroarrayNodeTests) MicroarrayNode init should return new object w/ correct attributes ... ok test_init_empty (test_seqsim.test_microarray.MicroarrayNodeTests) MicroarrayNode empty init should return new object as expected ... ok test_mutate (test_seqsim.test_microarray.MicroarrayNodeTests) Microarray mutate should set arrays appropriately ... ok test_geometric_mean (test_seqsim.test_microarray_normalize.microarray_normalize_tests) geometric_mean should return geometric mean. ... ok test_logzscores (test_seqsim.test_microarray_normalize.microarray_normalize_tests) logzscores should perform zscores on log of a ... ok test_make_empirical_quantile_normalizer (test_seqsim.test_microarray_normalize.microarray_normalize_tests) make_empirical_quantile_normalizer should convert a to dist of data ... ok test_make_normal_quantile_normalizer (test_seqsim.test_microarray_normalize.microarray_normalize_tests) make_normal_quantile_normalizer should sample from normal dist. ... ok test_make_quantile_normalizer (test_seqsim.test_microarray_normalize.microarray_normalize_tests) make_quantile_normalizer should sample from right distribution. ... ok test_quantiles (test_seqsim.test_microarray_normalize.microarray_normalize_tests) quantiles should convert array to quantiles within each column ... ok test_ranks (test_seqsim.test_microarray_normalize.microarray_normalize_tests) ranks should convert array to ranks within each column ... ok test_zscores (test_seqsim.test_microarray_normalize.microarray_normalize_tests) zscores should convert array to zscores within each column ... ok test_shuffle_between (test_seqsim.test_randomization.randomization_tests) shuffle_between should shuffle between specified chars ... ok test_shuffle_except (test_seqsim.test_randomization.randomization_tests) shuffle_except_indices should shuffle all except specified indices ... ok test_shuffle_except_indices (test_seqsim.test_randomization.randomization_tests) shuffle_except_indices should shuffle all except specified indices ... ok test_shuffle_range (test_seqsim.test_randomization.randomization_tests) shuffle_range should shuffle only inside range ... ok test_options (test_seqsim.test_searchpath.SearchNodeTests) Should return a copy of real options ... ok test_removeOption_noneLeft (test_seqsim.test_searchpath.SearchNodeTests) removeOption should cull options and return F when none left. ... ok test_removeOption_someLeft (test_seqsim.test_searchpath.SearchNodeTests) removeOption should cull options and return T when some left. ... ok test_init_noArg (test_seqsim.test_searchpath.SearchNodeTests_private) Init should correctly set private properties w/no arg ... ok test_clearNodes (test_seqsim.test_searchpath.SearchPathTests) Should empty path stack and variable forbidden ... ok test_findAllowedOption_currentAllowed (test_seqsim.test_searchpath.SearchPathTests) Should return true when current option is allowed ... ok test_findAllowedOption_none (test_seqsim.test_searchpath.SearchPathTests) Should return false if curr option is bad and no good exist ... ok test_findAllowedOption_otherAllowed (test_seqsim.test_searchpath.SearchPathTests) Should return true when curr option is bad but another is good ... ok test_generate_correctAlph (test_seqsim.test_searchpath.SearchPathTests) Should get correct alphabet even if node is popped then readded ... ok test_generate_fullCoverage (test_seqsim.test_searchpath.SearchPathTests) With no constraints, should produce all possible triplets ... ok test_generate_multiple (test_seqsim.test_searchpath.SearchPathTests) Should be able to call generate multiple times to extend path ... ok test_generate_nonePossible (test_seqsim.test_searchpath.SearchPathTests) Should return null if no path can match constraints ... ok test_generate_withForbidden (test_seqsim.test_searchpath.SearchPathTests) With 2 triplet constraints, should produce all others ... ok test_removeOption_empty (test_seqsim.test_searchpath.SearchPathTests) Should return False if removing option leads to empty stack ... ok test_removeOption_recurse (test_seqsim.test_searchpath.SearchPathTests) Should correctly remove empty node and curr option of next ... ok test_removeOption_simple (test_seqsim.test_searchpath.SearchPathTests) Should correctly remove option from untapped node ... ok test_add_node_first (test_seqsim.test_searchpath.SearchPathTests_private) add_node should correctly add first node and increase top index. ... ok test_add_node_subsequent (test_seqsim.test_searchpath.SearchPathTests_private) add_node should correctly add additional nodes and up top index. ... ok test_check_forbidden_seqs_fixed (test_seqsim.test_searchpath.SearchPathTests_private) Should return True if path includes a fixed forbidden seq ... ok test_check_forbidden_seqs_none (test_seqsim.test_searchpath.SearchPathTests_private) Should return False if path includes no forbidden seqs ... ok test_get_alphabet_badPosition (test_seqsim.test_searchpath.SearchPathTests_private) Should raise error if input isn't castable to nonneg int ... ok test_get_alphabet_default (test_seqsim.test_searchpath.SearchPathTests_private) Should return default alphabet if none defined for position ... ok test_get_alphabet_exists (test_seqsim.test_searchpath.SearchPathTests_private) Should return alphabet for position when one exists ... ok test_get_forbidden_lengths (test_seqsim.test_searchpath.SearchPathTests_private) get_forbidden_lengths should return dict of forbidden seq lens ... ok test_get_nmer (test_seqsim.test_searchpath.SearchPathTests_private) get_nmer should return correct nmer for n <= length of stack ... ok test_get_nmer_badArg (test_seqsim.test_searchpath.SearchPathTests_private) get_nmer should error if given a non integer-castable n ... ok test_get_nmer_len0 (test_seqsim.test_searchpath.SearchPathTests_private) get_nmer should return an empty string if n is 0 ... ok test_get_nmer_len1 (test_seqsim.test_searchpath.SearchPathTests_private) get_nmer should return correct result for nmer 1 on full stack ... ok test_get_nmer_tooLong (test_seqsim.test_searchpath.SearchPathTests_private) get_nmer should return None for n > length of stack ... ok test_get_top (test_seqsim.test_searchpath.SearchPathTests_private) Should return a reference to top node on stack if there is one ... ok test_get_top_None (test_seqsim.test_searchpath.SearchPathTests_private) Should return None if stack is empty ... ok test_init_badAlphabets (test_seqsim.test_searchpath.SearchPathTests_private) Init should fail if alphabets param is not dictionary-like ... ok test_init_noDefault (test_seqsim.test_searchpath.SearchPathTests_private) Init should fail if alphabets param has no 'default' key ... ok test_init_noForbid (test_seqsim.test_searchpath.SearchPathTests_private) Init should correctly set private properties w/o forbid list ... ok test_init_withForbid (test_seqsim.test_searchpath.SearchPathTests_private) Init should correctly set private properties, w/forbid list ... ok test_top_index (test_seqsim.test_searchpath.SearchPathTests_private) Should return index of top node when one exists ... ok test_top_index_None (test_seqsim.test_searchpath.SearchPathTests_private) Should return None when stack has no entries ... ok test_value (test_seqsim.test_searchpath.SearchPathTests_private) Should return string of node values when nodes exist ... ok test_value_empty (test_seqsim.test_searchpath.SearchPathTests_private) Should return empty string when path is empty ... ok test_assignLength (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignLength should set branch length ... ok test_assignPs (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignPs should assign multiple scaled P matrices ... ok test_assignQ_multiple (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should propagate multiple Qs ... ok test_assignQ_multiple_overwrite (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should allow overwrite ... ok test_assignQ_single_overwrite (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should overwrite root Q if new Q passed ... ok test_assignQ_single_passed (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should propagate single Q param down tree ... ok test_assignQ_single_set (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should propagate single Q if set ... ok test_assignQ_special (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode assignQ should work with special Qs ... ok test_evolve (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode evolve should work on a starting vector ... ok test_evolveSeqs (test_seqsim.test_tree.OldPhyloNodeTests) PhlyoNode evolveSeqs should evolve multiple sequences ... ok test_makeIdIndex (test_seqsim.test_tree.OldPhyloNodeTests) RangeNode makeIdIndex should assign ids to every node ... ok test_accumulateAttr (test_seqsim.test_tree.RangeTreeTests) RangeNode accumulateAttr should accumulate attr in right direction ... ok test_accumulateChildAttr (test_seqsim.test_tree.RangeTreeTests) RangeNode accumulateChildAttr should work as expected ... ok test_addChildren (test_seqsim.test_tree.RangeTreeTests) RangeNode add_children should add specified # children to list ... ok test_assignIds (test_seqsim.test_tree.RangeTreeTests) RangeNode assignIds should work as expected ... ok test_assignLevelsFromLeaves (test_seqsim.test_tree.RangeTreeTests) RangeNode assignLevelsFromLeaves should match hand-calculated levels ... ok test_assignLevelsFromRoot (test_seqsim.test_tree.RangeTreeTests) RangeNode assignLevelsFromRoot should match hand-calculated levels ... ok test_attrFromList (test_seqsim.test_tree.RangeTreeTests) RangeNode attrFromList should set values correctly ... ok test_attrToList (test_seqsim.test_tree.RangeTreeTests) RangeNode attrToList should return correct list of attr ... ok test_delAttr (test_seqsim.test_tree.RangeTreeTests) RangeNode delAttr should delete attr from self and children ... ok test_filter (test_seqsim.test_tree.RangeTreeTests) RangeNode filter should keep or omit selected nodes. ... ok test_fromBreakpoints (test_seqsim.test_tree.RangeTreeTests) RangeNode fromBreakpoints should have correct topology ... ok test_indexByAttr (test_seqsim.test_tree.RangeTreeTests) RangeNode indexByAttr should make index using correct attr ... ok test_indexbyFunc (test_seqsim.test_tree.RangeTreeTests) RangeNode indexByFunc should make index from function ... ok test_leafLcaDepths (test_seqsim.test_tree.RangeTreeTests) RangeNode leafLcaDepths should return expected depths ... ok test_outgroupLast (test_seqsim.test_tree.RangeTreeTests) RangeNode outgroupLast should reorder nodes to put outgroup last ... ok test_propagateAttr (test_seqsim.test_tree.RangeTreeTests) RangeNode propagateAttr should send attr down tree, unless set ... ok test_randomLeaf (test_seqsim.test_tree.RangeTreeTests) RandomLeaf should hit all leaf nodes equally ... ok test_randomNode (test_seqsim.test_tree.RangeTreeTests) RandomNode should hit all nodes equally ... ok test_randomNodeAtLevel (test_seqsim.test_tree.RangeTreeTests) RangeNode randomNodeAtLevel should return random node at correct level ... ok test_randomNodeWithNLeaves (test_seqsim.test_tree.RangeTreeTests) RandomNodeWithNLeaves should return node with correct # leaves ... ok test_str (test_seqsim.test_tree.RangeTreeTests) RangeNode should round-trip Newick string corrrectly. ... ok test_toBreakpoints (test_seqsim.test_tree.RangeTreeTests) RangeNode toBreakpoints should give expected list ... ok test_traverse (test_seqsim.test_tree.RangeTreeTests) RangeTree traverse should visit all nodes in correct order ... ok test_BalancedTree (test_seqsim.test_tree.treeTests) BalancedTree should return a balanced tree ... ok test_CombTree (test_seqsim.test_tree.treeTests) CombTree should return correct topology ... ok test_LineTree (test_seqsim.test_tree.treeTests) LineTree should return correct number of nodes ... ok test_RandomTree (test_seqsim.test_tree.treeTests) RandomTree should return correct number of nodes ... ok test_StarTree (test_seqsim.test_tree.treeTests) StarTree should return correct star topology and # nodes ... ok test_balanced_breakpoints (test_seqsim.test_tree.treeTests) balanced_breakpoints should produce expected arrays. ... ok test_init (test_seqsim.test_tree.treeTests) Make sure keyword arguments are being passed to baseclass ... ok test_ConflictMatrix_PairedRegions_overlap (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix __init__: raises error on overlapping PairedRegions ... ok test_ConflictMatrix_Pairs_overlap (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix __init__: raises error on overlapping pairs ... ok test_conflictCliques (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix conflictCliques: full and empty Pairs ... ok test_conflict_matrix_from_PairedRegions (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix __init__: PairedRegions as input, w/wo conflict ... ok test_conflict_matrix_from_pairs (test_struct.test_knots.ConflictMatrixTests) ConflixtMatrix __init__: Pairs as input, w/wo conflict ... ok test_conflicting (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix conflicting: full and empty Pairs ... ok test_conflictsOf (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix conflictsOf: with/without conflicts ... ok test_nonConflicting (test_struct.test_knots.ConflictMatrixTests) ConflictMatrix nonConflicting: full and empty Pairs ... ok test_contains_true (test_struct.test_knots.DPTests) contains_true: should return True if True in input ... ok test_dp_matrix_multi_artificial (test_struct.test_knots.DPTests) dp_matrix_multi: test on artificial structure ... ok test_dp_matrix_multi_lsu (test_struct.test_knots.DPTests) dp_matrix_multi: test on LSU rRNA domain I case ... ok test_dp_matrix_multi_toy (test_struct.test_knots.DPTests) dp_matrix_multi: test on initial toy example ... ok test_empty_matrix (test_struct.test_knots.DPTests) empty_matrix: valid input and error ... ok test_hydrogen_bonds (test_struct.test_knots.DPTests) hydrogen_bonds: score GC, AU, and GU base pairs ... ok test_matrix_solutions (test_struct.test_knots.DPTests) matrix_solutions: should return contents of top-right cell ... ok test_num_bps (test_struct.test_knots.DPTests) num_bps: should return length of paired region ... ok test_opt_all_knot (test_struct.test_knots.DPTests) opt_all: single/multiple solution(s) ... ok test_opt_all_nested (test_struct.test_knots.DPTests) opt_all: should return input when already nested ... ok test_opt_all_overlap (test_struct.test_knots.DPTests) opt_all: should raise error on overlapping pairs ... ok test_opt_all_scoring1 (test_struct.test_knots.DPTests) opt_all: one optimal in bps, both optimal in energy ... ok test_opt_all_scoring2 (test_struct.test_knots.DPTests) opt_all: both optimal in bps, one optimal in energy ... ok test_opt_all_scoring3 (test_struct.test_knots.DPTests) opt_all: one optimal in bps, the other optimal in energy ... ok test_opt_all_some_non_conflicting (test_struct.test_knots.DPTests) opt_all: some conflicting, other not ... ok test_opt_single_property (test_struct.test_knots.DPTests) opt_single_property: three properties ... ok test_opt_single_random (test_struct.test_knots.DPTests) opt_single_random: should return single solution ... ok test_pick_multi_best_max (test_struct.test_knots.DPTests) pick_multi_best: max, full and empty list ... ok test_pick_multi_best_min (test_struct.test_knots.DPTests) pick_multi_best: min, full and empty list ... ok test_pick_multi_best_saturated (test_struct.test_knots.DPTests) pick_multi_best: should only include saturated solutions ... ok test_add_back_non_conflicting (test_struct.test_knots.EliminationMethodsTests) add_back_non_conflicting: should add all non-confl regions ... ok test_add_back_non_conflicting_order (test_struct.test_knots.EliminationMethodsTests) add_back_non_conflicting: should add 5' side first ... ok test_elim_mc_circular (test_struct.test_knots.EliminationMethodsTests) conflict_elimination: find_max_conflicts, circular removal ... ok test_elim_min_gain (test_struct.test_knots.EliminationMethodsTests) conflict_elimination: find_min_gain, simple case ... ok test_elim_min_gain_circular (test_struct.test_knots.EliminationMethodsTests) conflict_elimination: find_min_gain, circular removal ... ok test_elim_most_conflict (test_struct.test_knots.EliminationMethodsTests) conflict_elimination: find_max_conflicts, simple case ... ok test_find_max_conflicts (test_struct.test_knots.EliminationMethodsTests) find_max_conflicts: simple case ... ok test_find_max_conflicts_on_start (test_struct.test_knots.EliminationMethodsTests) find_max_conflicts: in case of equal conflicts and gain ... ok test_find_min_gain (test_struct.test_knots.EliminationMethodsTests) find_min_gain: differentiate on gain only ... ok test_find_min_gain_conf (test_struct.test_knots.EliminationMethodsTests) find_min_gain: in case of equal gain, differentiate on conflicts ... ok test_find_min_gain_start (test_struct.test_knots.EliminationMethodsTests) find_min_gain: in case of equal gain and number of conflicts ... ok test_inc_length (test_struct.test_knots.IncrementalMethodsTests) inc_length: should handle standard input ... ok test_inc_length_rev (test_struct.test_knots.IncrementalMethodsTests) inc_length: should prefer 3' side when reversed is True ... ok test_inc_order_forward (test_struct.test_knots.IncrementalMethodsTests) nested_in_order: starting at 5' end ... ok test_inc_order_reversed (test_struct.test_knots.IncrementalMethodsTests) nested_in_order: starting at 3' end ... ok test_inc_range (test_struct.test_knots.IncrementalMethodsTests) inc_range: should handle normal input ... ok test_inc_range_empty (test_struct.test_knots.IncrementalMethodsTests) inc_range: should handle empty or pseudoknot-free pairs ... ok test_nussinov_fill (test_struct.test_knots.NussinovTests) nussinov_fill: basic test ... ok test_nussinov_restricted (test_struct.test_knots.NussinovTests) nussinov_restricted: basic test ... ok test_nussinov_restricted_bi (test_struct.test_knots.NussinovTests) nussinov_restricted: include bifurcation ... ok test_nussinov_traceback (test_struct.test_knots.NussinovTests) nussinov_traceback: basic test ... ok test_PairedRegionFromPairs (test_struct.test_knots.PairedRegionTests) PairedRegionFromPairs: should handle valid input ... ok test_PairedRegionFromPairs_invalid (test_struct.test_knots.PairedRegionTests) PairedRegionFromPairs: conflicts and error checking ... ok test_conflicting (test_struct.test_knots.PairedRegionTests) PairedRegion conflicting: identical, nested and pseudoknot ... ok test_downstream (test_struct.test_knots.PairedRegionTests) PairedRegions downstream: single and multiple pair(s) ... ok test_eq (test_struct.test_knots.PairedRegionTests) PairedRegion __eq__: should use pairs and IDs ... ok test_init_valid (test_struct.test_knots.PairedRegionTests) PairedRegion __init__: should work as expected on valid input ... ok test_init_weird (test_struct.test_knots.PairedRegionTests) PairedRegion __init__: no error checking ... ok test_len (test_struct.test_knots.PairedRegionTests) PairedRegion __len__: should return number of pairs ... ok test_overlapping (test_struct.test_knots.PairedRegionTests) PairedRegion overlapping: identical and different regions ... ok test_paired (test_struct.test_knots.PairedRegionTests) PairedRegion paired: single and multiple pair(s) ... ok test_regionRange (test_struct.test_knots.PairedRegionTests) PairedRegion regionRange: single and multiple pair(s) ... ok test_score (test_struct.test_knots.PairedRegionTests) PairedRegion score: should take arbitrary scoring function ... ok test_str (test_struct.test_knots.PairedRegionTests) PairedRegion __str__: should print pairs ... ok test_upstream (test_struct.test_knots.PairedRegionTests) PairedRegions upstream: single and multiple pair(s) ... ok test_PairedRegionsFromPairs (test_struct.test_knots.PairedRegionsTests) PairedRegionsFromPairs: should work on valid input ... ok test_PairedRegionsFromPairs_conflict (test_struct.test_knots.PairedRegionsTests) PairedRegionsFromPairs: should raise error on overlapping pairs ... ok test_boundaries (test_struct.test_knots.PairedRegionsTests) PairedRegions boundaries: full and empty ... ok test_byId (test_struct.test_knots.PairedRegionsTests) PairedRegions byId: unique IDs and duplicates ... ok test_byStartEnd (test_struct.test_knots.PairedRegionsTests) PairedRegions byStartEnd: unique and duplicate keys ... ok test_conflictCliques (test_struct.test_knots.PairedRegionsTests) PairedRegions conflictCliques: should work when IDs are unique ... ok test_conflicting (test_struct.test_knots.PairedRegionsTests) PairedRegions conflicting: works when IDs are set and unique ... ok test_conflicting_no_ids (test_struct.test_knots.PairedRegionsTests) PairedRegions conflicting: raises error on duplicate IDs ... ok test_downstream (test_struct.test_knots.PairedRegionsTests) PairedRegions upstream: full and empty ... ok test_enumeratedBoundaries (test_struct.test_knots.PairedRegionsTests) PairedRegions enumeratedBoundaries: full and empty ... ok test_eq (test_struct.test_knots.PairedRegionsTests) PairedRegions __eq__: with/without IDs, in or out of order ... ok test_highestEnd (test_struct.test_knots.PairedRegionsTests) PairedRegions highestEnd: full and empty object ... ok test_init (test_struct.test_knots.PairedRegionsTests) PairedRegions __init__: should accept list of PairedRegion objects ... ok test_init_no_validation (test_struct.test_knots.PairedRegionsTests) PairedRegions __init__: does not perform validation ... ok test_invertedEnumeratedBoundaries (test_struct.test_knots.PairedRegionsTests) PairedRegions invertedEnumeratedBoundaries: full and empty ... ok test_lowestStart (test_struct.test_knots.PairedRegionsTests) PairedRegions lowestStart: full and empty object ... ok test_merge (test_struct.test_knots.PairedRegionsTests) PairedRegions merge: different, duplicates, empty ... ok test_ne (test_struct.test_knots.PairedRegionsTests) PairedRegions __ne__: with/without IDs, in or out of order ... ok test_non_conflicting (test_struct.test_knots.PairedRegionsTests) PairedRegions nonConflicting: works when IDs are set and unique ... ok test_non_conflicting_no_ids (test_struct.test_knots.PairedRegionsTests) PairedRegions nonConflicting: raises error on duplicate IDs ... ok test_numberOfRegions (test_struct.test_knots.PairedRegionsTests) PairedRegions numberOfRegions: full and empty ... ok test_pairedPos (test_struct.test_knots.PairedRegionsTests) PairedRegions pairedPos: full and empty ... ok test_sortedIds (test_struct.test_knots.PairedRegionsTests) PairedRegions sortedIds: full and empty list ... ok test_str (test_struct.test_knots.PairedRegionsTests) PairedRegions __str__: full and empty list ... ok test_toPairs (test_struct.test_knots.PairedRegionsTests) PairedRegions toPairs: good data ... ok test_totalLength (test_struct.test_knots.PairedRegionsTests) PairedRegions totalLength: full and empty ... ok test_totalScore (test_struct.test_knots.PairedRegionsTests) PairedRegions totalScore: full, empty, None ... ok test_upstream (test_struct.test_knots.PairedRegionsTests) PairedRegions upstream: full and empty ... ok test_adjust_base (test_struct.test_pairs_util.GappedUngappedTests) adjust_base: should work for pairs object or list of pairs ... ok test_adjust_base_None (test_struct.test_pairs_util.GappedUngappedTests) adjust_base: should keep Nones or duplicates, ignore conflicts ... ok test_adjust_base_structures (test_struct.test_pairs_util.GappedUngappedTests) adjust_pairs_structures: simple structure ... ok test_adjust_pairs_from_mapping_confl (test_struct.test_pairs_util.GappedUngappedTests) adjust_pairs_from_mapping: should handle conflicts, pseudo, dupl ... ok test_degap_model_seq (test_struct.test_pairs_util.GappedUngappedTests) degap_model_seq: replacement for broken method ... ok test_degap_seq (test_struct.test_pairs_util.GappedUngappedTests) degap_seq: Sequence, ModelSequence, old_cogent, string ... ok test_delete_gaps_from_pairs (test_struct.test_pairs_util.GappedUngappedTests) delete_gaps_from_pairs: should work on standard input ... ok test_delete_gaps_from_pairs_weird (test_struct.test_pairs_util.GappedUngappedTests) delete_gaps_from_pairs: should ignore conflicts etc ... ok test_gapped_to_ungapped (test_struct.test_pairs_util.GappedUngappedTests) gapped_to_ungapped: Sequence, ModelSequence, old_cogent, string ... ok test_get_gap_list (test_struct.test_pairs_util.GappedUngappedTests) get_gap_list: Sequence, ModelSequence, old_cogent, string ... ok test_get_gap_symbol (test_struct.test_pairs_util.GappedUngappedTests) get_gap_symbol: Sequence, ModelSequence, old_cogent, string ... ok test_insert_gaps_in_pairs (test_struct.test_pairs_util.GappedUngappedTests) insert_gaps_in_pairs: should work with normal and conflicts ... ok test_ungapped_to_gapped (test_struct.test_pairs_util.GappedUngappedTests) ungapped_to_gapped: Sequence, ModelSequence, old_cogent, string ... ok test_all_metrics (test_struct.test_pairs_util.GardnerMetricsTest) all_metrics: check against compare_ct.pm ... ok test_all_metrics_pseudo (test_struct.test_pairs_util.GardnerMetricsTest) all_metrics: pseudoknot in ref, check against compare_ct.pm ... ok test_all_metrics_weird_input (test_struct.test_pairs_util.GardnerMetricsTest) all_metrics: should work when ref or prediction empty or no seqs ... ok test_approximate_correlation (test_struct.test_pairs_util.GardnerMetricsTest) approximate_correlation: check against compare_ct.pm ... ok test_cc_bad_pred (test_struct.test_pairs_util.GardnerMetricsTest) correlation_coefficient: should give 0 when TP=0 ... ok test_conflicts (test_struct.test_pairs_util.GardnerMetricsTest) all metrics should raise error when conflicts in one of the structs ... ok test_correlation_coefficient (test_struct.test_pairs_util.GardnerMetricsTest) correlation_coefficient: check against compare_ct.pm ... ok test_extract_seqs (test_struct.test_pairs_util.GardnerMetricsTest) extract_seqs: should handle different input formats ... ok test_get_all_pairs (test_struct.test_pairs_util.GardnerMetricsTest) get_all_pairs: should return the number of possible pairs ... ok test_get_counts (test_struct.test_pairs_util.GardnerMetricsTest) get_counts: should work with all parameters ... ok test_get_counts_pseudo (test_struct.test_pairs_util.GardnerMetricsTest) get_counts: should work when pseudo in ref -> classification off ... ok test_mcc (test_struct.test_pairs_util.GardnerMetricsTest) mcc: check against compare_ct.pm ... ok test_selectivity (test_struct.test_pairs_util.GardnerMetricsTest) selectivity: check against compare_ct.pm ... ok test_selectivity_dupl (test_struct.test_pairs_util.GardnerMetricsTest) selectivity: duplicates and Nones shouldn't influence the calc. ... ok test_selectivity_empty (test_struct.test_pairs_util.GardnerMetricsTest) selectivity: should handle empty reference/predicted structure ... ok test_selectivity_general (test_struct.test_pairs_util.GardnerMetricsTest) selectivity: should work in general ... ok test_sensitivity (test_struct.test_pairs_util.GardnerMetricsTest) sensitivity: check against compare_ct.pm ... ok test_sensitivity_dupl (test_struct.test_pairs_util.GardnerMetricsTest) sensitivity: should handle duplicates, pseudo, None ... ok test_sensitivity_empty (test_struct.test_pairs_util.GardnerMetricsTest) sensitivity: should work on emtpy Pairs ... ok test_sensitivity_general (test_struct.test_pairs_util.GardnerMetricsTest) sensitivity: should work in general ... ok test_adjust_base (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) adjust_base: should work for pairs object or list of pairs ... ok test_adjust_base_None (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) adjust_base: should keep Nones or duplicates, ignore conflicts ... ok test_adjust_pairs_from_mapping (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) adjust_pairs_from_mapping: should work both ways ... ok test_delete_gaps_from_pairs (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) delete_gaps_from_pairs: should work on standard input ... ok test_delete_gaps_from_pairs_weird (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) delete_gaps_from_pairs: should ignore conflicts etc ... ok test_gapped_to_ungapped_duplicates (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: should work when pairs contains duplicates ... ok test_gapped_to_ungapped_general (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: should return object of right type ... ok test_gapped_to_ungapped_general_seq (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: when input is Sequence obj, treat as string ... ok test_gapped_to_ungapped_no_gaps (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: should return same pairs when no gaps ... ok test_gapped_to_ungapped_out_of_order (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: should work when pairs are out of order ... ok test_gapped_to_ungapped_pseudo (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: shouldn't care about pseudoknots ... ok test_gapped_to_ungapped_simple (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) gapped_to_ungapped: should work on simple case ... ok test_insert_gaps_in_pairs (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) insert_gaps_in_pairs: should work with normal and conflicts ... ok test_ungapped_to_gapped (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) ungapped_to_gapped: should work for basic case ... ok test_ungapped_to_gapped_duplicates (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) ungapped_to_gapped: should work when pairs are duplicated ... ok test_ungapped_to_gapped_general (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) ungapped_to_gapped: should return object of right type ... ok test_ungapped_to_gapped_out_of_order (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) ungapped_to_gapped: should work when pairs out of order ... ok test_ungapped_to_gapped_simple (test_struct.test_pairs_util.OldAdjustmentFunctionsTests) ungapped_to_gapped: should work on basic case ... ok test_compare_pairs (test_struct.test_pairs_util.PairsComparisonTests) compare_pairs: should work on simple case ... ok test_compare_pairs_both_empty (test_struct.test_pairs_util.PairsComparisonTests) compare_pairs: should return 1.0 when both lists are empty ... ok test_compare_pairs_mapping (test_struct.test_pairs_util.PairsComparisonTests) compare_pairs_mapping: should work with correct mapping ... ok test_compare_pairs_weird (test_struct.test_pairs_util.PairsComparisonTests) compare_pairs: should handle conflicts, duplicates, pseudo, None ... ok test_compare_random_to_correct (test_struct.test_pairs_util.PairsComparisonTests) comapre_random_to_correct: should return correct fraction ... ok test_pairs_intersection (test_struct.test_pairs_util.PairsComparisonTests) pairs_intersection: should work on simple case ... ok test_pairs_intersection_duplicates (test_struct.test_pairs_util.PairsComparisonTests) pairs_intersection: should work on flipped pairs and duplicates ... ok test_pairs_union (test_struct.test_pairs_util.PairsComparisonTests) pairs_union: should work on simple case ... ok test_union_duplicates (test_struct.test_pairs_util.PairsComparisonTests) pairs_union: should work on flipped base pairs and duplicates ... ok test_directed (test_struct.test_rna2d.PairsTests) Pairs directed() should change all pairs so that a 0) ... ok test_str (test_struct.test_rna2d.StemTests) Stem str should print Start, End and Length as a tuple ... ok test_init_empty (test_struct.test_rna2d.StructureStringInitTests) StructureString initialization should accept an empty string ... ok test_init_invalid_string (test_struct.test_rna2d.StructureStringInitTests) StructureString should raise ValueError if invalid chars ... ok test_init_long_nested (test_struct.test_rna2d.StructureStringInitTests) StructureString should accept long structure w/ many nested pairs ... ok test_init_no_pairs (test_struct.test_rna2d.StructureStringInitTests) StructureString should allow a structure with no pairs ... ok test_init_one_helix (test_struct.test_rna2d.StructureStringInitTests) StructureString should allow a structure with one helix ... ok test_init_too_few_pairs_opened (test_struct.test_rna2d.StructureStringInitTests) StructureString should raise IndexError if too few open pairs ... ok test_init_too_many_pairs_opened (test_struct.test_rna2d.StructureStringInitTests) StructureString should raise IndexError if too many open pairs ... ok test_getitem (test_struct.test_rna2d.StructureStringTests) StructureString struct[index] should return char at index in struct ... ok test_getslice (test_struct.test_rna2d.StructureStringTests) StructureString struct[a:b] should return slice from a to b ... ok test_len (test_struct.test_rna2d.StructureStringTests) StructureString len() should match structure length ... ok test_str (test_struct.test_rna2d.StructureStringTests) StructureString str() should print structure and energy, if known ... ok test_toPairs (test_struct.test_rna2d.StructureStringTests) StructureString toPairs() should return Pairs object ... ok test_toPartners (test_struct.test_rna2d.StructureStringTests) StructureString toPartners() should return Partners object ... ok test_toTree (test_struct.test_rna2d.StructureStringTests) StructureString toTree should produce correct tree ... ok test_breakBadPairs (test_struct.test_rna2d.ViennaNodeTests) StructureNode breakBadPairs should eliminate mispaired bases. ... ok test_classify (test_struct.test_rna2d.ViennaNodeTests) ViennaNode classify should return correct classification string ... ok test_collapse (test_struct.test_rna2d.ViennaNodeTests) StructureNode collapse should collapse consecutive pairs from self ... ok test_collapseAll (test_struct.test_rna2d.ViennaNodeTests) StructureNode collapseAll should collapse consecutive pairs ... ok test_expand (test_struct.test_rna2d.ViennaNodeTests) StructureNode expand should extend helices. ... ok test_expandAll (test_struct.test_rna2d.ViennaNodeTests) StructureNode expandAll should act recursively ... ok test_extendHelices (test_struct.test_rna2d.ViennaNodeTests) StructureNode extendHelices should extend all helices ... ok test_extendHelix (test_struct.test_rna2d.ViennaNodeTests) StructureNode extendHelix should extend the helix as far as possible ... ok test_fitSeq (test_struct.test_rna2d.ViennaNodeTests) StructureNode fitSeq should adjust structure to match sequence ... ok test_pairAfter (test_struct.test_rna2d.ViennaNodeTests) StructureNode pairAfter should create pairs after a node ... ok test_pairBefore (test_struct.test_rna2d.ViennaNodeTests) StructureNode pairBefore should make a pair before the current node ... ok test_pairChildren (test_struct.test_rna2d.ViennaNodeTests) StructureNode PairChildren should make the correct pairs ... ok test_renumber (test_struct.test_rna2d.ViennaNodeTests) ViennaNode renumber should assign correct numbers to nodes ... ok test_str (test_struct.test_rna2d.ViennaNodeTests) ViennaNode str should return Vienna-format string ... ok test_unpair (test_struct.test_rna2d.ViennaNodeTests) StructureNode unpair should break a base pair and add correct nodes ... ok test_init_empty (test_struct.test_rna2d.WussStructureInitTests) StructureString initialization should accept an empty string ... ok test_init_invalid_string (test_struct.test_rna2d.WussStructureInitTests) StructureString should raise ValueError if invalid chars ... ok test_init_long_nested (test_struct.test_rna2d.WussStructureInitTests) StructureString should accept long structure w/ many nested pairs ... ok test_init_no_pairs (test_struct.test_rna2d.WussStructureInitTests) StructureString should allow a structure with no pairs ... ok test_init_one_helix (test_struct.test_rna2d.WussStructureInitTests) StructureString should allow a structure with one helix ... ok test_init_too_few_pairs_opened (test_struct.test_rna2d.WussStructureInitTests) StructureString should raise IndexError if too few open pairs ... ok test_init_too_many_pairs_opened (test_struct.test_rna2d.WussStructureInitTests) StructureString should raise IndexError if too many open pairs ... ok test_getitem (test_struct.test_rna2d.WussStructureTests) StructureString struct[index] should return char at index in struct ... ok test_getslice (test_struct.test_rna2d.WussStructureTests) StructureString struct[a:b] should return slice from a to b ... ok test_len (test_struct.test_rna2d.WussStructureTests) StructureString len() should match structure length ... ok test_str (test_struct.test_rna2d.WussStructureTests) StructureString str() should print structure and energy, if known ... ok test_toPairs (test_struct.test_rna2d.WussStructureTests) StructureString toPairs() should return Pairs object ... ok test_toPartners (test_struct.test_rna2d.WussStructureTests) StructureString toPartners() should return Partners object ... ok test_toTree (test_struct.test_rna2d.WussStructureTests) StructureString toTree should produce correct tree ... ok test_wuss_toPairs (test_struct.test_rna2d.WussStructureTests) WussStructure toPairs() should return a valid Pairs object ... ok test_wuss_toPartners (test_struct.test_rna2d.WussStructureTests) WussStructure toPartners() should return valid Partners object ... ok test_0import (test_struct.test_asa.asaTest) tests if can import _asa cython extension. ... ok test_1import (test_struct.test_asa.asaTest) tests if can import asa. ... ok test__prepare_entities (test_struct.test_asa.asaTest) ... ok test_asa_loop (test_struct.test_asa.asaTest) tests if inner asa_loop (cython) performs correctly ... ok test_asa_xtra (test_struct.test_asa.asaTest) test internal asa ... ok test_asa_xtra_stride (test_struct.test_asa.asaTest) test asa via stride ... ok test_compare (test_struct.test_asa.asaTest) compares internal asa to stride. ... ok test_crystal (test_struct.test_asa.asaTest) compares asa within unit cell. ... ok test_uc (test_struct.test_asa.asaTest) compares asa within unit cell. ... ok test_0import (test_struct.test_contact.asaTest) tests if can import _contact cython extension. ... ok test_1import (test_struct.test_contact.asaTest) tests if can import contact. ... ok test_chains (test_struct.test_contact.asaTest) compares contacts diff chains ... ok test_crystal (test_struct.test_contact.asaTest) "compares contacts diff unit-cell-mates ... ok test_symmetry (test_struct.test_contact.asaTest) compares contacts diff symmetry mates ... ok test_xtradata (test_struct.test_annotation.AnnotationTest) tests if an full_id's in the data dict are correctly parsed. ... ok test_einput (test_struct.test_selection.AnnotationTest) tests einput. ... ok test_select (test_struct.test_selection.AnnotationTest) tests select. ... ok test_0expand_symmetry (test_struct.test_manipulation.ManipulationTest) tests the expansion of a asu to a unit-cell. ... ok test_1expand_crystal (test_struct.test_manipulation.ManipulationTest) tests the expansion of a unit-cell to a crystal ... ok test_clean_ical (test_struct.test_manipulation.ManipulationTest) tests the clean ical function which cleans structures. ... ok test_cal_var_args (test_util.test_unit_test.FakeRandomTests) FakeRandom __call__ should ignore extra args ... ok test_call_constant (test_util.test_unit_test.FakeRandomTests) FakeRandom __call__ should return next item from list if constant ... ok test_call_constant_wrap (test_util.test_unit_test.FakeRandomTests) FakeRandom __call__ should wrap for one-item list if specified ... ok test_call_var (test_util.test_unit_test.FakeRandomTests) FakeRandom __call__ should work with a multi-item list ... ok test_call_var_wrap (test_util.test_unit_test.FakeRandomTests) FakeRandom __call__ should work with a multi-item wrapped list ... ok test_assertContains (test_util.test_unit_test.TestCaseTests) assertContains should raise exception if item not in test set ... ok test_assertEqualItems (test_util.test_unit_test.TestCaseTests) assertEqualItems should raise exception if items not equal ... ok test_assertEqual_None (test_util.test_unit_test.TestCaseTests) assertEqual should not raise exception with two copies of None ... ok test_assertEqual_equal (test_util.test_unit_test.TestCaseTests) assertEqual should not raise exception when values test equal ... ok test_assertEqual_nested_array (test_util.test_unit_test.TestCaseTests) ... ok test_assertEqual_numbers (test_util.test_unit_test.TestCaseTests) assertEqual should not raise exception with integer and float zero ... ok test_assertEqual_shape_mismatch (test_util.test_unit_test.TestCaseTests) assertEqual should raise when obs and exp shapes mismatch ... ok test_assertEqual_unequal (test_util.test_unit_test.TestCaseTests) assertEqual should raise exception when values differ ... ok test_assertFloatEqualAbs_equal (test_util.test_unit_test.TestCaseTests) assertFloatEqualAbs should not raise exception when values within eps ... ok test_assertFloatEqualAbs_mixed (test_util.test_unit_test.TestCaseTests) assertFloatEqualAbs should work on lists of mixed types. ... ok test_assertFloatEqualAbs_shape_mismatch (test_util.test_unit_test.TestCaseTests) assertFloatEqualAbs should raise when obs and exp shapes mismatch ... ok test_assertFloatEqualAbs_threshold (test_util.test_unit_test.TestCaseTests) assertFloatEqualAbs should raise exception when eps is very small ... ok test_assertFloatEqualAbs_unequal (test_util.test_unit_test.TestCaseTests) assertFloatEqualAbs should raise exception when values differ by >eps ... ok test_assertFloatEqualList_equal (test_util.test_unit_test.TestCaseTests) assertFloatEqual should work on two lists of similar values ... ok test_assertFloatEqualList_unequal (test_util.test_unit_test.TestCaseTests) assertFloatEqual should fail on two lists of dissimilar values ... ok test_assertFloatEqualRel_equal (test_util.test_unit_test.TestCaseTests) assertFloatEqualRel should not raise exception when values within eps ... ok test_assertFloatEqualRel_mixed (test_util.test_unit_test.TestCaseTests) assertFloatEqualRel should work on lists of mixed types. ... ok test_assertFloatEqualRel_shape_mismatch (test_util.test_unit_test.TestCaseTests) assertFloatEqualRel should raise when obs and exp shapes mismatch ... ok test_assertFloatEqualRel_unequal (test_util.test_unit_test.TestCaseTests) assertFloatEqualRel should raise exception when values differ by >eps ... ok test_assertFloatEqual_mixed (test_util.test_unit_test.TestCaseTests) assertFloatEqual should work on equal lists of mixed types. ... ok test_assertFloatEqual_mixed_unequal (test_util.test_unit_test.TestCaseTests) assertFloatEqual should work on unequal lists of mixed types. ... ok test_assertFloatEqual_shape_mismatch (test_util.test_unit_test.TestCaseTests) assertFloatEqual should raise when obs and exp shapes mismatch ... ok test_assertGreaterThan_None (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise exception if compared to None ... ok test_assertGreaterThan_equal (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise exception if equal ... ok test_assertGreaterThan_floats_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when observed <= value ... ok test_assertGreaterThan_floats_list_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when any elements are <= value ... ok test_assertGreaterThan_floats_list_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when all elements are > value ... ok test_assertGreaterThan_floats_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when observed > value ... ok test_assertGreaterThan_mixed_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when observed <= value ... ok test_assertGreaterThan_mixed_list_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when a single element is <= value ... ok test_assertGreaterThan_mixed_list_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when all elements are > value ... ok test_assertGreaterThan_mixed_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when observed > value ... ok test_assertGreaterThan_numbers_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when observed <= value ... ok test_assertGreaterThan_numbers_list_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should raise when a single element is <= value ... ok test_assertGreaterThan_numbers_list_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when all elements are > value ... ok test_assertGreaterThan_numbers_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when observed > value ... ok test_assertGreaterThan_numpy_array_false (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when any element is <= value ... ok test_assertGreaterThan_numpy_array_true (test_util.test_unit_test.TestCaseTests) assertGreaterThan should pass when all elements are > value ... ok test_assertIsBetween_None (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when compared to None ... ok test_assertIsBetween_bounds (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise if min_value >= max_value ... ok test_assertIsBetween_equal (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when a value is equal to either bound ... ok test_assertIsBetween_floats_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when out of bounds ... ok test_assertIsBetween_floats_list_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when any elements are out of bounds ... ok test_assertIsBetween_floats_list_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when all elements are in bounds ... ok test_assertIsBetween_floats_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when in bounds ... ok test_assertIsBetween_mixed_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when out of bounds ... ok test_assertIsBetween_mixed_list_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when any elements are out of bounds ... ok test_assertIsBetween_mixed_list_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when all elements are in bounds ... ok test_assertIsBetween_mixed_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when in bounds ... ok test_assertIsBetween_numbers_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when out of bounds ... ok test_assertIsBetween_numbers_list_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when any elements are out of bounds ... ok test_assertIsBetween_numbers_list_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when all elements are in bounds ... ok test_assertIsBetween_numbers_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when in bounds ... ok test_assertIsBetween_numpy_array_false (test_util.test_unit_test.TestCaseTests) assertIsBetween should raise when any elements is out of bounds ... ok test_assertIsBetween_numpy_array_true (test_util.test_unit_test.TestCaseTests) assertIsBetween should pass when all elements are in bounds ... ok test_assertIsNotBetween_None (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when compared against None ... ok test_assertIsNotBetween_bounds (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise if min_value >= max_value ... ok test_assertIsNotBetween_equals (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when equal on either bound ... ok test_assertIsNotBetween_float_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when a number is in bounds ... ok test_assertIsNotBetween_float_list_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when any element is in bounds ... ok test_assertIsNotBetween_float_list_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when all elements are out of bounds ... ok test_assertIsNotBetween_float_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when a number is not in bounds ... ok test_assertIsNotBetween_mixed_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when a number is in bounds ... ok test_assertIsNotBetween_mixed_list_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when any element is in bounds ... ok test_assertIsNotBetween_mixed_list_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when all elements are not in bounds ... ok test_assertIsNotBetween_mixed_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when a number is not in bounds ... ok test_assertIsNotBetween_numbers_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when a number is in bounds ... ok test_assertIsNotBetween_numbers_list_false (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should raise when any element is in bounds ... ok test_assertIsNotBetween_numbers_list_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when all elements are out of bounds ... ok test_assertIsNotBetween_numbers_true (test_util.test_unit_test.TestCaseTests) assertIsNotBetween should pass when a number is not in bounds ... ok test_assertIsPermutation_false (test_util.test_unit_test.TestCaseTests) assertIsPermutation should raise when a is not a permutation of b ... ok test_assertIsPermutation_true (test_util.test_unit_test.TestCaseTests) assertIsPermutation should pass when a is a permutation of b ... ok test_assertIsProb_None (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when compared against None ... ok test_assertIsProb_float_false (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when compared against invalid numbers ... ok test_assertIsProb_float_list_false (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when any element is not a prob ... ok test_assertIsProb_float_list_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when all elements are probs ... ok test_assertIsProb_float_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when compared against valid numbers ... ok test_assertIsProb_mixed_list_false (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when any element is not a prob ... ok test_assertIsProb_mixed_list_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when all elements are probs ... ok test_assertIsProb_numbers_false (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when compared against invalid numbers ... ok test_assertIsProb_numbers_list_false (test_util.test_unit_test.TestCaseTests) assertIsProb should raise when any element is not a prob ... ok test_assertIsProb_numbers_list_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when all elements are probs ... ok test_assertIsProb_numbers_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when compared against valid numbers ... ok test_assertIsProb_numpy_array_true (test_util.test_unit_test.TestCaseTests) assertIsProb should pass when all elements are probs ... ok test_assertLessThan_None (test_util.test_unit_test.TestCaseTests) assertLessThan should raise exception if compared to None ... ok test_assertLessThan_equal (test_util.test_unit_test.TestCaseTests) assertLessThan should raise exception if equal ... ok test_assertLessThan_floats_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when observed >= value ... ok test_assertLessThan_floats_list_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when a single element is >= value ... ok test_assertLessThan_floats_list_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when all elements are < value ... ok test_assertLessThan_floats_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when observed < value ... ok test_assertLessThan_mixed_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when observed >= value ... ok test_assertLessThan_mixed_list_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when a single element is >= value ... ok test_assertLessThan_mixed_list_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when all elements are < value ... ok test_assertLessThan_mixed_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when observed < value ... ok test_assertLessThan_numbers_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when observed >= value ... ok test_assertLessThan_numbers_list_false (test_util.test_unit_test.TestCaseTests) assertLessThan should raise when a single element is >= value ... ok test_assertLessThan_numbers_list_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when all elements are < value ... ok test_assertLessThan_numbers_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when observed < value ... ok test_assertLessThan_numpy_array_false (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when any element is >= value ... ok test_assertLessThan_numpy_array_true (test_util.test_unit_test.TestCaseTests) assertLessThan should pass when all elements are < value ... ok test_assertNotContains (test_util.test_unit_test.TestCaseTests) assertNotContains should raise exception if item in test set ... ok test_assertNotEqualItems (test_util.test_unit_test.TestCaseTests) assertNotEqualItems should raise exception if all items equal ... ok test_assertNotEqual_None (test_util.test_unit_test.TestCaseTests) assertNotEqual should raise exception with two copies of None ... ok test_assertNotEqual_equal (test_util.test_unit_test.TestCaseTests) assertNotEqual should raise exception when values differ ... ok test_assertNotEqual_numbers (test_util.test_unit_test.TestCaseTests) assertNotEqual should raise exception with integer and float zero ... ok test_assertNotEqual_unequal (test_util.test_unit_test.TestCaseTests) assertNotEqual should not raise exception when values differ ... ok test_assertNotSameObj_false (test_util.test_unit_test.TestCaseTests) assertSameObj should raise when 'a is b' ... ok test_assertNotSameObj_true (test_util.test_unit_test.TestCaseTests) assertNotSameObj should pass when 'a is not b' ... ok test_assertSameItems (test_util.test_unit_test.TestCaseTests) assertSameItems should raise exception if items not same ... ok test_assertSameObj_false (test_util.test_unit_test.TestCaseTests) assertSameObj should raise when 'a is not b' ... ok test_assertSameObj_true (test_util.test_unit_test.TestCaseTests) assertSameObj should pass when 'a is b' ... ok test_assertSimilarFreqs_false (test_util.test_unit_test.TestCaseTests) assertSimilarFreqs should raise when p < pvalue ... ok test_assertSimilarFreqs_numpy_array_false (test_util.test_unit_test.TestCaseTests) assertSimilarFreqs should raise when p < pvalue ... ok test_assertSimilarFreqs_numpy_array_true (test_util.test_unit_test.TestCaseTests) assertSimilarFreqs should pass when p > pvalue ... ok test_assertSimilarFreqs_true (test_util.test_unit_test.TestCaseTests) assertSimilarFreqs should pass when p > pvalue ... ok test_assertSimilarMeans_one_obs_false (test_util.test_unit_test.TestCaseTests) assertSimilarMeans should raise when p < pvalue ... ok test_assertSimilarMeans_one_obs_true (test_util.test_unit_test.TestCaseTests) assertSimilarMeans should pass when p > pvalue ... ok test_assertSimilarMeans_twosample_false (test_util.test_unit_test.TestCaseTests) assertSimilarMeans should raise when p < pvalue ... ok test_assertSimilarMeans_twosample_true (test_util.test_unit_test.TestCaseTests) assertSimilarMeans should pass when p > pvalue ... ok test_set_suite_pvalue (test_util.test_unit_test.TestCaseTests) Should set the suite pvalue ... ok test_abs_diff (test_util.test_array.ArrayMathTests) abs_diff should calculate element-wise sum of abs(first-second) ... ok test_carteisan_product (test_util.test_array.ArrayMathTests) cartesian_product should return expected results. ... ok test_classifiers (test_util.test_array.ArrayMathTests) classifiers should return all the 1D classifiers of samples ... ok test_col_uncertainty (test_util.test_array.ArrayMathTests) column_uncertainty: should handle pos/neg/zero/empty arrays ... ok test_column_degeneracy (test_util.test_array.ArrayMathTests) column_degeneracy: should work with different cutoff values ... ok test_combine_dimensions (test_util.test_array.ArrayMathTests) combine_dimensions should aggregate expected dimensions ... ok test_count_alphabet (test_util.test_array.ArrayMathTests) count_alphabet should return correct counts ... ok test_count_simple (test_util.test_array.ArrayMathTests) count_simple should return correct counts ... ok test_euclidean_distance (test_util.test_array.ArrayMathTests) euclidean_distance: should return dist between 2 vectors or matrices ... ok test_euclidean_distance_unexpected (test_util.test_array.ArrayMathTests) euclidean_distance: works always when frames are aligned. UNEXPECTED! ... ok test_hamming_distance_diff_length (test_util.test_array.ArrayMathTests) hamming_distance: truncates at shortest sequence ... ok test_hamming_distance_same_length (test_util.test_array.ArrayMathTests) hamming_distance: should return # of chars different ... ok test_has_neg_off_diags (test_util.test_array.ArrayMathTests) has_neg_off_diags should be same as has_neg_off_diags_naive ... ok test_has_neg_off_diags_naive (test_util.test_array.ArrayMathTests) has_neg_off_diags_naive should return True if any off-diags negative ... ok test_is_complex (test_util.test_array.ArrayMathTests) is_complex should return True on matrix with complex values ... ok test_is_significantly_complex (test_util.test_array.ArrayMathTests) is_significantly_complex should return True on complex matrix ... ok test_ln_2 (test_util.test_array.ArrayMathTests) ln_2: should be constant ... ok test_log2 (test_util.test_array.ArrayMathTests) log2: should work fine on positive/negative numbers and zero ... ok test_merge_samples (test_util.test_array.ArrayMathTests) merge_samples should keep the sample label ... ok test_minimize_error_count (test_util.test_array.ArrayMathTests) minimize_error_count should return correct classifier ... ok test_minimize_error_rate (test_util.test_array.ArrayMathTests) minimize_error_rate should return correct classifier ... ok test_mutate_array (test_util.test_array.ArrayMathTests) mutate_array should return mutated copy ... ok test_non_diag (test_util.test_array.ArrayMathTests) non_diag should return non-diag elements from flattened matrices ... ok test_norm (test_util.test_array.ArrayMathTests) norm: should return vector or matrix norm ... ok test_norm_diff (test_util.test_array.ArrayMathTests) norm_diff should calculate per-element rms difference ... ok test_only_nonzero (test_util.test_array.ArrayMathTests) only_nonzero should return only items whose first element is nonzero ... /build/python-cogent-1.9/cogent/util/array.py:464: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. return take(a, numpy.ravel(nonzero(a[first_element_selector])), axis=0) ok test_perturb_off_diag (test_util.test_array.ArrayMathTests) perturb_off_diag should change all off_diag elements. ... ok test_perturb_one_off_diag (test_util.test_array.ArrayMathTests) perturb_element should perturb a random off-diagonal element ... ok test_row_degeneracy (test_util.test_array.ArrayMathTests) row_degeneracy: should work with different cutoff values and arrays ... ok test_row_uncertainty (test_util.test_array.ArrayMathTests) row_uncertainty: should handle pos/neg/zero/empty arrays as expected ... ok test_safe_log (test_util.test_array.ArrayMathTests) safe_log: should handle pos/neg/zero/empty arrays as expected ... ok test_safe_p_log_p (test_util.test_array.ArrayMathTests) safe_p_log_p: should handle pos/neg/zero/empty arrays as expected ... ok test_scale_row_sum (test_util.test_array.ArrayMathTests) scale_row_sum should give same result as scale_row_sum_naive ... ok test_scale_row_sum_naive (test_util.test_array.ArrayMathTests) scale_row_sum_naive should scale rows to correct values ... ok test_scale_trace (test_util.test_array.ArrayMathTests) scale_trace should scale trace to correct values ... ok test_sort_merged_samples_by_value (test_util.test_array.ArrayMathTests) sort_merged_samples_by_value should keep label associations ... ok test_split_dimension (test_util.test_array.ArrayMathTests) split_dimension should unpack specified dimension ... ok test_sq_diff (test_util.test_array.ArrayMathTests) sq_diff should calculate element-wise sum square of abs(first-second) ... ok test_sum_neg_off_diags (test_util.test_array.ArrayMathTests) sum_neg_off_diags should return same as sum_neg_off_diags_naive ... ok test_sum_neg_off_diags_naive (test_util.test_array.ArrayMathTests) sum_neg_off_diags_naive should return the sum of negative off-diags ... ok test_with_diag (test_util.test_array.ArrayMathTests) with_diag should add diagonal to matrix ... ok test_without_diag (test_util.test_array.ArrayMathTests) without_diag should omit diagonal from matrix ... ok test_gapped_to_ungapped (test_util.test_array.arrayTests) gapped_to_ungapped should match hand-calculated results ... ok test_masked_to_unmasked (test_util.test_array.arrayTests) masked_to_unmasked should match hand-calculated results ... ok test_pairs_to_array (test_util.test_array.arrayTests) pairs_to_array should match hand-calculated results ... ok test_ungapped_to_gapped (test_util.test_array.arrayTests) ungapped_to_gapped should match hand-calculated results ... ok test_unmasked_to_masked (test_util.test_array.arrayTests) unmasked_to_masked should match hand-calculated results ... ok test_colKeys (test_util.test_dict2d.Dict2DTests) Dict2D colKeys should find all the keys of component cols ... ok test_cols (test_util.test_dict2d.Dict2DTests) Dict2D Cols property should return list in correct order ... ok test_copy (test_util.test_dict2d.Dict2DTests) Dict2D copy should copy data and selected attributes ... ok test_fill (test_util.test_dict2d.Dict2DTests) Dict2D fill should fill in specified values ... ok test_fromDicts (test_util.test_dict2d.Dict2DTests) Dict2D.fromDicts should construct from dict of dicts ... ok test_fromIndices (test_util.test_dict2d.Dict2DTests) Dict2D.fromIndices should construct from list of indices ... ok test_fromLists (test_util.test_dict2d.Dict2DTests) Dict2D.fromLists should construct from list of lists ... ok test_getColIndices (test_util.test_dict2d.Dict2DTests) Dict2D getColIndices should return list of indices of matching cols ... ok test_getCols (test_util.test_dict2d.Dict2DTests) Dict2D getCols should return object with specified cols only ... ok test_getColsIf (test_util.test_dict2d.Dict2DTests) Dict2D getColsIf should return new Dict2D with matching cols ... ok test_getItemIndices (test_util.test_dict2d.Dict2DTests) Dict2D getItemIndices should return indices when f(item) is True ... ok test_getItems (test_util.test_dict2d.Dict2DTests) Dict2D getItems should return list of relevant items ... ok test_getItemsIf (test_util.test_dict2d.Dict2DTests) Dict2D getItemsIf should return list of items when f(item) is True ... ok test_getRowIndices (test_util.test_dict2d.Dict2DTests) Dict2D getRowIndices should return indices of rows where f(x) True ... ok test_getRows (test_util.test_dict2d.Dict2DTests) Dict2D getRows should get specified rows ... ok test_getRowsIf (test_util.test_dict2d.Dict2DTests) Dict2D getRowsIf should return object with rows wher f(x) is True ... ok test_guess_input_type_fromDict (test_util.test_dict2d.Dict2DTests) Dict2D init can correctly guess input type: Dict ... ok test_guess_input_type_fromIndices (test_util.test_dict2d.Dict2DTests) Dict2D init can correctly guess input type: Indices ... ok test_guess_input_type_fromLists (test_util.test_dict2d.Dict2DTests) Dict2D init can correctly guess input type: Lists ... ok test_init (test_util.test_dict2d.Dict2DTests) Dict2D init should work as expected ... ok test_init_without_data (test_util.test_dict2d.Dict2DTests) Dict2D init functions correctly without a data parameter ... ok test_items (test_util.test_dict2d.Dict2DTests) Dict2D Items property should return list in correct order ... ok test_pad (test_util.test_dict2d.Dict2DTests) Dict2D pad should fill empty slots with default, but not make square ... ok test_purge (test_util.test_dict2d.Dict2DTests) Dict2D purge should delete unwanted keys at both levels ... ok test_reflect (test_util.test_dict2d.Dict2DTests) Dict2D reflect should reflect square matrices across diagonal. ... ok test_rowKeys (test_util.test_dict2d.Dict2DTests) Dict2D rowKeys should find all the keys of component rows ... ok test_rows (test_util.test_dict2d.Dict2DTests) Dict2D Rows property should return list in correct order ... ok test_scale (test_util.test_dict2d.Dict2DTests) Dict2D scale should apply f(x) to each d[i][j] ... ok test_setDiag (test_util.test_dict2d.Dict2DTests) Dict2D setDiag should set diagonal to specified value ... ok test_sharedColKeys (test_util.test_dict2d.Dict2DTests) Dict2D sharedColKeys should find keys shared by all component cols ... ok test_square (test_util.test_dict2d.Dict2DTests) Dict2D square should ensure that all d[i][j] exist ... ok test_toDelimited (test_util.test_dict2d.Dict2DTests) Dict2D toDelimited should return delimited string for printing ... ok test_toLists (test_util.test_dict2d.Dict2DTests) Dict2D toLists should convert dict into list of lists ... ok test_transpose (test_util.test_dict2d.Dict2DTests) Dict2D transpose should work on both dense and sparse matrices, in place ... ok test_contains (test_util.test_misc.ClassCheckerTests) ClassChecker should return True only if given instance of class ... ok test_copy (test_util.test_misc.ClassCheckerTests) copy.copy should work correctly on ClassChecker ... ok test_deepcopy (test_util.test_misc.ClassCheckerTests) copy.deepcopy should work correctly on ClassChecker ... ok test_init_bad (test_util.test_misc.ClassCheckerTests) ClassChecker should raise TypeError if initialized with non-class ... ok test_init_good (test_util.test_misc.ClassCheckerTests) ClassChecker should init OK when initialized with classes ... ok test_str (test_util.test_misc.ClassCheckerTests) ClassChecker str should be the same as str(self.Classes) ... ok test_parse_command_line_parameters (test_util.test_misc.CommandLineParserTests) parse_command_line_parameters returns without error ... ok test_Constraint (test_util.test_misc.ConstrainedContainerTests) ConstrainedContainer should only allow valid constraints to be set ... ok test_itemIsValid (test_util.test_misc.ConstrainedContainerTests) ConstrainedContainer should use constraint for checking item ... ok test_matchesConstraint (test_util.test_misc.ConstrainedContainerTests) ConstrainedContainer matchesConstraint should return true if items ok ... ok test_otherIsValid (test_util.test_misc.ConstrainedContainerTests) ConstrainedContainer should use constraint for checking other ... ok test_sequenceIsValid (test_util.test_misc.ConstrainedContainerTests) ConstrainedContainer should use constraint for checking sequence ... ok test_copy (test_util.test_misc.ConstrainedDictTests) ConstrainedDict copy should retain constraint ... ok test_fromkeys (test_util.test_misc.ConstrainedDictTests) ConstrainedDict instance fromkeys should retain constraint ... ok test_init_bad_data (test_util.test_misc.ConstrainedDictTests) ConstrainedDict should fail init with items not in constraint ... ok test_init_good_data (test_util.test_misc.ConstrainedDictTests) ConstrainedDict should init OK if list matches constraint ... ok test_init_sequence (test_util.test_misc.ConstrainedDictTests) ConstrainedDict should init from sequence, unlike normal dict ... ok test_setdefault (test_util.test_misc.ConstrainedDictTests) ConstrainedDict setdefault shouldn't allow bad keys ... ok test_setitem (test_util.test_misc.ConstrainedDictTests) ConstrainedDict setitem should work only if key in constraint ... ok test_setitem_masks (test_util.test_misc.ConstrainedDictTests) ConstrainedDict setitem should work only if key in constraint ... ok test_update (test_util.test_misc.ConstrainedDictTests) ConstrainedDict should allow update only of compliant data ... ok test_add_prevents_bad_data (test_util.test_misc.ConstrainedListTests) ConstrainedList should allow addition only of compliant data ... ok test_append (test_util.test_misc.ConstrainedListTests) ConstrainedList append should work only if item in constraint ... ok test_extend (test_util.test_misc.ConstrainedListTests) ConstrainedList extend should work only if all items in constraint ... ok test_getslice (test_util.test_misc.ConstrainedListTests) ConstrainedList getslice should remember constraint ... ok test_iadd_prevents_bad_data (test_util.test_misc.ConstrainedListTests) ConstrainedList should allow in-place addition only of compliant data ... ok test_imul (test_util.test_misc.ConstrainedListTests) ConstrainedList imul should preserve constraint ... ok test_init_bad_data (test_util.test_misc.ConstrainedListTests) ConstrainedList should fail init with items not in constraint ... ok test_init_good_data (test_util.test_misc.ConstrainedListTests) ConstrainedList should init OK if list matches constraint ... ok test_insert (test_util.test_misc.ConstrainedListTests) ConstrainedList insert should work only if item in constraint ... ok test_mul (test_util.test_misc.ConstrainedListTests) ConstrainedList mul should preserve constraint ... ok test_rmul (test_util.test_misc.ConstrainedListTests) ConstrainedList rmul should preserve constraint ... ok test_setitem (test_util.test_misc.ConstrainedListTests) ConstrainedList setitem should work only if item in constraint ... ok test_setitem_masks (test_util.test_misc.ConstrainedListTests) ConstrainedList setitem with masks should transform input ... ok test_setslice (test_util.test_misc.ConstrainedListTests) ConstrainedList setslice should fail if slice has invalid chars ... ok test_add_prevents_bad_data (test_util.test_misc.ConstrainedStringTests) ConstrainedString should allow addition only of compliant string ... ok test_getitem (test_util.test_misc.ConstrainedStringTests) ConstrainedString getitem should handle slice objects ... ok test_getslice (test_util.test_misc.ConstrainedStringTests) ConstrainedString getslice should remember constraint ... ok test_init_bad_data (test_util.test_misc.ConstrainedStringTests) ConstrainedString should fail init if unknown chars in string ... ok test_init_good_data (test_util.test_misc.ConstrainedStringTests) ConstrainedString should init OK if string matches constraint ... ok test_init_masks (test_util.test_misc.ConstrainedStringTests) ConstrainedString should init OK with masks ... ok test_mul (test_util.test_misc.ConstrainedStringTests) ConstrainedString mul amd rmul should retain constraint ... ok test_copy (test_util.test_misc.DelegatorTests) copy.copy should work correctly on Delegator ... ok test_deepcopy (test_util.test_misc.DelegatorTests) copy.deepcopy should work correctly on Delegator ... ok test_getattr (test_util.test_misc.DelegatorTests) Delegator should find attributes in correct places ... ok test_init (test_util.test_misc.DelegatorTests) Delegator should init OK when data supplied ... ok test_setattr (test_util.test_misc.DelegatorTests) Delegator should set attributes in correct places ... ok test_copy (test_util.test_misc.FunctionWrapperTests) copy should work for FunctionWrapper objects ... ok test_init (test_util.test_misc.FunctionWrapperTests) FunctionWrapper should initialize with any callable ... ok test_get (test_util.test_misc.MappedDictTests) MappedDict get should automatically map key. ... ok test_getitem (test_util.test_misc.MappedDictTests) MappedDict getitem should automatically map key. ... ok test_has_key (test_util.test_misc.MappedDictTests) MappedDict has_key should automatically map key. ... ok test_setitem_masks (test_util.test_misc.MappedDictTests) MappedDict setitem should work only if key in constraint ... ok test_setitem_masks (test_util.test_misc.MappedListTests) MappedList setitem with masks should transform input ... ok test_init_masks (test_util.test_misc.MappedStringTests) MappedString should init OK with masks ... ok test_DictFromFirst (test_util.test_misc.UtilsTests) DictFromFirst should return correct first positions ... ok test_DictFromLast (test_util.test_misc.UtilsTests) DictFromLast should return correct last positions ... ok test_DictFromPos (test_util.test_misc.UtilsTests) DictFromPos should return correct lists of positions ... ok test_DistanceFromMatrix (test_util.test_misc.UtilsTests) DistanceFromMatrix should return correct elements ... ok test_InverseDict (test_util.test_misc.UtilsTests) InverseDict should invert dict's keys and values ... ok test_InverseDictMulti (test_util.test_misc.UtilsTests) InverseDictMulti should invert keys and values, keeping all keys ... ok test_PairsFromGroups (test_util.test_misc.UtilsTests) PairsFromGroups should return dict with correct pairs ... ok test_add_lowercase (test_util.test_misc.UtilsTests) add_lowercase should add lowercase version of each key w/ same val ... ok test_add_lowercase_tuple (test_util.test_misc.UtilsTests) add_lowercase should deal with tuples correctly ... ok test_caps_from_underscores (test_util.test_misc.UtilsTests) caps_from_underscores should become CapsFromUnderscores ... ok test_combinate (test_util.test_misc.UtilsTests) Should return combinations ... ok test_create_dir (test_util.test_misc.UtilsTests) create_dir creates dir and fails meaningful. ... ok test_deep_list (test_util.test_misc.UtilsTests) should convert nested tuple to nested list ... ok test_deep_tuple (test_util.test_misc.UtilsTests) Should convert a nested list to a nested tuple ... ok test_extract_delimited_bad_delimiters (test_util.test_misc.UtilsTests) extract_delimited should raise error if delimiters identical ... ok test_extract_delimited_indexed (test_util.test_misc.UtilsTests) extract_delimited should return correct field with starting index ... ok test_extract_delimited_missing_right (test_util.test_misc.UtilsTests) extract_delimited should raise error if right delimiter missing ... ok test_extract_delimited_normal (test_util.test_misc.UtilsTests) extract_delimited should return correct field if present, or None ... ok test_find_all (test_util.test_misc.UtilsTests) find_all should return list of all occurrences ... ok test_find_many (test_util.test_misc.UtilsTests) find_many should return list of all occurrences of all items ... ok test_flatten (test_util.test_misc.UtilsTests) flatten should remove one level of nesting from nested sequences ... ok test_flatten_no_change (test_util.test_misc.UtilsTests) flatten should not change non-nested sequences (except to list) ... ok test_getNewId (test_util.test_misc.UtilsTests) should return a random 12 digit id ... ok test_get_merged_spans (test_util.test_misc.UtilsTests) tests merger of overlapping spans ... ok test_get_random_directory_name (test_util.test_misc.UtilsTests) get_random_directory_name functions as expected ... ok test_get_run_start_indices (test_util.test_misc.UtilsTests) return indices corresponding to start of a run of identical values ... ok test_handle_error_codes (test_util.test_misc.UtilsTests) handle_error_codes raises the right error. ... ok test_identity (test_util.test_misc.UtilsTests) should return same object ... ok test_if_ (test_util.test_misc.UtilsTests) implementation of c-like tertiary operator ... ok test_independent_spans (test_util.test_misc.UtilsTests) get_independent_coords returns truly non-overlapping (decorated) spans ... ok test_is_char (test_util.test_misc.UtilsTests) is_char(obj) should return True when obj is a char ... ok test_is_char_or_noniterable (test_util.test_misc.UtilsTests) is_char_or_noniterable should return True or False ... ok test_is_iterable (test_util.test_misc.UtilsTests) is_iterable should return True for iterables ... ok test_is_str_or_noniterable (test_util.test_misc.UtilsTests) is_str_or_noniterable should return True or False ... ok test_iterable (test_util.test_misc.UtilsTests) iterable(x) should return x or [x], always an iterable result ... ok test_list_flatten (test_util.test_misc.UtilsTests) list_flatten should remove all nesting, str is untouched ... ok test_max_index (test_util.test_misc.UtilsTests) max_index should return index of largest item, last if tie ... ok test_merged_by_value_spans (test_util.test_misc.UtilsTests) correctly merge adjacent spans with the same value ... ok test_min_index (test_util.test_misc.UtilsTests) min_index should return index of smallest item, first if tie ... ok test_not_list_tuple (test_util.test_misc.UtilsTests) not_list_tuple(obj) should return False when obj is list or tuple ... ok test_recursive_flatten (test_util.test_misc.UtilsTests) recursive_flatten should remove all nesting from nested sequences ... ok test_recursive_flatten_max_depth (test_util.test_misc.UtilsTests) recursive_flatten should not remover more than max_depth levels ... ok test_recursive_flatten_old (test_util.test_misc.UtilsTests) Should flatten nested lists ... ok test_remove_files (test_util.test_misc.UtilsTests) Remove files functions as expected ... ok test_safe_md5 (test_util.test_misc.UtilsTests) Make sure we have the expected md5 ... ok test_select_empty (test_util.test_misc.UtilsTests) select should raise error if indexing into empty sequence ... ok test_select_mapping (test_util.test_misc.UtilsTests) select should return the values corresponding to a list of keys ... ok test_select_sequence (test_util.test_misc.UtilsTests) select should work on a sequence with a list of indices ... ok test_sort_order (test_util.test_misc.UtilsTests) sort_order should return the ordered indices of items ... ok test_sort_order_cmpfunc (test_util.test_misc.UtilsTests) sort_order should use cmpfunc if passed ... ok test_sort_order_empty (test_util.test_misc.UtilsTests) sort_order should return empty list on empty sequence ... ok test_toString (test_util.test_misc.UtilsTests) should stringify an object ... ok test_unflatten (test_util.test_misc.UtilsTests) unflatten should turn a 1D sequence into a 2D list ... ok test_unflatten_bad_row_width (test_util.test_misc.UtilsTests) unflatten should raise ValueError with row_width < 1 ... ok test_unreserve (test_util.test_misc.UtilsTests) unreserve should trim trailing underscore if present. ... ok test_unzip (test_util.test_misc.UtilsTests) unzip(items) should be the inverse of zip(*items) ... ok test_generateCombinations (test_util.test_misc.generateCombinationsTests) function should return all combinations of given length ... ok test_generateCombinations_badArgs (test_util.test_misc.generateCombinationsTests) function should error if args are not castable to right type. ... ok test_generateCombinations_emptyAlphabet (test_util.test_misc.generateCombinationsTests) function should return empty list if alphabet arg is [], "" ... ok test_generateCombinations_singleAlphabet (test_util.test_misc.generateCombinationsTests) function should return correct value when alphabet is one char ... ok test_generateCombinations_singleLength (test_util.test_misc.generateCombinationsTests) function should return correct values if length is 1 ... ok test_generateCombinations_zeroLength (test_util.test_misc.generateCombinationsTests) function should return empty list if length arg is 0 ... ok test_makeNonnegInt_castable (test_util.test_misc.makeNonnegIntTests) Should return nonneg int version of a castable input ... ok test_makeNonnegInt_noncastable (test_util.test_misc.makeNonnegIntTests) Should raise a special NonnegIntError if input isn't castable ... ok test_makeNonnegInt_unchanged (test_util.test_misc.makeNonnegIntTests) Should return an input nonneg int unchanged ... ok test_NestedSplitter (test_util.test_misc.reverse_complementTests) NestedSplitter should make a function which return expected list ... ok test_app_path (test_util.test_misc.reverse_complementTests) app_path should return correct paths ... ok test_curry (test_util.test_misc.reverse_complementTests) curry should generate the function with parameters setted ... ok test_get_items_except (test_util.test_misc.reverse_complementTests) get_items_except should return all items of seq not in indices ... ok test_not_none (test_util.test_misc.reverse_complementTests) not_none should return True if none of the items is None ... ok test_reverse_complement_DNA (test_util.test_misc.reverse_complementTests) reverse_complement should correctly return reverse complement of DNA ... ok test_reverse_complement_RNA (test_util.test_misc.reverse_complementTests) reverse_complement should correctly return reverse complement of RNA ... ok test_reverse_complement_caseSensitive (test_util.test_misc.reverse_complementTests) reverse_complement should convert bases without changing case ... ok test_reverse_complement_emptySeq (test_util.test_misc.reverse_complementTests) reverse_complement should return empty string if given empty sequence ... ok test_reverse_complement_noSeq (test_util.test_misc.reverse_complementTests) reverse_complement should return error if given no sequence argument ... ok test_reverse_complement_nonNucleicSeq (test_util.test_misc.reverse_complementTests) reverse_complement should just reverse any chars but ACGT/U ... ok test_call_empty (test_util.test_organizer.FilterTests) Empty Filter should return True when called on anything ... ok test_call_full (test_util.test_organizer.FilterTests) Filter should return True if the object satisfies all criteria ... ok test_init (test_util.test_organizer.FilterTests) Filter should init as expected ... ok test_init_empty (test_util.test_organizer.GroupListTests) Empty GroupList should init OK ... ok test_init_full (test_util.test_organizer.GroupListTests) GroupList should init OK with data and groups ... ok test_double_org_empty_list (test_util.test_organizer.OrganizerTests) Organizer should return [] when applied to [] ... ok test_double_org_full_list (test_util.test_organizer.OrganizerTests) Organizer should handle multiple filters correctly ... ok test_empty_org_empty_list (test_util.test_organizer.OrganizerTests) Empty Organizer should return [] when applied to [] ... ok test_empty_org_full_list (test_util.test_organizer.OrganizerTests) Empty organizer, applied to full list, should return the original ... ok test_full_org_empty_list (test_util.test_organizer.OrganizerTests) Organizer should return [] when applied to [] ... ok test_full_org_full_list (test_util.test_organizer.OrganizerTests) Organizer should return correct organization ... ok test_init_empty (test_util.test_organizer.OrganizerTests) Empty Organizer should init correctly ... ok test_init_full (test_util.test_organizer.OrganizerTests) Organizer should init correctly with multiple functions ... ok test_multiple_func (test_util.test_organizer.OrganizerTests) Organizer should handle filter with multiple functions correctly ... ok test_regroup (test_util.test_organizer.organizerTests) regroup: should groups with identical hierarchy-info together ... ok test_build_alphabet_map_handles_all_ids_and_defs_wo_error (test_util.test_recode_alignment.RecodeAlignmentTests) build_alphabet_map: handles all pre-defined alphabets w/o error ... ok test_build_alphabet_map_handles_bad_data (test_util.test_recode_alignment.RecodeAlignmentTests) build_alphabet_map: bad data raises error ... ok test_build_alphabet_map_w_alphabet_def (test_util.test_recode_alignment.RecodeAlignmentTests) build_alphabet_map: returns correct dict when given alphabet_def ... ok test_build_alphabet_map_w_alphabet_id (test_util.test_recode_alignment.RecodeAlignmentTests) build_alphabet_map: returns correct dict when given alphabet_id ... ok test_recode_dense_alignment (test_util.test_recode_alignment.RecodeAlignmentTests) recode_dense_alignment: recode alignment to charge_2 alpha works ... ok test_recode_dense_alignment_handles_all_ids_and_defs_wo_error (test_util.test_recode_alignment.RecodeAlignmentTests) recode_dense_alignment: handles pre-defined alphabets w/o error ... ok test_recode_dense_alignment_leaves_original_alignment_intact (test_util.test_recode_alignment.RecodeAlignmentTests) recode_dense_alignment: leaves input alignment intact ... ok test_recode_dense_alignment_to_orig (test_util.test_recode_alignment.RecodeAlignmentTests) recode_dense_alignment: recode aln to orig returns original aln ... ok test_recode_freq_vector (test_util.test_recode_alignment.RecodeAlignmentTests) recode_freq_vector: bg freqs updated to reflect recoded alphabet ... ok test_recode_freq_vector_ignores (test_util.test_recode_alignment.RecodeAlignmentTests) recode_freq_vector: ignored chars are ignored ... ok test_recode_count_matrix_2_states (test_util.test_recode_alignment.RecodeMatrixTests) recode_count_matrix: returns correct result with 2-state alphabet ... ok test_recode_count_matrix_3_states (test_util.test_recode_alignment.RecodeMatrixTests) recode_count_matrix: returns correct result with 3-state alphabet ... ok test_recode_count_matrix_3_states_ambig_ignored (test_util.test_recode_alignment.RecodeMatrixTests) recode_count_matrix: correct result w 3-state alphabet w ambig chars ... ok test_recode_count_matrix_no_change (test_util.test_recode_alignment.RecodeMatrixTests) recode_count_matrix: no changes applied when they shouldn't be ... ok test_recode_counts_and_freqs (test_util.test_recode_alignment.RecodeMatrixTests) recode_counts_and_freqs: functions as expected ... ok test_util/test_table.rst Doctest: test_table.rst ... ok test_comb (test_util.test_transform.Filter_Criteria_Tests) comb should return correct combinations ... ok test_cross_comb (test_util.test_transform.Filter_Criteria_Tests) cross_comb should produce correct combinations ... ok test_exclude_chars (test_util.test_transform.Filter_Criteria_Tests) exclude_chars returns string containing only chars not in exclude ... ok test_exclude_if_more (test_util.test_transform.Filter_Criteria_Tests) exclude_if_more should be True if #items in s <= x ... ok test_exclude_if_more_other (test_util.test_transform.Filter_Criteria_Tests) exclude_if_more_other should be True if #other items <= x ... ok test_find_all (test_util.test_transform.Filter_Criteria_Tests) find_all should be True if all words appear in the string ... ok test_find_any (test_util.test_transform.Filter_Criteria_Tests) find_any should be True if one of the words is in the string ... ok test_find_no (test_util.test_transform.Filter_Criteria_Tests) find_no should be True if none of the words in the string ... ok test_first (test_util.test_transform.Filter_Criteria_Tests) first should return first occurrence where f(s) ... ok test_first_in_set (test_util.test_transform.Filter_Criteria_Tests) first_in_set should return first occurrence ... ok test_first_index (test_util.test_transform.Filter_Criteria_Tests) first_index should return index of first occurrence where f(s) ... ok test_first_index_in_set (test_util.test_transform.Filter_Criteria_Tests) first_index_in_set should return index of first occurrence ... ok test_first_index_not_in_set (test_util.test_transform.Filter_Criteria_Tests) first_index_not_in_set should return index of first occurrence ... ok test_first_not_in_set (test_util.test_transform.Filter_Criteria_Tests) first_not_in_set should return first occurrence ... ok test_float_from_string (test_util.test_transform.Filter_Criteria_Tests) float_from_string should ignore funny chars ... ok test_keep_chars (test_util.test_transform.Filter_Criteria_Tests) keep_chars returns a string containing only chars in keep ... ok test_keep_if_more (test_util.test_transform.Filter_Criteria_Tests) keep_if_more should be True if #items in s > x ... ok test_keep_if_more_other (test_util.test_transform.Filter_Criteria_Tests) keep_if_more_other should be True if #other items > x ... ok test_last (test_util.test_transform.Filter_Criteria_Tests) last should return last occurrence where f(s) ... ok test_last_in_set (test_util.test_transform.Filter_Criteria_Tests) last_in_set should return last occurrence ... ok test_last_index (test_util.test_transform.Filter_Criteria_Tests) last_index should return index of last occurrence where f(s) ... ok test_last_index_in_set (test_util.test_transform.Filter_Criteria_Tests) last_index_in_set should return index of last occurrence ... ok test_last_index_not_in_set (test_util.test_transform.Filter_Criteria_Tests) last_index_not_in_set should return index of last occurrence ... ok test_last_not_in_set (test_util.test_transform.Filter_Criteria_Tests) last_not_in_set should return last occurrence ... ok test_make_trans (test_util.test_transform.Filter_Criteria_Tests) make_trans should return trans table mapping chars to default ... ok test_perm (test_util.test_transform.Filter_Criteria_Tests) perm should return correct permutations ... ok test_reorder (test_util.test_transform.Filter_Criteria_Tests) reorder should always use the same order when invoked ... ok test_reorder_inplace (test_util.test_transform.Filter_Criteria_Tests) reorder_inplace should replace object's data with new order ... ok test_trans_all (test_util.test_transform.Filter_Criteria_Tests) trans_all should return trans table mapping all bad chars to x ... ok test_trans_except (test_util.test_transform.Filter_Criteria_Tests) trans_except should return trans table mapping non-good chars to x ... ok test_for_seq (test_util.test_transform.SequenceFunctionsTests) for_seq should return the correct function ... ok test_per_longest (test_util.test_transform.SequenceFunctionsTests) per_longest should divide by max(len(x), len(y)) ... ok test_per_shortest (test_util.test_transform.SequenceFunctionsTests) per_shortest should divide by min(len(x), len(y)) ... ok test_all (test_util.test_transform.metafunctionsTests) all should return a function returning True if all components True ... ok test_any (test_util.test_transform.metafunctionsTests) any should return a function returning True if any component True ... ok test_apply_each (test_util.test_transform.metafunctionsTests) apply_each should apply each function to args, kwargs ... ok test_bool_each (test_util.test_transform.metafunctionsTests) bool_each should return boolean version of applying each f to args ... ok test_bools (test_util.test_transform.metafunctionsTests) bools should convert items to True or False. ... ok test_both (test_util.test_transform.metafunctionsTests) both should return True if both components True ... ok test_compose (test_util.test_transform.metafunctionsTests) compose should return function returning f(g(x)) ... ok test_compose_many (test_util.test_transform.metafunctionsTests) compose_many should return composition of all args ... ok test_conjoin (test_util.test_transform.metafunctionsTests) conjoin should return True if all components True ... ok test_disjoin (test_util.test_transform.metafunctionsTests) disjoin should return True if any component True ... ok test_either (test_util.test_transform.metafunctionsTests) either should return function returning True if either component True ... ok test_extract_field (test_util.test_transform.metafunctionsTests) extract_field should apply constructor to field, or return None ... ok test_has_field (test_util.test_transform.metafunctionsTests) has_field should return True if specified field exists. ... ok test_identity (test_util.test_transform.metafunctionsTests) identity should return x ... ok test_index (test_util.test_transform.metafunctionsTests) index should index objects by specified field or identity ... ok test_negate (test_util.test_transform.metafunctionsTests) negate should return True if no component True ... ok test_neither (test_util.test_transform.metafunctionsTests) neither should return function returning True if each component False ... ok test_none (test_util.test_transform.metafunctionsTests) none should return a function returning True if no component True ... ok test_test_container (test_util.test_transform.metafunctionsTests) test_container should return True or False in a typesafe way. ... ok test_test_field (test_util.test_transform.metafunctionsTests) test_field should return boolean result of applying constructor ... ok test_calc_data_point_locations_custom_spacing (test_draw.test_distribution_plots.DistributionPlotsTests) _calc_data_point_locations() should return an array containing ... ok test_calc_data_point_locations_default_spacing (test_draw.test_distribution_plots.DistributionPlotsTests) _calc_data_point_locations() should return an array containing ... ok test_calc_data_point_locations_invalid_widths (test_draw.test_distribution_plots.DistributionPlotsTests) _calc_data_point_locations() should raise a ValueError ... ok test_calc_data_point_ticks (test_draw.test_distribution_plots.DistributionPlotsTests) _calc_data_point_ticks() should return an array containing the ... ok test_color_box_plot (test_draw.test_distribution_plots.DistributionPlotsTests) _color_box_plot() should not throw an exception when passed the ... ok test_create_legend (test_draw.test_distribution_plots.DistributionPlotsTests) _create_box_plot_legend() should create a legend on valid input. ... ok test_create_legend_invalid_input (test_draw.test_distribution_plots.DistributionPlotsTests) Test raises error on bad input. ... ok test_create_plot (test_draw.test_distribution_plots.DistributionPlotsTests) _create_plot() should return a tuple containing a Figure and ... ok test_generate_box_plots (test_draw.test_distribution_plots.DistributionPlotsTests) generate_box_plots() should return a valid Figure object. ... ok test_generate_comparative_plots_bar (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should return a valid barchart Figure ... ok test_generate_comparative_plots_box (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should return a valid boxplot Figure ... ok test_generate_comparative_plots_empty_marker_list (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should use the predefined list of ... ok test_generate_comparative_plots_error (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should raise a ValueError for an ... ok test_generate_comparative_plots_insufficient_colors (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should work even when there aren't ... ok test_generate_comparative_plots_insufficient_symbols (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should work even when there aren't ... ok test_generate_comparative_plots_scatter (test_draw.test_distribution_plots.DistributionPlotsTests) generate_comparative_plots() should return a valid scatterplot ... ok test_get_distribution_markers_bad_marker_type (test_draw.test_distribution_plots.DistributionPlotsTests) _get_distribution_markers() should raise a ValueError. ... ok test_get_distribution_markers_empty_marker_list (test_draw.test_distribution_plots.DistributionPlotsTests) _get_distribution_markers() should return a list of predefined ... ok test_get_distribution_markers_insufficient_markers (test_draw.test_distribution_plots.DistributionPlotsTests) _get_distribution_markers() should return a wrapped list of ... ok test_get_distribution_markers_null_marker_list (test_draw.test_distribution_plots.DistributionPlotsTests) _get_distribution_markers() should return a list of predefined ... ok test_get_distribution_markers_zero_markers (test_draw.test_distribution_plots.DistributionPlotsTests) _get_distribution_markers() should return an empty list. ... ok test_plot_bar_data (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_bar_data() should return a list of Rectangle objects. ... ok test_plot_bar_data_bad_error_bar_type (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_bar_data() should raise an exception on bad error bar type. ... ok test_plot_bar_data_empty (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_bar_data() should not error when given empty list of data, ... ok test_plot_box_data (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_box_data() should return a dictionary for Line2D's. ... ok test_plot_box_data_empty (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_box_data() should not error when given empty list of data, ... ok test_plot_scatter_data_empty (test_draw.test_distribution_plots.DistributionPlotsTests) _plot_scatter_data() should not error when given empty list of data, ... ok test_set_axes_options (test_draw.test_distribution_plots.DistributionPlotsTests) _set_axes_options() should set the labels on the axes and not raise ... ok test_set_axes_options_bad_ylim (test_draw.test_distribution_plots.DistributionPlotsTests) _set_axes_options() should raise an exception when given non-numeric ... ok test_set_axes_options_ylim (test_draw.test_distribution_plots.DistributionPlotsTests) _set_axes_options() should set the y-axis limits. ... ok test_set_figure_size (test_draw.test_distribution_plots.DistributionPlotsTests) Test setting a valid figure size. ... ok test_set_figure_size_defaults (test_draw.test_distribution_plots.DistributionPlotsTests) Test setting a figure size using matplotlib defaults. ... ok test_set_figure_size_invalid (test_draw.test_distribution_plots.DistributionPlotsTests) Test setting a figure size using invalid dimensions. ... ok test_set_figure_size_long_labels (test_draw.test_distribution_plots.DistributionPlotsTests) Test setting a figure size that has really long labels. ... /usr/lib/python2.7/dist-packages/matplotlib/tight_layout.py:182: UserWarning: The bottom and top margins cannot be made large enough to accommodate all axes decorations. warnings.warn('The bottom and top margins cannot be made large ' ok test_validate_input_all_valid_input (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should return valid information about the data ... ok test_validate_input_empty (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError if empty data is passed ... ok test_validate_input_empty_deeply_nested (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should pass for deeply nested empty data. ... ok test_validate_input_empty_nested (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError if empty nested data is ... ok test_validate_input_invalid_data_point_names (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError on data_point_names that ... ok test_validate_input_invalid_num_samples (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError if an inconsistent ... ok test_validate_input_invalid_sample_names (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError on sample_names that are ... ok test_validate_input_null (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_input() should raise a ValueError if null data is passed ... ok test_validate_x_values_invalid_x_tick_labels (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_x_values() should raise a ValueError on an invalid number ... ok test_validate_x_values_invalid_x_values (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_x_values() should raise a ValueError on an invalid number ... ok test_validate_x_values_nonnumber_x_values (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_x_values() should raise a ValueError on x_values that ... ok test_validate_x_values_valid_x_values (test_draw.test_distribution_plots.DistributionPlotsTests) _validate_x_values() should not throw an exception. ... ok test_call (test_app.test_formatdb.FormatDbTests) FormatDb: Calling on a nucleotide data functions as expected ... ok test_keep_everything_scorer (test_app.test_blast.BlastTests) keep_everything_scorer should keep all ids found. ... ok test_make_shotgun_scorer (test_app.test_blast.BlastTests) make_shotgun_scorer should keep ids matching n queries ... ok test_make_subject_match_scorer (test_app.test_blast.BlastTests) make_subject_match_scorer should keep ids matching n queries ... ok test_seqs_to_stream (test_app.test_blast.BlastTests) seqs_to_stream should iterate over seqs ... ok test_index_fasta (test_app.test_cdbfasta.cdbfastaTests) Index a fasta! ... ok test_index_fastq (test_app.test_cdbfasta.cdbfastaTests) Index a fastq!!! ... ok test_version (test_app.test_cdbfasta.cdbfastaTests) make sure the expected version string is produced ... ok test_query_indexed_seqs_fasta (test_app.test_cdbfasta.cdbyankTests) pull out some sequences ... ok test_query_indexed_seqs_fastq (test_app.test_cdbfasta.cdbyankTests) pull out some sequences ... ok test_version (test_app.test_cdbfasta.cdbyankTests) make sure the expected version string is produced ... ok test_base_command (test_app.test_clearcut.ClearcutTests) Clearcut BaseCommand should return the correct BaseCommand ... ok test_build_tree_from_alignment (test_app.test_clearcut.ClearcutTests) Clearcut should return a tree built from the passed alignment ... ok test_build_tree_from_distance_matrix (test_app.test_clearcut.ClearcutTests) build_tree_from_distance_matrix builds a tree from a dict2d ... ok test_changing_working_dir (test_app.test_clearcut.ClearcutTests) Clearcut BaseCommand should change according to WorkingDir ... ok test_general_cleanUp (test_app.test_clearcut.ClearcutTests) Last test executed: cleans up all files initially created ... ok test_matrix_input_from_dict2d (test_app.test_clearcut.ClearcutTests) matrix_input_from_dict2d formats dict2d object into distance matrix ... ok test_align (test_app.test_dialign.DialignTests) test aligning samples ... ok test_base_command (test_app.test_dialign.DialignTests) Dialign BaseCommand should return the correct BaseCommand ... ok test_cleaning_up (test_app.test_dialign.DialignTests) not a test, just removes the temp files ... ok test_base_command (test_app.test_fasttree.FastTreeTests) ... ok test_build_tree_from_alignment (test_app.test_fasttree.FastTreeTests) ... ok test_change_working_dir (test_app.test_fasttree.FastTreeTests) ... ok test_add_seqs_to_alignment (test_app.test_muscle_v38.MuscleTests) Should add sequences to an alignment ... ok test_align_and_build_tree (test_app.test_muscle_v38.MuscleTests) Should align and build a tree from a set of sequences ... ok test_align_two_alignments (test_app.test_muscle_v38.MuscleTests) Should align to multiple sequence alignments ... ok test_align_unaligned_seqs (test_app.test_muscle_v38.MuscleTests) align_unaligned_seqs should work as expected ... ok test_aln_tree_seqs (test_app.test_muscle_v38.MuscleTests) aln_tree_seqs returns the muscle alignment and tree from iteration2 ... ok test_aln_tree_seqs_spaces (test_app.test_muscle_v38.MuscleTests) aln_tree_seqs should work on filename with spaces ... ok test_base_command (test_app.test_muscle_v38.MuscleTests) Muscle BaseCommand should return the correct BaseCommand ... ok test_build_tree_from_alignment (test_app.test_muscle_v38.MuscleTests) Muscle should return a tree built from the passed alignment ... ok test_changing_working_dir (test_app.test_muscle_v38.MuscleTests) Muscle BaseCommand should change according to WorkingDir ... ok test_maxmb (test_app.test_muscle_v38.MuscleTests) maxmb option should not break Muscle ... ok test_base_command (test_app.test_cd_hit.CD_HIT_EST_Tests) CD_HIT_EST BaseCommand should return the correct BaseCommand ... ok test_changing_working_dir (test_app.test_cd_hit.CD_HIT_EST_Tests) CD_HIT_EST BaseCommand should change according to WorkingDir ... ok test_clean_cluster_seq_id (test_app.test_cd_hit.CD_HIT_SupportMethodTests) clean_cluster_seq_id returns a cleaned sequence id ... ok test_parse_cdhit_clstr_file (test_app.test_cd_hit.CD_HIT_SupportMethodTests) parse_cdhit_clstr_file returns the correct clusters ... ok test_base_command (test_app.test_cd_hit.CD_HIT_Tests) CD_HIT BaseCommand should return the correct BaseCommand ... ok test_changing_working_dir (test_app.test_cd_hit.CD_HIT_Tests) CD_HIT BaseCommand should change according to WorkingDir ... ok test_align_subject_to_pdb (test_format.test_pdb_color.PdbColorTests) Tests for align_subject_to_pdb function. ... ok test_chains_to_seqs_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for chains_to_seqs function using nucleotide pdb chains. ... ok test_chains_to_seqs_protein (test_format.test_pdb_color.PdbColorTests) Tests for chains_to_seqs function using protein pdb chains. ... ok test_get_aligned_muscle (test_format.test_pdb_color.PdbColorTests) Tests for get_aligned_muscle function. ... ok test_get_best_muscle_hits (test_format.test_pdb_color.PdbColorTests) Tests for get_best_muscle_hits function. ... ok test_get_chains_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for get_chains function using nucleotide pdb lines. ... ok test_get_chains_protein (test_format.test_pdb_color.PdbColorTests) Tests for get_chains function using protein pdb lines. ... ok test_get_matching_chains (test_format.test_pdb_color.PdbColorTests) Tests for get_matching_chains function. ... ok test_make_color_list (test_format.test_pdb_color.PdbColorTests) Tests for make_color_list function. ... ok test_ungapped_to_pdb_nucleotide (test_format.test_pdb_color.PdbColorTests) Tests for ungapped_to_pdb function using nucleotide pdb chains. ... ok test_ungapped_to_pdb_protein (test_format.test_pdb_color.PdbColorTests) Tests for ungapped_to_pdb function using protein pdb chains. ... ok ---------------------------------------------------------------------- Ran 3397 tests in 114.297s OK # restore original tests file mv tests/alltests.py~ tests/alltests.py find tests -name "*.pyc" -delete make[1]: Leaving directory '/build/python-cogent-1.9' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py install --root /build/python-cogent-1.9/debian/python-cogent running install running build running build_py running build_ext running install_lib creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7 creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/kegg_pos.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/bowtie.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/locuslink.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/cmfinder.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/column.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/knetfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/flowgram.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/flowgram_collection.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/hmmscan.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/carnac.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/dynalign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/cigar.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/binary_sff.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/mothur.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/phylip.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/fastq.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/comrna.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/dialign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/unafold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/table.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/macsim.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/bpseq.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/tree_xml.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rnashapes.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/fasta.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/pdb.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rnaview.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rfam.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/pknotsrg.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/msms.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/cut.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/greengenes.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/sfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/clustal.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/kegg_fasta.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/gcg.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/aaindex.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rna_fold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/unigene.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/gbseq.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/kegg_taxonomy.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/ncbi_taxonomy.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/structure.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/dotur.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/gibbs.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/record.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rnaalifold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/pfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/tinyseq.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/meme.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/gff.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/psl.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/ilm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/consan.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/cutg.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/flowgram_parser.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/ct.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/ebi.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rdb.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/contrafold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/nupack.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/paml_matrix.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rna_plot.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/newick.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/blast.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/rnaforester.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/sequence.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/sprinzl.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/agilent_microarray.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/blast_xml.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/infernal.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/nexus.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/record_finder.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/stockholm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/foldalign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/kegg_ko.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/paml.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/mfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/stride.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/genbank.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/cove.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/mage.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/parse/illumina_sequence.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/align.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/algorithm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_pairwise_pogs.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/indel_model.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/indel_positions.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/pairwise.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/pycompare.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_compare.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/_pairwise_seqs.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights/methods.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/weights/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/dp_calculation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/traceback.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/align/progressive.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif/k_word.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/motif/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/consensus.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/nj.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/least_squares.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/tree_space.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/maximum_likelihood.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/distance.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/phylo/tree_collection.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_solved_models.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/solved_models.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_pairwise_distance.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/simulate.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/pairwise_distance.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/best_likelihood.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/_likelihood_tree.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/coevolution.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/models.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/substitution_calculation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/likelihood_calculation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/motif_prob_model.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/substitution_model.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/bootstrap.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/parameter_controller.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/predicate.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/likelihood_tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/discrete_markov.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/evolve/likelihood_function.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/usage.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/analysis.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/birth_death.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/markov.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/randomization.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/searchpath.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/microarray_normalize.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/microarray.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/seqsim/sequence_generators.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/nucleic_properties.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/energy_params.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/protein_properties.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/ligand_properties.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/molecular_weight.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/data/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/pdb_color.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/motif.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/phylip.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/table.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/fasta.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/pdb.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/clustal.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/bedgraph.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/structure.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/text_tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/alignment.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/xyzrn.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/nexus.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/rna_struct.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/stockholm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/format/mage.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/sffinfo.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/fastq_join.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/cmfinder.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/knetfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/carnac.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/dynalign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rtax.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/vienna_package.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/mothur.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/cdbfasta.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/flash.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/pplacer.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/comrna.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/seqprep.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/dialign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/formatdb.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/unafold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/raxml.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rnashapes.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/clearcut.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rdp_classifier.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/uclust.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rnaview.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/pknotsrg.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/msms.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/fasttree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/sfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/gctmpca.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/cd_hit.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/sfffile.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/muscle_v38.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/dotur.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/raxml_v730.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/usearch.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rnaalifold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/pfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rdp_classifier20.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/ilm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/consan.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/muscle.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/mafft.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/blat.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/clustalw.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/parsinsert.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/contrafold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/guppy.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/nupack.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/blast.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/rnaforester.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/fasttree_v1.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/pandaseq.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/infernal.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/parameters.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/foldalign.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/mfold.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/stride.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/bwa.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/app/cove.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/approximate_mds.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/nmds.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/metric_scaling.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/goodness_of_fit.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/procrustes.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/cluster/UPGMA.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/pairs_util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/dihedral.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/_contact.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/rna2d.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/manipulation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/annotation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/_asa.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/selection.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/contact.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/knots.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/struct/asa.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/feature_level.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/genome.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/related_region.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/assembly.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/region.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/species.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/host.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/name.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/compara.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/database.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/sequence.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ensembl/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/pdb.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/rfam.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/ncbi.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/db/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/location.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/usage.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/info.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/bitvector.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/entity.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/annotation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/alphabet.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/genetic_code.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/moltype.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/profile.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/alignment.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/core/sequence.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/option_parsing.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/progress_display.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/dict_array.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/trie.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/table.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/dict2d.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/recode_alignment.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/parallel.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/transform.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/checkpointing.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/warning.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/modules.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/terminal.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/datatypes.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/update_version.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/misc.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/unit_test.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/array.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/util/organizer.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/_period.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix_exponentiation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/fit_function.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/simannealingoptimiser.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/distance_transform.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix_logarithm.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix_exponential_integration.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/optimisers.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix/distance.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/matrix/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/svd.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/scipy_optimisers.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/function_optimisation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/markov.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/period.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac/fast_tree.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac/fast_unifrac.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/unifrac/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/solve.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/scipy_optimize.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/geometry.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/jackknife.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/distribution.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/rarefaction.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/alpha_diversity.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/kendall.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/test.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/period.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/histogram.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai/adaptor.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai/get_by_cai.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/cai/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/information_criteria.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/ks.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/stats/special.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/spatial/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/maths/spatial/ckd3.so -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/dotplot.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/distribution_plots.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/rlg2mpl.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/compatibility.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/linear.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/fancy_arrow.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/arrow_rates.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/legend.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/codon_usage.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/dinuc.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/util.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/dendrogram.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/draw/multivariate_plot.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw creating /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation/setting.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation/__init__.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation/scope.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation/calculation.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation copying /build/python-cogent-1.9/.pybuild/cpython2_2.7_cogent/build/cogent/recalculation/definition.py -> /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/kegg_pos.py to kegg_pos.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/bowtie.py to bowtie.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/locuslink.py to locuslink.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/cmfinder.py to cmfinder.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/column.py to column.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/knetfold.py to knetfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/flowgram.py to flowgram.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/flowgram_collection.py to flowgram_collection.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/hmmscan.py to hmmscan.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/carnac.py to carnac.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/dynalign.py to dynalign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/cigar.py to cigar.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/binary_sff.py to binary_sff.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/mothur.py to mothur.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/phylip.py to phylip.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/fastq.py to fastq.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/comrna.py to comrna.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/dialign.py to dialign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/unafold.py to unafold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/table.py to table.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/macsim.py to macsim.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/bpseq.py to bpseq.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/tree_xml.py to tree_xml.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rnashapes.py to rnashapes.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/fasta.py to fasta.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/pdb.py to pdb.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rnaview.py to rnaview.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rfam.py to rfam.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/pknotsrg.py to pknotsrg.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/msms.py to msms.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/cut.py to cut.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/greengenes.py to greengenes.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/sfold.py to sfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/clustal.py to clustal.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/kegg_fasta.py to kegg_fasta.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/gcg.py to gcg.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/aaindex.py to aaindex.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rna_fold.py to rna_fold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/unigene.py to unigene.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/gbseq.py to gbseq.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/kegg_taxonomy.py to kegg_taxonomy.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/ncbi_taxonomy.py to ncbi_taxonomy.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/structure.py to structure.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/dotur.py to dotur.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/gibbs.py to gibbs.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/tree.py to tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/record.py to record.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rnaalifold.py to rnaalifold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/pfold.py to pfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/tinyseq.py to tinyseq.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/meme.py to meme.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/gff.py to gff.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/psl.py to psl.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/ilm.py to ilm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/consan.py to consan.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/cutg.py to cutg.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/flowgram_parser.py to flowgram_parser.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/ct.py to ct.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/ebi.py to ebi.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rdb.py to rdb.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/contrafold.py to contrafold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/nupack.py to nupack.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/paml_matrix.py to paml_matrix.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rna_plot.py to rna_plot.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/newick.py to newick.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/blast.py to blast.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/rnaforester.py to rnaforester.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/sequence.py to sequence.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/sprinzl.py to sprinzl.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/agilent_microarray.py to agilent_microarray.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/blast_xml.py to blast_xml.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/infernal.py to infernal.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/nexus.py to nexus.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/record_finder.py to record_finder.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/stockholm.py to stockholm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/foldalign.py to foldalign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/kegg_ko.py to kegg_ko.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/paml.py to paml.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/mfold.py to mfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/stride.py to stride.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/genbank.py to genbank.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/cove.py to cove.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/mage.py to mage.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/parse/illumina_sequence.py to illumina_sequence.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/align.py to align.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/algorithm.py to algorithm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/indel_model.py to indel_model.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/indel_positions.py to indel_positions.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/pairwise.py to pairwise.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/pycompare.py to pycompare.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights/methods.py to methods.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/weights/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/dp_calculation.py to dp_calculation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/traceback.py to traceback.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/progressive.py to progressive.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif/k_word.py to k_word.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/motif/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/consensus.py to consensus.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/nj.py to nj.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/least_squares.py to least_squares.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/tree_space.py to tree_space.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/maximum_likelihood.py to maximum_likelihood.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/distance.py to distance.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/phylo/tree_collection.py to tree_collection.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/solved_models.py to solved_models.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/simulate.py to simulate.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/pairwise_distance.py to pairwise_distance.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/best_likelihood.py to best_likelihood.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/coevolution.py to coevolution.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/models.py to models.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py to substitution_calculation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_calculation.py to likelihood_calculation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/motif_prob_model.py to motif_prob_model.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/substitution_model.py to substitution_model.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/bootstrap.py to bootstrap.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/parameter_controller.py to parameter_controller.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/predicate.py to predicate.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_tree.py to likelihood_tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/discrete_markov.py to discrete_markov.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/likelihood_function.py to likelihood_function.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/usage.py to usage.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/analysis.py to analysis.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/birth_death.py to birth_death.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/markov.py to markov.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/randomization.py to randomization.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/searchpath.py to searchpath.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/microarray_normalize.py to microarray_normalize.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/tree.py to tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/microarray.py to microarray.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/seqsim/sequence_generators.py to sequence_generators.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/nucleic_properties.py to nucleic_properties.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/energy_params.py to energy_params.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/protein_properties.py to protein_properties.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/ligand_properties.py to ligand_properties.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/molecular_weight.py to molecular_weight.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/data/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/pdb_color.py to pdb_color.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/motif.py to motif.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/phylip.py to phylip.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/table.py to table.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/fasta.py to fasta.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/pdb.py to pdb.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/clustal.py to clustal.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/bedgraph.py to bedgraph.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/structure.py to structure.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/text_tree.py to text_tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/alignment.py to alignment.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/xyzrn.py to xyzrn.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/nexus.py to nexus.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/rna_struct.py to rna_struct.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/stockholm.py to stockholm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/format/mage.py to mage.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/sffinfo.py to sffinfo.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/fastq_join.py to fastq_join.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/cmfinder.py to cmfinder.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/knetfold.py to knetfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/carnac.py to carnac.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/dynalign.py to dynalign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rtax.py to rtax.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/vienna_package.py to vienna_package.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/mothur.py to mothur.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/cdbfasta.py to cdbfasta.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/flash.py to flash.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/pplacer.py to pplacer.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/comrna.py to comrna.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/seqprep.py to seqprep.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/dialign.py to dialign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/formatdb.py to formatdb.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/unafold.py to unafold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/raxml.py to raxml.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rnashapes.py to rnashapes.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/clearcut.py to clearcut.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier.py to rdp_classifier.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/uclust.py to uclust.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rnaview.py to rnaview.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/pknotsrg.py to pknotsrg.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/msms.py to msms.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/fasttree.py to fasttree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/sfold.py to sfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/gctmpca.py to gctmpca.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/cd_hit.py to cd_hit.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/sfffile.py to sfffile.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/muscle_v38.py to muscle_v38.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/dotur.py to dotur.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/raxml_v730.py to raxml_v730.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/usearch.py to usearch.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rnaalifold.py to rnaalifold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/pfold.py to pfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rdp_classifier20.py to rdp_classifier20.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/ilm.py to ilm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/consan.py to consan.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/muscle.py to muscle.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/mafft.py to mafft.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/blat.py to blat.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/clustalw.py to clustalw.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/parsinsert.py to parsinsert.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/contrafold.py to contrafold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/guppy.py to guppy.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/nupack.py to nupack.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/blast.py to blast.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/rnaforester.py to rnaforester.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/fasttree_v1.py to fasttree_v1.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/pandaseq.py to pandaseq.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/infernal.py to infernal.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/parameters.py to parameters.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/foldalign.py to foldalign.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/mfold.py to mfold.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/stride.py to stride.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/bwa.py to bwa.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/app/cove.py to cove.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/approximate_mds.py to approximate_mds.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/nmds.py to nmds.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/metric_scaling.py to metric_scaling.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/goodness_of_fit.py to goodness_of_fit.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/procrustes.py to procrustes.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/cluster/UPGMA.py to UPGMA.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/pairs_util.py to pairs_util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/dihedral.py to dihedral.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/rna2d.py to rna2d.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/manipulation.py to manipulation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/annotation.py to annotation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/selection.py to selection.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/contact.py to contact.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/knots.py to knots.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/asa.py to asa.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/feature_level.py to feature_level.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/genome.py to genome.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/related_region.py to related_region.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/assembly.py to assembly.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/region.py to region.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/species.py to species.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/host.py to host.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/name.py to name.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/compara.py to compara.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/database.py to database.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/sequence.py to sequence.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ensembl/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/pdb.py to pdb.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/rfam.py to rfam.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/ncbi.py to ncbi.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/db/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/location.py to location.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/usage.py to usage.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/info.py to info.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/bitvector.py to bitvector.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/entity.py to entity.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/annotation.py to annotation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/tree.py to tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/alphabet.py to alphabet.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/genetic_code.py to genetic_code.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/moltype.py to moltype.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/profile.py to profile.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/alignment.py to alignment.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/core/sequence.py to sequence.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/option_parsing.py to option_parsing.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/progress_display.py to progress_display.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/dict_array.py to dict_array.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/trie.py to trie.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/table.py to table.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/dict2d.py to dict2d.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/recode_alignment.py to recode_alignment.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/parallel.py to parallel.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/transform.py to transform.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/checkpointing.py to checkpointing.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/warning.py to warning.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/modules.py to modules.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/terminal.py to terminal.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/datatypes.py to datatypes.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/update_version.py to update_version.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/misc.py to misc.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/unit_test.py to unit_test.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/array.py to array.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/util/organizer.py to organizer.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponentiation.py to matrix_exponentiation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/fit_function.py to fit_function.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/simannealingoptimiser.py to simannealingoptimiser.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/distance_transform.py to distance_transform.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix_logarithm.py to matrix_logarithm.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix_exponential_integration.py to matrix_exponential_integration.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/optimisers.py to optimisers.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix/distance.py to distance.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/matrix/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/svd.py to svd.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimisers.py to scipy_optimisers.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/function_optimisation.py to function_optimisation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/markov.py to markov.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/period.py to period.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_tree.py to fast_tree.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac/fast_unifrac.py to fast_unifrac.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/unifrac/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/solve.py to solve.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/scipy_optimize.py to scipy_optimize.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/geometry.py to geometry.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/jackknife.py to jackknife.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/distribution.py to distribution.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/rarefaction.py to rarefaction.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/alpha_diversity.py to alpha_diversity.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/kendall.py to kendall.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/test.py to test.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/period.py to period.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/histogram.py to histogram.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/adaptor.py to adaptor.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/get_by_cai.py to get_by_cai.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/cai/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/information_criteria.py to information_criteria.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/ks.py to ks.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/stats/special.py to special.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/dotplot.py to dotplot.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/distribution_plots.py to distribution_plots.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/rlg2mpl.py to rlg2mpl.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/compatibility.py to compatibility.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/linear.py to linear.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/fancy_arrow.py to fancy_arrow.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/arrow_rates.py to arrow_rates.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/legend.py to legend.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/codon_usage.py to codon_usage.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/dinuc.py to dinuc.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/util.py to util.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/dendrogram.py to dendrogram.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/draw/multivariate_plot.py to multivariate_plot.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation/setting.py to setting.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation/__init__.py to __init__.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation/scope.py to scope.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation/calculation.py to calculation.pyc byte-compiling /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/recalculation/definition.py to definition.pyc running install_egg_info running egg_info creating cogent.egg-info writing requirements to cogent.egg-info/requires.txt writing cogent.egg-info/PKG-INFO writing top-level names to cogent.egg-info/top_level.txt writing dependency_links to cogent.egg-info/dependency_links.txt writing manifest file 'cogent.egg-info/SOURCES.txt' reading manifest file 'cogent.egg-info/SOURCES.txt' writing manifest file 'cogent.egg-info/SOURCES.txt' Copying cogent.egg-info to /build/python-cogent-1.9/debian/python-cogent/usr/lib/python2.7/dist-packages/cogent-1.9.egg-info Skipping SOURCES.txt running install_scripts dh_install -O--buildsystem=pybuild debian/rules override_dh_installdocs make[1]: Entering directory '/build/python-cogent-1.9' dh_installdocs rm -rf debian/python-cogent/usr/share/doc/python-cogent/html/_sources find debian -name doctrees -type d | xargs rm -rf make[1]: Leaving directory '/build/python-cogent-1.9' dh_installchangelogs -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 fs:343: renaming _compare.so to _compare.i386-linux-gnu.so I: dh_python2 fs:343: renaming _pairwise_pogs.so to _pairwise_pogs.i386-linux-gnu.so I: dh_python2 fs:343: renaming _pairwise_seqs.so to _pairwise_seqs.i386-linux-gnu.so I: dh_python2 fs:343: renaming _likelihood_tree.so to _likelihood_tree.i386-linux-gnu.so I: dh_python2 fs:343: renaming _pairwise_distance.so to _pairwise_distance.i386-linux-gnu.so I: dh_python2 fs:343: renaming _solved_models.so to _solved_models.i386-linux-gnu.so I: dh_python2 fs:343: renaming _asa.so to _asa.i386-linux-gnu.so I: dh_python2 fs:343: renaming _contact.so to _contact.i386-linux-gnu.so I: dh_python2 fs:343: renaming _period.so to _period.i386-linux-gnu.so I: dh_python2 fs:343: renaming ckd3.so to ckd3.i386-linux-gnu.so dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild debian/rules override_dh_compress make[1]: Entering directory '/build/python-cogent-1.9' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/build/python-cogent-1.9' dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild debian/rules override_dh_shlibdeps make[1]: Entering directory '/build/python-cogent-1.9' dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_pairwise_pogs.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/spatial/ckd3.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_solved_models.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_pairwise_seqs.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/_contact.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_likelihood_tree.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/align/_compare.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/evolve/_pairwise_distance.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/struct/_asa.i386-linux-gnu.so debian/python-cogent/usr/lib/python2.7/dist-packages/cogent/maths/_period.i386-linux-gnu.so were not linked against libpthread.so.0 (they use none of the library's symbols) dh_numpy make[1]: Leaving directory '/build/python-cogent-1.9' dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-cogent: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cogent: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package python-cogent: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cogent: substitution variable ${python:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python-cogent-dbgsym' in '../python-cogent-dbgsym_1.9-14_i386.deb'. dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_1.9-14_all.deb'. dpkg-deb: building package 'python-cogent' in '../python-cogent_1.9-14_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-cogent_1.9-14_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/18050/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/18050/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/18050 and its subdirectories I: Current time: Mon Jun 29 01:37:57 +14 2020 I: pbuilder-time-stamp: 1593344277