I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 14 04:10:48 +14 2025 I: pbuilder-time-stamp: 1765635048 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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: Copying source file I: copying [python-cogent_2024.5.7a1+dfsg-3.dsc] I: copying [./python-cogent_2024.5.7a1+dfsg.orig.tar.xz] I: copying [./python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 5 16:52:40 2024 gpgv: using RSA key D54C3BFAFFB042DE382DA5D741CE7F0B9F1B8B32 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-cogent_2024.5.7a1+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting python-cogent in python-cogent-2024.5.7a1+dfsg dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg.orig.tar.xz dpkg-source: info: unpacking python-cogent_2024.5.7a1+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying sphinx.patch dpkg-source: info: applying fix_interpreter.patch dpkg-source: info: applying remove-jupyter-sphinx.patch dpkg-source: info: applying ignore_tests_accessing_network.patch dpkg-source: info: applying skip-parallel-tests-on-single-cpu-systems.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1098549/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-amd64. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 13 14:10 /bin/sh -> /bin/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/1098549/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1098549/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=18c7a6dca6d9462f81ac8c8e12283d12 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=1098549 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/r-b-build.9V06TGWp/pbuilderrc_52DQ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9V06TGWp/b2 --logfile b2/build.log python-cogent_2024.5.7a1+dfsg-3.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1098549/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: amd64 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: architecture-is-64-bit, architecture-is-little-endian, cython3, debhelper-compat (= 13), dh-sequence-python3, flit, libjs-requirejs, pandoc, pybuild-plugin-pyproject, python3-all-dev, python3-chardet, python3-isort, python3-jupyter-sphinx-theme, python3-jupyterlab-server, python3-matplotlib, python3-nbsphinx, python3-numba, python3-numpy, python3-numpydoc, python3-pandas, python3-plotly, python3-pydata-sphinx-theme, python3-pytest, python3-pytest-cov, python3-pytest-xdist, python3-scipy, python3-scitrack, python3-sphinx, python3-sphinx-bootstrap-theme, python3-sphinx-design, python3-sphinx-gallery, python3-sphinxcontrib.bibtex, python3-stevedore, python3-tinydb, python3-tqdm, python3-typing-extensions dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19970 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 architecture-is-64-bit; however: Package architecture-is-64-bit is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on flit; however: Package flit is not installed. pbuilder-satisfydepends-dummy depends on libjs-requirejs; however: Package libjs-requirejs is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-chardet; however: Package python3-chardet is not installed. pbuilder-satisfydepends-dummy depends on python3-isort; however: Package python3-isort is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyter-sphinx-theme; however: Package python3-jupyter-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-jupyterlab-server; however: Package python3-jupyterlab-server is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nbsphinx; however: Package python3-nbsphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-numba; however: Package python3-numba is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-plotly; however: Package python3-plotly is not installed. pbuilder-satisfydepends-dummy depends on python3-pydata-sphinx-theme; however: Package python3-pydata-sphinx-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cov; however: Package python3-pytest-cov is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-scitrack; however: Package python3-scitrack is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-bootstrap-theme; however: Package python3-sphinx-bootstrap-theme is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-design; however: Package python3-sphinx-design is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-gallery; however: Package python3-sphinx-gallery is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.bibtex; however: Package python3-sphinxcontrib.bibtex is not installed. pbuilder-satisfydepends-dummy depends on python3-stevedore; however: Package python3-stevedore is not installed. pbuilder-satisfydepends-dummy depends on python3-tinydb; however: Package python3-tinydb is not installed. pbuilder-satisfydepends-dummy depends on python3-tqdm; however: Package python3-tqdm is not installed. pbuilder-satisfydepends-dummy depends on python3-typing-extensions; however: Package python3-typing-extensions 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} flit{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-glyphicons-halflings{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jupyter-sphinx-theme-common{a} libarchive-zip-perl{a} libargon2-1{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhwloc15{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-bootstrap{a} libjs-bootswatch{a} libjs-jquery{a} libjs-jquery-hotkeys{a} libjs-jquery-isonscreen{a} libjs-jquery-metadata{a} libjs-jquery-tablesorter{a} libjs-jquery-throttle-debounce{a} libjs-jquery-ui{a} libjs-requirejs{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm14t64{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnorm1t64{a} libnsl2{a} libnuma1{a} libopenjp2-7{a} libpfm4{a} libpgm-5.3-0t64{a} libpipeline1{a} libpng16-16t64{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsodium23{a} libssh2-1t64{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libz3-4{a} libzmq5{a} llvm-14{a} llvm-14-linker-tools{a} llvm-14-runtime{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} pandoc{a} pandoc-data{a} po-debconf{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python-tinycss2-common{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-anyio{a} python3-appdirs{a} python3-argon2{a} python3-arrow{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-bleach{a} python3-brotli{a} python3-bs4{a} python3-build{a} python3-certifi{a} python3-cffi-backend{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-colorama{a} python3-commonmark{a} python3-contourpy{a} python3-coverage{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-execnet{a} python3-fastjsonschema{a} python3-fonttools{a} python3-fqdn{a} python3-fs{a} python3-html5lib{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-isoduration{a} python3-isort{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-json-pointer{a} python3-json5{a} python3-jsonschema{a} python3-jsonschema-specifications{a} python3-jupyter-client{a} python3-jupyter-core{a} python3-jupyter-events{a} python3-jupyter-server{a} python3-jupyter-server-terminals{a} python3-jupyter-sphinx-theme{a} python3-jupyterlab-pygments{a} python3-jupyterlab-server{a} python3-kiwisolver{a} python3-latexcodec{a} python3-llvmlite{a} python3-lxml{a} python3-lz4{a} python3-markdown-it{a} python3-markupsafe{a} python3-matplotlib{a} python3-mdurl{a} python3-minimal{a} python3-mistune{a} python3-more-itertools{a} python3-mpmath{a} python3-nbclient{a} python3-nbconvert{a} python3-nbformat{a} python3-nbsphinx{a} python3-numba{a} python3-numpy{a} python3-numpydoc{a} python3-overrides{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pandocfilters{a} python3-pbr{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-plotly{a} python3-pluggy{a} python3-prometheus-client{a} python3-psutil{a} python3-ptyprocess{a} python3-py{a} python3-pybtex{a} python3-pybtex-docutils{a} python3-pydata-sphinx-theme{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytest-cov{a} python3-pytest-xdist{a} python3-pythonjsonlogger{a} python3-recommonmark{a} python3-referencing{a} python3-requests{a} python3-rfc3339-validator{a} python3-rfc3986-validator{a} python3-rich{a} python3-roman{a} python3-rpds-py{a} python3-scipy{a} python3-scitrack{a} python3-send2trash{a} python3-setuptools{a} python3-six{a} python3-sniffio{a} python3-snowballstemmer{a} python3-soupsieve{a} python3-sphinx{a} python3-sphinx-bootstrap-theme{a} python3-sphinx-design{a} python3-sphinx-gallery{a} python3-sphinxcontrib.bibtex{a} python3-stevedore{a} python3-sympy{a} python3-tabulate{a} python3-tenacity{a} python3-terminado{a} python3-tinycss2{a} python3-tinydb{a} python3-tk{a} python3-toml{a} python3-tomli-w{a} python3-tornado{a} python3-tqdm{a} python3-traitlets{a} python3-typeguard{a} python3-typeshed{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-uritemplate{a} python3-urllib3{a} python3-webcolors{a} python3-webencodings{a} python3-websocket{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3-zmq{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} x11-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: binfmt-support curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libhwloc-plugins libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules llvm-14-dev lynx numba-doc optipng publicsuffix python3-accessible-pygments python3-bottleneck python3-cssselect python3-gi python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pip python3-rfc3987 python3-tables shared-mime-info systemd wget xdg-user-dirs 0 packages upgraded, 315 newly installed, 0 to remove and 0 not upgraded. Need to get 208 MB of archives. After unpacking 1048 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-hotkeys all 0~20130707+git2d51e3a9+dfsg-2.1 [11.5 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-3 [255 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 24 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-10 [97.2 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.3 [2184 B] Get: 39 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b5 [307 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 72 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 97 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1 [118 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 python3-tomli-w all 1.0.0-2 [8012 B] Get: 103 http://deb.debian.org/debian unstable/main amd64 flit all 3.9.0-2 [93.4 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-3 [162 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libjs-bootstrap all 3.4.1+dfsg-3 [172 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libjs-bootswatch all 3.3.7+dfsg2-1.1 [133 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-bootstrap-theme all 0.8.1-5 [422 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 jupyter-sphinx-theme-common all 0.0.6+ds1-12 [12.6 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libargon2-1 amd64 0~20190702+dfsg-4+b2 [21.4 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-isonscreen all 1.2.0-1.1 [3196 B] Get: 133 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-metadata all 12-4 [6532 B] Get: 134 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-tablesorter all 1:2.31.3+dfsg1-4 [184 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-throttle-debounce all 1.1+dfsg.1-2 [12.2 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjs-requirejs all 2.3.7+ds+~2.1.37-1 [196 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libllvm14t64 amd64 1:14.0.6-20 [21.9 MB] Get: 147 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.6-3+b2 [147 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b1 [221 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libpfm4 amd64 4.13.0+git83-g91970fe-1 [368 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 158 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2021.12.0-1 [48.9 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2021.12.0-1 [14.4 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2021.12.0-1 [87.8 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 llvm-14-runtime amd64 1:14.0.6-20 [481 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 llvm-14-linker-tools amd64 1:14.0.6-20 [1292 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 llvm-14 amd64 1:14.0.6-20 [11.8 MB] Get: 175 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.44.0-2 [53.4 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.14.0-1 [5701 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python-tinycss2-common all 1.3.0-1 [31.9 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-sniffio all 1.3.1-1 [7120 B] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-anyio all 4.6.0-1 [59.2 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 1.17.1-1 [87.1 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-argon2 amd64 21.1.0-2 [22.8 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1258 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-arrow all 1.3.0-1.1 [64.7 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.14.0-1 [111 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-webencodings all 0.5.1-5 [11.1 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-html5lib all 1.2-1 [92.2 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-bleach all 6.2.0-1 [51.2 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b5 [318 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-soupsieve all 2.6-1 [38.3 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-bs4 all 4.12.3-3 [133 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-click all 8.1.7-2 [94.3 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-commonmark all 0.9.1-6 [45.3 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.0-2 [215 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-coverage amd64 7.6.0+dfsg1-2 [175 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-execnet all 2.1.1-1 [40.2 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-fastjsonschema all 2.20.0-1 [21.8 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1 [1251 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b4 [25.2 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.13.1-5 [16.7 MB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.54.1-4 [1429 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-fqdn all 1.5.1-2 [7592 B] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-isoduration all 20.11.0+git20211126.ae0bd61-2 [12.3 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-isort all 5.13.2-2 [71.7 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b1 [13.6 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-json-pointer all 2.4-2 [14.6 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-json5 all 0.9.25-1 [21.9 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-rpds-py amd64 0.20.1-1 [252 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-referencing all 0.35.1-1 [23.5 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9020 B] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-jsonschema all 4.19.2-5 [71.4 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-traitlets all 5.14.3+really5.14.3-1 [70.9 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-core all 5.7.2-4 [35.1 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-tornado amd64 6.4.1-3 [349 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-py all 1.11.0-2 [88.7 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-zmq amd64 24.0.1-5+b2 [269 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-client all 8.6.2-3 [91.5 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-pythonjsonlogger all 3.1.0-1 [14.4 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-rfc3339-validator all 0.1.4-2 [4060 B] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-rfc3986-validator all 0.1.1-2 [4884 B] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-mdurl all 0.1.2-1 [9444 B] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-markdown-it all 3.0.0-2 [62.5 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 257 http://deb.debian.org/debian unstable/main amd64 python3-rich all 13.7.1-1 [201 kB] Get: 258 http://deb.debian.org/debian unstable/main amd64 python3-uritemplate all 4.1.1-3 [10.6 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 python3-webcolors all 1.13-1 [15.3 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1 [134 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-events all 0.10.0-3 [18.2 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 python3-ptyprocess all 0.7.0-6 [14.5 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 python3-terminado all 0.18.1-1 [17.3 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server-terminals all 0.5.3-2 [13.9 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-pygments all 0.2.2-3 [6096 B] Get: 266 http://deb.debian.org/debian unstable/main amd64 python3-mistune all 3.0.2-2 [33.2 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 python3-nbformat all 5.9.1-1 [45.1 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 python3-nbclient all 0.8.0-1 [64.0 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 python3-pandocfilters all 1.5.1-1 [23.7 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 python3-tinycss2 all 1.3.0-1 [22.1 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 python3-nbconvert all 7.16.4-2 [158 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 python3-overrides all 7.7.0-2 [14.2 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 python3-prometheus-client all 0.19.0+ds1-1 [35.0 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 python3-send2trash all 1.8.2-1 [16.5 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 python3-websocket all 1.8.0-2 [45.5 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-server all 2.14.2-4 [212 kB] Get: 277 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 python3-nbsphinx all 0.9.4+ds-1.1 [39.6 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 python3-jupyter-sphinx-theme all 0.0.6+ds1-12 [2968 B] Get: 283 http://deb.debian.org/debian unstable/main amd64 python3-jupyterlab-server all 2.25.2-1 [50.9 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-2 [60.9 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 python3-latexcodec all 3.0.0-1 [17.5 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 python3-llvmlite amd64 0.42.0-1+b1 [180 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1 [502 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.0-1 [103 kB] Get: 290 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.12.6-1 [9428 B] Get: 291 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.4.0-1 [79.4 kB] Get: 292 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3 [5560 kB] Get: 294 http://deb.debian.org/debian unstable/main amd64 python3-numba amd64 0.59.1+dfsg-3 [1732 kB] Get: 295 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [4389 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 python3-pbr all 6.1.0-3 [56.6 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 python3-tenacity all 8.4.2+really8.4.1-1 [46.0 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 python3-plotly all 5.20.0+dfsg-1 [2726 kB] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-pybtex all 0.24.0-4 [74.6 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-pybtex-docutils all 1.0.2-1 [8064 B] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-pydata-sphinx-theme all 0.15.4+dfsg-2 [40.3 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cov all 5.0.0-1 [26.8 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 python3-pytest-xdist all 3.6.1-1 [44.4 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 python3-scitrack all 2024.10.8-1 [9420 B] Get: 310 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-design all 0.6.1-1 [883 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-gallery all 0.16.0-1 [392 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.bibtex all 2.6.2-1 [32.4 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 python3-stevedore all 5.3.0-3 [20.9 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 python3-tinydb all 3.15.2-4 [20.8 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 python3-tqdm all 4.67.0-1 [90.2 kB] Fetched 208 MB in 3s (76.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libjs-jquery. (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 ... 19970 files and directories currently installed.) Preparing to unpack .../libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-hotkeys. Preparing to unpack .../libjs-jquery-hotkeys_0~20130707+git2d51e3a9+dfsg-2.1_all.deb ... Unpacking libjs-jquery-hotkeys (0~20130707+git2d51e3a9+dfsg-2.1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... 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 ... 20316 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../07-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... 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 ... 21378 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-bootstrap (3.4.1+dfsg-3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libtbbbind-2-5:amd64 (2021.12.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libjs-jquery-metadata (12-4) ... Setting up libjs-jquery-isonscreen (1.2.0-1.1) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libllvm14t64:amd64 (1:14.0.6-20) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libjs-jquery-tablesorter (1:2.31.3+dfsg1-4) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up llvm-14-linker-tools (1:14.0.6-20) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libzmq5:amd64 (4.3.5-1+b3) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up python3.12-tk (3.12.7-3) ... Setting up libtbb12:amd64 (2021.12.0-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3.13-tk (3.13.0-1) ... Setting up llvm-14-runtime (1:14.0.6-20) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up sphinx-common (7.4.7-4) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up llvm-14 (1:14.0.6-20) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... 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Setting up python3-recommonmark (0.7.1+ds-5) ... /usr/lib/python3/dist-packages/recommonmark/transform.py:254: SyntaxWarning: invalid escape sequence '\w' match = re.search('[ ]?[\w_-]+::.*', language) Setting up python3-numpydoc (1.6.0-2) ... Setting up python3-pydata-sphinx-theme (0.15.4+dfsg-2) ... Setting up python3-jupyter-sphinx-theme (0.0.6+ds1-12) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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 I: Building the package I: user script /srv/workspace/pbuilder/1098549/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1098549/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-cogent_2024.5.7a1+dfsg-3_source.changes dpkg-buildpackage: info: source package python-cogent dpkg-buildpackage: info: source version 2024.5.7a1+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' #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/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules binary dh binary --with sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3 * Building wheel... Successfully built cogent3-2024.5.7a1-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module debian/rules execute_after_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' set -x; cd doc; PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg http_proxy='127.0.0.1:9' /usr/bin/make html + cd doc + PYTHONPATH=/build/reproducible-path/python-cogent-2024.5.7a1+dfsg + http_proxy=127.0.0.1:9 + /usr/bin/make html make[2]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v7.4.7 loading translations [en]... done making output directory... done WARNING: html_static_path entry '_static' does not exist WARNING: The config value `today' has type `date', defaults to `str'. checking bibtex cache... out of date parsing bibtex file /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cogent3.bib... parsed 21 entries building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 176 source files that are out of date updating environment: [new config] 176 added, 0 changed, 0 removed reading sources... [ 1%] COGENT3_LICENSE reading sources... [ 1%] api/__init__/cogent3.__init__.available_apps reading sources... [ 2%] api/__init__/cogent3.__init__.available_codes reading sources... [ 2%] api/__init__/cogent3.__init__.available_models reading sources... [ 3%] api/__init__/cogent3.__init__.available_moltypes reading sources... [ 3%] api/__init__/cogent3.__init__.get_code reading sources... [ 4%] api/__init__/cogent3.__init__.get_model reading sources... [ 5%] api/__init__/cogent3.__init__.get_moltype reading sources... [ 5%] api/__init__/cogent3.__init__.load_aligned_seqs reading sources... [ 6%] api/__init__/cogent3.__init__.load_annotations reading sources... [ 6%] api/__init__/cogent3.__init__.load_delimited reading sources... [ 7%] api/__init__/cogent3.__init__.load_seq reading sources... [ 7%] api/__init__/cogent3.__init__.load_table reading sources... [ 8%] api/__init__/cogent3.__init__.load_tree reading sources... 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[ 91%] examples/manipulating_tree_nodes reading sources... [ 91%] examples/neutral_test reading sources... [ 92%] examples/parallel reading sources... [ 93%] examples/parametric_bootstrap reading sources... [ 93%] examples/period_estimation reading sources... [ 94%] examples/phylo_by_ls reading sources... [ 94%] examples/rate_heterogeneity reading sources... [ 95%] examples/relative_rate reading sources... [ 95%] examples/scope_model_params_on_trees reading sources... [ 96%] examples/simple reading sources... [ 97%] examples/simulate_alignment reading sources... [ 97%] examples/testing_multi_loci reading sources... [ 98%] index reading sources... [ 98%] install reading sources... [ 99%] licenses reading sources... [ 99%] pycogent reading sources... [100%] templates/class WARNING: autodoc: failed to import function '__init__.available_apps' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_codes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_models' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.available_moltypes' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_code' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_model' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.get_moltype' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_annotations' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_delimited' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.load_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_aligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_seq' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_tree' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.make_unaligned_seqs' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function '__init__.open_data_store' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/alignment.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst SequenceCollection Alignment ArrayAlignment WARNING: autodoc: failed to import class 'core.alignment.Alignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.ArrayAlignment' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.alignment.SequenceCollection' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/alphabet.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Alphabet WARNING: autodoc: failed to import class 'core.alphabet.Alphabet' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/annotation.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Feature WARNING: autodoc: failed to import class 'core.annotation.Feature' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/annotation_db.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst BasicAnnotationDb GffAnnotationDb GenbankAnnotationDb WARNING: autodoc: failed to import class 'core.annotation_db.BasicAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GenbankAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.annotation_db.GffAnnotationDb' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.composable.define_app' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataMember' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.DataStoreDirectory' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.data_store.ReadOnlyDataStoreZipped' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'app.io.register_datastore_reader' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'app.sqlite_data_store.DataStoreSqlite' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.genetic_code.GeneticCode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/genetic_code.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst GeneticCode WARNING: autodoc: failed to import class 'core.moltype.MolType' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/moltype.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst MolType WARNING: autodoc: failed to import class 'core.sequence.DnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.ProteinSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'core.sequence.RnaSequence' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/sequence.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst DnaSequence RnaSequence ProteinSequence WARNING: autodoc: failed to import class 'parse.table.FilteringParser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Columns' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import class 'util.table.Table' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst Table Columns /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/table.rst:15: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst FilteringParser WARNING: autodoc: failed to import class 'core.tree.PhyloNode' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/tree.rst:6: ERROR: Unknown directive type "autosummary". .. autosummary:: :toctree: classes :template: class.rst PhyloNode WARNING: autodoc: failed to import class 'util.deserialise.register_deserialiser' from module 'cogent3'; the following exception was raised: No module named 'cogent3' WARNING: autodoc: failed to import function 'util.deserialise.deserialise_object' from module 'cogent3'; the following exception was raised: No module named 'cogent3' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app codon_aligner = get_app("progressive_align", "codon") aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "codon", distance="paralinear") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" codon_aligner = get_app("progressive_align", "codon", guide_tree=tree) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "codon", guide_tree=tree, indel_rate=0.001, indel_length=0.01 ) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: codon_aligner = get_app("progressive_align", "CNFHKY", guide_tree=tree, param_vals=dict(omega=0.1, kappa=3) ) aligned = codon_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-codon.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") seqs = loader("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app nt_aligner = get_app("progressive_align", "nucleotide") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: nt_aligner = get_app("progressive_align", "nucleotide", distance="TN93") aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "nucleotide", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: tree = "((Chimp:0.001,Human:0.001):0.0076,Macaque:0.01,((Rat:0.01,Mouse:0.01):0.02,Mouse_Lemur:0.02):0.01)" nt_aligner = get_app("progressive_align", "F81", guide_tree=tree) aligned = nt_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-nucleotide.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", format="fasta") to_aa = get_app("translate_seqs") process = loader + to_aa seqs = process("data/SCA1-cds.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app aa_aligner = get_app("progressive_align", "protein") aligned = aa_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aa_aligner = get_app("progressive_align", "protein", distance="paralinear") aligned = aa_aligner(seqs) aligned /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/align-protein.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligned.info /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-sample.rst:6: WARNING: toctree contains reference to nonexisting document 'app/app_cookbook/sample-trim-stop' /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/index-writers.rst:5: WARNING: Explicit markup ends without a blank line; unexpected unindent. /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/brca1-bats.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="protein", format="phylip") aln = load_aligned_app("data/abglobin_aa.phylip") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:59: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-aligned.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[0].read()[:50]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import get_app, open_data_store from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name # create lf object to write load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") lf = gn_model_app(aln).lf out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") # write with the same identifier as the write_json example write_json_app = get_app("write_json", data_store=out_dstore) data_member = write_json_app(lf, identifier="gn_params.json") path_to_dstore = data_member.data_store.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-json.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_json_app = get_app("load_json") lf = load_json_app(f"{path_to_dstore}/gn_params.json") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_tsv_app = get_app("load_tabular", sep="\t") tsv_data = load_tsv_app("data/stats.tsv") tsv_data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import NamedTemporaryFile tmpdir = NamedTemporaryFile(dir=".") path_to_csv_file = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-tabular.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app tsv_data.write(path_to_csv_file, sep=",") load_csv_app = get_app("load_tabular", sep=",") csv_data = load_csv_app(path_to_csv_file) csv_data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="protein") seqs = load_unaligned_app("data/inseqs_protein.fasta") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = open_data_store(path_to_dir, suffix="tsv", mode="w") load_unaligned_app = get_app("load_unaligned", format="fasta", moltype="dna") jdist = get_app("jaccard_dist") writer = get_app("write_tabular", out_dstore, format="tsv") process = load_unaligned_app + jdist + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/load-unaligned.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) print(result[1].read()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_alns_app = get_app("concat", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln1 = make_aligned_seqs({"s1": "AAA", "s2": "CAA", "s3": "AAA"}, moltype="dna") aln2 = make_aligned_seqs({"s1": "GCG", "s2": "GGG", "s3": "GGT"}, moltype="dna") aln1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = concat_alns_app([aln1, aln2]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs, get_app concat_missing = get_app("concat", moltype="dna", intersect=False) aln3 = make_aligned_seqs({"s4": "GCG", "s5": "GGG"}, moltype="dna") result = concat_missing([aln1, aln3]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-concat.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app concat_delim = get_app("concat", join_seq="N", moltype="dna") result = concat_delim([aln1, aln2]) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="protein", format="phylip") aln = loader("data/abglobin_aa.phylip") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_20 = get_app("fixed_length", length=20) first_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app skip_10_take_20 = get_app("fixed_length", length=20, start=10) skip_10_take_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-fixed-len.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_20 = get_app("fixed_length", length=20, random=True) random_20(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_unaligned", moltype="dna", format="fasta") aln = loader("data/SCA1-cds.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app over_240s = get_app("min_length", 240) aln_fltrd = over_240s(aln) aln_fltrd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-min-len.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(path_to_dir, mode="w", suffix="fasta") writer = get_app("write_seqs", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "---ACC---TT-", "s2": "---ACC---TT-", "s3": "---ACC---TT-", "s4": "--AACCG-GTT-", "s5": "--AACCGGGTTT", "s6": "AGAACCGGGTT-", "s7": "------------", }, moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_frac_05 = get_app("omit_bad_seqs", gap_fraction=0.5) omit_frac_05(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-bad.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_quant_08 = get_app("omit_bad_seqs", quantile=0.8) omit_quant_08(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GACG", "s2": "GATGATGYT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens = get_app("omit_degenerates", moltype="dna") result = omit_degens(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degens_keep_gaps = get_app("omit_degenerates", moltype="dna", gap_is_degen=False) result = omit_degens_keep_gaps(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-degen.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_degenerates_app = get_app("omit_degenerates", moltype="dna", motif_length=2) result = omit_degenerates_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs data = { "a": "ACGT", "b": "ACG-", # identical to 'a' except has a gap "c": "ACGG", # duplicate "d": "ACGG", # duplicate "e": "AGTC", # unique } aln = make_aligned_seqs(data, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_shorter_duplicate = get_app("omit_duplicated", moltype="dna", choose="longest") omit_shorter_duplicate(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_all_duplicates = get_app("omit_duplicated", moltype="dna", choose=None) omit_all_duplicates(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( { "s1": "ATCG", "s2": "ATYG", # matches s1 with ambiguity "s3": "GGTA", }, moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-duplicated.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app app_dna = get_app("omit_duplicated", mask_degen=True, choose="longest", moltype="dna") app_dna(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna") result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna") result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-omit-gap.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: omit_gap_pos_app = get_app( "omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna" ) result = omit_gap_pos_app(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app first_3 = get_app("take_n_seqs", number=3) first_3(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app random_n = get_app("take_n_seqs", random=True, number=3, seed=1) random_n(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln1 = loader("data/primate_brca1.fasta") aln2 = loader("data/brca1.fasta") aln1.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-n-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: fixed_choice = get_app("take_n_seqs", number=2, random=True, fixed_choice=True) result1 = fixed_choice(aln1).names result2 = fixed_choice(aln2).names result1 == result2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs({"s1": "ACGACGACG", "s2": "GATGATGAT"}, moltype="dna") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos3 = get_app("take_codon_positions", 3, moltype="dna") result = take_pos3(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app take_pos12 = get_app("take_codon_positions", 1, 2, moltype="dna") result = take_pos12(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln_ff = make_aligned_seqs({"s1": "GCAAGCGTTTAT", "s2": "GCTTTTGTCAAT"}) take_fourfold = get_app("take_codon_positions", fourfold_degenerate=True, moltype="dna") result = take_fourfold(aln_ff) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + cpos3 + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-pos.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore = process.apply_to(fasta_seq_dstore) out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app loader = get_app("load_aligned", moltype="dna") aln = loader("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla") ape_aln = greater_ape_selector(aln) ape_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs hrg_aln = process("data/primate_brca1.fasta") hrg_aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-take-seqs.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app no_galagos = get_app("take_named_seqs", "Galago", negate=True) no_galago_aln = no_galagos(hrg_aln) no_galago_aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst:6: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) no_stops = get_app("trim_stop_codons", gc=1) no_stops(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store dstore = open_data_store("data", suffix="fasta", limit=2) reader = get_app("load_aligned", format="fasta", moltype="dna") min_length = get_app("min_length", 300) out_dstore = open_data_store(f"{path_to_dir}.sqlitedb", mode="w") writer = get_app("write_db", out_dstore) process = reader + min_length + writer result = process.apply_to(dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-db.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: out_dstore is result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # Load the alignment load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") # Fit the GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) model_result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-json.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store # Initialise the write_json app with a data store out_dstore = open_data_store(path_to_dir, mode="w", suffix="json") write_json_app = get_app("write_json", data_store=out_dstore) write_json_app(model_result.lf, identifier="gn_params.json") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app load_aligned_app = get_app("load_aligned", moltype="dna", format="fasta") aln = load_aligned_app("data/primate_brca1.fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store seq_dstore = open_data_store(path_to_dir, suffix="phylip", mode="w") write_seqs_app = get_app("write_seqs", data_store=seq_dstore, format="phylip") result = write_seqs_app(aln) result.read()[:50] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import open_data_store fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_unaligned", format="fasta", moltype="dna") keep_translatable = get_app("select_translatable") translate = get_app("translate_seqs") writer = get_app("write_seqs", out_dstore, format="fasta") process = loader + keep_translatable + translate + writer /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = process.apply_to(fasta_seq_dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-seqs.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app # load alignment load_aligned_app = get_app("load_aligned", moltype="dna") aln = load_aligned_app("data/primate_brca1.fasta") # fit GN model gn_model_app = get_app("model", "GN", tree="data/primate_brca1.tree") model_result = gn_model_app(aln) # tabulate the model result tabulator = get_app("tabulate_stats") model_result_tab = tabulator(model_result) motif_params = model_result_tab["motif params"] print(type(motif_params)) motif_params /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="csv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="csv") write_tabular_app(motif_params, identifier="gn_model_results.csv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") write_tabular_app = get_app("write_tabular", data_store=out_dstore, format="tsv") write_tabular_app(motif_params, identifier="gn_model_results.tsv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/write-tabular.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import get_app, open_data_store loader = get_app("load_unaligned", moltype="dna") jdist = get_app("jaccard_dist") out_dstore = open_data_store(path_to_dir, mode="w", suffix="tsv") writer = get_app("write_tabular", data_store=out_dstore, format="tsv") process = loader + jdist + writer in_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2) result = process.apply_to(in_dstore) result.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-get.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app just_nucs = get_app("omit_degenerates", moltype="dna") just_nucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-help.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import app_help app_help("omit_degenerates") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from tempfile import TemporaryDirectory tmpdir = TemporaryDirectory(dir=".") path_to_dir = tmpdir.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app, open_data_store out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w") loader = get_app("load_aligned", format="fasta", moltype="dna") cpos3 = get_app("take_codon_positions", 3) writer = get_app("write_seqs", out_dstore, format="fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = loader("data/primate_brca1.fasta") just3rd = cpos3(data) m = writer(just3rd) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:138: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: process = loader + cpos3 + writer m = process("data/primate_brca1.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data", suffix="fasta", mode="r") result = process.apply_to(dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result = process.apply_to(dstore, show_progress=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/app-overview.rst:205: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import shutil shutil.rmtree(path_to_dir, ignore_errors=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_apps available_apps() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/available-apps.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: available_apps(name_filter="load") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store dstore = open_data_store("data/raw.zip", suffix="fa", mode="r") print(dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m = dstore[0] m /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:102: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for m in dstore[:5]: print(m) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: m.read()[:20] # truncating /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore = open_data_store("data/demo-locked.sqlitedb") dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.unlock(force=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.summary_logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dstore.logs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(dstore.logs[0].read()[:225]) # truncated for clarity /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import open_data_store in_dstore = open_data_store("data/raw.zip", suffix="fa") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = open_data_store("translated.sqlitedb", mode="w") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app load = get_app("load_unaligned", moltype="dna") translate = get_app("translate_seqs") write = get_app("write_db", data_store=out_dstore) app = load + translate + write app /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore = app.apply_to(in_dstore) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.validate() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.summary_not_completed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:232: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: len(out_dstore.not_completed) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:238: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: out_dstore.not_completed[:2] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib fn = pathlib.Path("translated.sqlitedb") fn.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/dstore.rst:11: WARNING: download file not readable: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/data/raw.zip /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app reader = get_app("load_aligned", format="fasta") select_seqs = get_app("take_named_seqs", "Mouse", "Human") aln = reader("data/primate_brca1.fasta") result = select_seqs(aln) assert result == False result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.origin /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.message /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = reader("primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: app = reader + select_seqs result = app("data/primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_overview/not-completed.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: result = app("primate_brca1.fasta") result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") gn = get_app("model", "GN", tree="data/primate_brca1.tree") result = gn(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reconstuctor = get_app("ancestral_states") states_result = reconstuctor(result) states_result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: states_result["edge.0"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-ancestral-states.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.tree.get_figure(contemporaneous=True).show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "BH", tree="data/primate_brca1.tree") result = model(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = result.tree fig = tree.get_figure() fig.scale_bar = "top right" fig.show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") stats = tabulator(result) stats /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-dt-nuc-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stats["edge motif motif2 params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") model = get_app("model", "GN", tree="data/primate_brca1.tree") result = model(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulator = get_app("tabulate_stats") tabulated = tabulator(result) tabulated /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["edge params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["global params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-extract-model-stats.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tabulated["motif params"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") tree = "data/primate_brca1.tree" null = get_app("model", "GTR", tree=tree, optimise_motif_probs=True) alt = get_app("model", "GN", tree=tree, optimise_motif_probs=True) hyp = get_app("hypothesis", null, alt) result = hyp(aln) type(result) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.LR, result.df, result.pvalue /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.null.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-hypothesis.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago") process = loader + select_seqs aln = process("data/primate_brca1.fasta") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN") gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) type(fitted) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lnL, fitted.nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.tree, fitted.alignment /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.total_length(length_as="paralinear") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", split_codons=True) fitted = gn(aln) fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted[3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") fig = tree.get_figure(contemporaneous=True) fig.style_edges( "Human", tip2="Orangutan", outgroup="Galago", line=dict(color="red") ) fig.show(width=500, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: time_het = get_app("model", "GN", tree=tree, time_het=[dict(tip_names=["Human", "Orangutan"], outgroup_name="Galago")], ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loader = get_app("load_aligned", format="fasta") aln = loader("data/primate_brca1.fasta") result = time_het(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-timehet.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3 import get_app tree = load_tree("data/primate_brca1.tree") gn = get_app("model", "GN", tree=tree) gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: gn = get_app("model", "GN", tree="data/primate_brca1.tree") gn /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted = gn(aln) fitted /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-model-with-tree.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fitted.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") omega_eq_1 = get_app("natsel_neutral", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = omega_eq_1(aln) type(result) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_neutral.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") sites_differ = get_app("natsel_sitehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False ) result = sites_differ(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_sitehet.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = result.alt.lf.get_bin_probs() bprobs[:, :20] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_aligned", format="fasta", moltype="dna") aln = loader("data/primate_brca1.fasta") hc_differ = get_app("natsel_timehet", "GNC", tree="data/primate_brca1.tree", optimise_motif_probs=False, tip1="Human", tip2="Chimpanzee", ) result = hc_differ(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_timehet.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: result.alt.lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_tutorials/evo-natsel_zhang.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ['Site Class', 'Proportion', 'Background Edges', 'Foreground Edges'] data = {'Site Class': array(['0', '1', '2a', '2b'], dtype=' 1', '0 < omega0 < 1'], dtype=' AlignedSeqsType: return val[:index] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: first4 = up_to(index=4) first4 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=dict(a="GCAAGCGTTTAT", b="GCTTTTGTCAAT"), array_align=False, moltype="dna" ) result = first4(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from typing import Union from cogent3.app.composable import define_app from cogent3.app.typing import SeqsCollectionType, SerialisableType T = Union[SeqsCollectionType, SerialisableType] @define_app def rename_seqs(seqs: SeqsCollectionType) -> T: """upper case names""" return seqs.rename_seqs(lambda x: x.upper()) renamer = rename_seqs() result = renamer(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/user_function.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app.composable import define_app from cogent3.app.typing import AlignedSeqsType, PairwiseDistanceType @define_app def get_dists(aln: AlignedSeqsType, calc="hamming") -> PairwiseDistanceType: return aln.distance_matrix(calc=calc, show_progress=False) percent_dist = get_dists(calc="pdist") result = percent_dist(aln) result /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT") my_seq.moltype.label /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq = make_seq("AGTACACTGGT", moltype="bytes") my_seq.moltype.label /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") rnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna") my_seq type(my_seq) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.name = "my_gene" my_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") my_seq.complement() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq.rc() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna") pep = my_seq.get_translation() type(pep) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:144: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna") rnaseq = my_seq.to_rna() rnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna") dnaseq = rnaseq.to_dna() dnaseq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:166: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq a = make_seq("AGTACACTGGT", moltype="dna") a.can_pair(a.complement()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a.can_pair(a.rc()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("AGTACACTGGT", moltype="dna") extra_seq = make_seq("CTGAC", moltype="dna") long_seq = my_seq + extra_seq long_seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: my_seq[1:6] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") pos3 = seq[2::3] assert str(pos3) == "GGGG" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq("ATGATGATGATG", moltype="dna") indices = [(i, i + 2) for i in range(len(seq))[::3]] pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices) pos12 = pos12.get_slice() assert str(pos12) == "ATATATAT" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:227: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rnaseq.shuffle() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/DNA_and_RNA_sequences.rst:234: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna") s.degap() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = make_unaligned_seqs(dna, moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} seqs = make_aligned_seqs(data=dna, moltype="dna", array_align=True) print(type(seqs)) seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/test.paml") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_seqs = make_aligned_seqs( [("seq0", "ATG-AGT-AGG"), ("seq4", "ATGCC------")], moltype="dna" ) new_aln = aln.add_seqs(new_seqs) new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:98: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, before_name="seq2") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new_aln = aln.add_seqs(new_seqs, after_name="seq2") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) ref_aln = make_aligned_seqs( [("seq3", "ATAGGATG"), ("seq0", "ATG-AGCG"), ("seq4", "ATGCTGGG")], moltype="dna", ) new_aln = aln.add_from_ref_aln(ref_aln) new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", ) new_aln = aln.get_degapped_relative_to("seq1") new_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( [("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG")], moltype="dna", array_align=False, ) seq = aln.get_seq("seq1") seq.name type(seq) seq.is_gapped() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = aln.get_gapped_seq("seq1") seq.is_gapped() seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn, moltype="dna") my_seq = seqs.seqs[0] my_seq[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(my_seq) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:200: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs(fn, moltype="dna") aln.seqs[0][:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/test.paml", moltype="dna") aln.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:216: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: new = aln.take_seqs(["Human", "HowlerMon"]) new.names /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs from cogent3.core.alignment import Alignment seq = load_unaligned_seqs("data/test.paml", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:237: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = Alignment(seq) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCTGGG")] aln = make_aligned_seqs(data=data) dna = aln.to_dna() dna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.to_moltype("dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:264: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("a", "ACG---"), ("b", "CCUGGG")] aln = make_aligned_seqs(data=data) rna = aln.to_rna() rna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:275: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = [("x", "TYV"), ("y", "TE-")] aln = make_aligned_seqs(data=data) prot = aln.to_protein() prot /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") degapped = aln.degap() print(type(degapped)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs dna = {"seq1": "ATGACC", "seq2": "ATCGCC"} aln = make_aligned_seqs(data=dna, moltype="dna") aln.write("sample.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:317: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.write("sample", format="fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.io import remove_files remove_files(["sample", "sample.fasta"], error_on_missing=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:332: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/long_testseqs.fasta") aln = Alignment(seq) fasta_align = aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) got = aln.to_phylip() print(got) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:357: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.core.alignment import Alignment seq = load_aligned_seqs("data/test.paml") aln = Alignment(seq) string_list = aln.to_dict().values() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:374: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs fn = "data/long_testseqs.fasta" aln = load_aligned_seqs(fn, moltype="dna") aln[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3 import load_unaligned_seqs fn = "data/long_testseqs.fasta" seqs = load_unaligned_seqs(fn) seqs[:24] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:396: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/test.paml") column_four = aln[3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:406: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") region = aln[50:70] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() type(col) list(col) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:430: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=False ) list(range(len(aln))[2::3]) indices = [(i, i + 1) for i in range(len(aln))[2::3]] indices /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pos3 = aln.add_feature(biotype="pos3", name="pos3", spans=indices) pos3 = pos3.get_slice() pos3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:452: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ATGATGATG---", "seq2": "ATGATGATGATG"}, array_align=True ) pos3 = aln[2::3] pos3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:472: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data={"seq1": "ACGTAA---", "seq2": "ACGACA---", "seq3": "ACGCAATGA"}, moltype="dna", ) new = aln.trim_stop_codons() new /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:485: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln = make_aligned_seqs( data={ "seq1": "ACGTAA---", "seq2": "ACGAC----", # terminal codon incomplete "seq3": "ACGCAATGA", }, moltype="dna", ) new = aln.trim_stop_codons(strict=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:504: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:519: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nucs = aln.no_degenerates() nucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:526: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trinucs = aln.no_degenerates(motif_length=3) trinucs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_variable_aln = aln.take_positions(pos) just_variable_aln[:10] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:546: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") pos = aln.variable_positions() just_constant_aln = aln.take_positions(pos, negate=True) just_constant_aln[:10] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:560: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") variable_codons = aln.filtered( lambda x: len(set(map(tuple, x))) > 1, motif_length=3 ) just_variable_aln[:9] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = aln.to_type(array_align=False) variable_codons = aln.filtered(lambda x: len(set("".join(x))) > 1, motif_length=3) just_variable_aln[:9] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:586: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta") aln.take_seqs(["Human", "Mouse"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:595: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs(["Human", "Mouse"], negate=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:604: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) def no_N_chars(s): return "N" not in s aln.take_seqs_if(no_N_chars) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:624: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.take_seqs_if(no_N_chars, negate=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:636: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGGTG---"), ("seq2", "ATGAAGGTGATG"), ("seq3", "ATGAAGGNGATG"), ], moltype="dna", ) counts = aln.counts() counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:651: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(motif_length=3) counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:656: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.counts(include_ambiguity=True) counts /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:670: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs() motif_probs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:680: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, load_aligned_seqs trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta", moltype="dna") motif_probs = aln.get_motif_probs(alphabet=trinuc_alphabet) for m in sorted(motif_probs, key=lambda x: motif_probs[x], reverse=True): print("%s %.3f" % (m, motif_probs[m])) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:694: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs(data=[("a", "AACAAC"), ("b", "AAGAAG")], moltype="dna") motif_probs = aln.get_motif_probs() assert motif_probs["T"] == 0.0 motif_probs = aln.get_motif_probs(pseudocount=1e-6) assert 0 < motif_probs["T"] <= 1e-6 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:706: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("a", "AACGTAAG"), ("b", "AACGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) motif_probs = aln.get_motif_probs(alphabet=dinuc_alphabet) assert motif_probs["AA"] == 0.25 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:716: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = [("my_seq", "AAAGTAAG")] aln = make_aligned_seqs(data=seqs, moltype="dna") my_seq = aln.get_seq("my_seq") my_seq.count("AA") "AAA".count("AA") "AAAA".count("AA") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:727: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq seq = make_seq(moltype="dna", seq="AAAGTAAG") seq di_nucs = [seq[i : i + 2] for i in range(len(seq) - 1)] sum([nn == "AA" for nn in di_nucs]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:742: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") col = aln[113:115].iter_positions() c1, c2 = list(col) c1, c2 list(filter(lambda x: x == "-", c1)) list(filter(lambda x: x == "-", c2)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") for column in aln[113:150].iter_positions(): ungapped = list(filter(lambda x: x == "-", column)) gap_fraction = len(ungapped) * 1.0 / len(column) print(gap_fraction) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:771: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[ ("seq1", "ATGAAGG-TG--"), ("seq2", "ATG-AGGTGATG"), ("seq3", "ATGAAG--GATG"), ], moltype="dna", ) seq_to_aln_map = aln.get_gapped_seq("seq1").gap_maps()[0] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:787: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq_to_aln_map[3] seq_to_aln_map[8] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:796: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln_to_seq_map = aln.get_gapped_seq("seq1").gap_maps()[1] aln_to_seq_map[3] aln_to_seq_map[8] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:804: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError seq_pos = aln_to_seq_map[7] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:818: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_runs(2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:832: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA---TG-"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) aln.omit_gap_pos(0.40) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:846: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = make_aligned_seqs( data=[ ("seq1", "ATGAA------"), ("seq2", "ATG-AGTGATG"), ("seq3", "AT--AG-GATG"), ], moltype="dna", ) filtered_aln = aln.omit_gap_seqs(0.50) filtered_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alignments.rst:861: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: filtered_aln.omit_gap_pos() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA, PROTEIN print(DNA.alphabet) print(PROTEIN.alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: PROTEIN.alphabet.moltype == PROTEIN /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dinuc_alphabet = DNA.alphabet.get_word_alphabet(2) print(dinuc_alphabet) trinuc_alphabet = DNA.alphabet.get_word_alphabet(3) print(trinuc_alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = "TAGT" indices = DNA.alphabet.to_indices(seq) indices /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/alphabet.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = DNA.alphabet.from_indices([0, 2, 3, 0]) seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import BasicAnnotationDb anno_db = BasicAnnotationDb() anno_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") gff_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gb_db = load_annotations(path="data/mycoplasma-genitalium.gb") gb_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: summary = gff_db.describe summary /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: anno_db.add_feature( seqid="NC_000908", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) anno_db.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.add_feature( seqid="seq1", biotype="gene", name="interesting_gene", spans=[(1, 4)], strand="+", ) gff_db.describe[-2:, :] # showing just last two rows /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mg_16s = list( gb_db.get_features_matching( name="MG_RS00775", biotype="gene", seqid="NC_000908" ) ) mg_16s /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogenes = list(gff_db.get_features_matching(biotype="pseudogene")) pseudogenes[:2] # showing just the first two /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: operon_cds = list( gff_db.get_features_matching(start=220600, end=229067, biotype="CDS") ) operon_cds /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:188: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: replication_records = list( gff_db.get_records_matching(attributes="replication", biotype="CDS") ) replication_records[0] # showing just the first match /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gb_db.num_matches(biotype="gene") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:215: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gb_db.count_distinct(biotype="gene", name=True) single_copy = total_genes[total_genes.columns["count"] == 1, :] len(single_copy) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:226: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: total_genes = gff_db.num_matches(biotype="gene") print("total genes: ", total_genes) genes = gff_db.count_distinct(biotype="gene", name=True) single_copy = genes[genes.columns["count"] == 1, :] print("single copy genes: ", len(single_copy)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:246: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: children = list(gff_db.get_feature_children(name="gene-MG_RS00035")) children /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: parents = list(gff_db.get_feature_parent(name="cds-WP_009885556.1")) parents /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:273: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(anno_db) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.compatible(gb_db) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: union_db = gb_db.union(anno_db) union_db.describe[-2:, :] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:307: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_db.update(anno_db) gff_db.describe[-2:, :] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:318: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3.core.annotation_db import GenbankAnnotationDb new_gb_db = GenbankAnnotationDb(source="m-genitalium-database.gbdb", db=anno_db) new_gb_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:331: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_annotations gff_db = load_annotations(path="data/mycoplasma-genitalium.gff") just_cds = gff_db.subset(biotype="CDS") just_cds.describe /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:354: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="NC_000908", moltype="dna", ) seq1.annotation_db = anno_db seq1.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq gb_seq = load_seq("data/mycoplasma-genitalium.gb") gb_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:389: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: gff_seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", ) gff_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:402: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = load_seq( "data/mycoplasma-genitalium.fa", annotation_path="data/mycoplasma-genitalium.gff", label_to_name=lambda x: x.split()[0], ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/annotation_db.rst:412: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib # clean up files path = pathlib.Path("m-genitalium-database.gbdb") path.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") aln, tree = tree_align("HKY85", seqs, show_progress=False) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = make_tree( "(((NineBande:0.013,Mouse:0.185):0.023,DogFaced:0.046):0.027,Human:0.034,HowlerMon:0.019)" ) params = {"kappa": 4.0} aln, tree = tree_align( "HKY85", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs, make_tree from cogent3.align.progressive import tree_align seqs = load_unaligned_seqs("data/test2.fasta", moltype="dna") tree = make_tree( "((NineBande:0.058,Mouse:0.595):0.079,DogFaced:0.142,(HowlerMon:0.062,Human:0.103):0.079)" ) params = {"kappa": 4.0, "omega": 1.3} aln, tree = tree_align( "MG94HKY", seqs, tree=tree, param_vals=params, show_progress=False ) aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs from cogent3.align.progressive import tree_align from cogent3.evolve.models import get_model seqs = [ ( "hum", "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", ), ( "mus", "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", ), ("rat", "CTGAACAAGCAGCCACTTTCAAACAAGAAA"), ] unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_DNA.get_translation() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs aligned_aa_seqs = [ ("hum", "KQIQESSENGSLAARQERQAQVNLT"), ("mus", "KQIQESGESGSLAARQERQAQVNLT"), ("rat", "LNKQ------PLS---------NKK"), ] aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_alignments.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA, aa_to_codon=True) aligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = aln.quick_tree(calc="TN93", show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tree = aln.quick_tree(calc="TN93", bootstrap=100, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = dists.quick_tree(show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.phylo import nj aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="TN93") tree = nj.nj(dists, show_progress=False) tree = tree.balanced() # purely for display print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo import nj dists = {("a", "b"): 2.7, ("c", "b"): 2.33, ("c", "a"): 0.73} tree = nj.nj(dists, show_progress=False) print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:76: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.phylo.least_squares import WLS from cogent3.util.deserialise import deserialise_object dists = deserialise_object("data/dists_for_phylo.json") ls = WLS(dists) stat, tree = ls.trex(a=5, k=5, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/building_phylogenies.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve.models import F81 from cogent3.phylo.maximum_likelihood import ML aln = load_aligned_seqs("data/primate_brca1.fasta") ml = ML(F81(), aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_distances available_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_distance_calculator, load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta") dist_calc = get_distance_calculator("tn93", alignment=aln) dist_calc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.run(show_progress=False) dists = dist_calc.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:54: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dist_calc.stderr /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_model, load_aligned_seqs from cogent3.evolve import distance aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") d = distance.EstimateDistances(aln, submodel=get_model("F81")) d.run(show_progress=False) dists = d.get_pairwise_distances() dists /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:82: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.max_pair() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.max_pair()] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") dists = aln.distance_matrix(calc="tn93", show_progress=False) dists.min_pair() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/calc_genetic_distance.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: dists[dists.min_pair()] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_models available_models() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model hky = get_model("HKY85") print(hky) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("GTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:56: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("CNFGTR", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model sub_mod = get_model("JTT92", with_rate=True, distribution="gamma") print(sub_mod) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:80: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:94: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_tree from cogent3.evolve.models import get_model sub_mod = get_model("F81") tree = make_tree("(a,b,(c,d))") lf = sub_mod.make_likelihood_function(tree) aln = make_aligned_seqs( [("a", "ACGT"), ("b", "AC-T"), ("c", "ACGT"), ("d", "AC-T")] ) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:112: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule( "omega", tip_names=["Human", "Orangutan"], outgroup_name="Galago", clade=True, init=0.5, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("CNFGTR") lf = sm.make_likelihood_function(tree, digits=2) lf.set_param_rule("omega", init=0.1, lower=1e-9, upper=20.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:190: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_param_rule("length", upper=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:207: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:222: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.models import get_model sm = get_model("GTR", with_rate=True, distribution="gamma") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree, bins=4, sites_independent=False, digits=2) lf.set_param_rule("bprobs", is_constant=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:239: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:253: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, max_restarts=5, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=False, global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:265: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False, max_restarts=5, tolerance=1e-8) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:276: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) try: lf.optimise( show_progress=False, limit_action="raise", max_evaluations=10, return_calculator=True, ) except ArithmeticError as err: print(err) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:303: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model sm = get_model("GTR") tree = load_tree("data/primate_brca1.tree") lf = sm.make_likelihood_function(tree) aln = load_aligned_seqs("data/primate_brca1.fasta") lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:321: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lnL = lf.lnL lnL /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:326: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nfp = lf.nfp nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:338: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:344: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_aic(second_order=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:353: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.get_bic() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:367: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: a_g = lf.get_param_value("A/G") a_g /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human = lf.get_param_value("length", "Human") human /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:380: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mprobs = lf.get_motif_probs() mprobs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tables = lf.get_statistics(with_motif_probs=True, with_titles=True) tables[0] # just displaying the first /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:398: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) null_lnL = lf.lnL null_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:423: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) lf.set_name("Alt Hypothesis") lf.optimise(local=True, show_progress=False) alt_lnL = lf.lnL alt_nfp = lf.nfp lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:434: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (alt_lnL - null_lnL) # the likelihood ratio statistic df = alt_nfp - null_nfp # the test degrees of freedom p = chi2.sf(LR, df) print(f"LR={LR:.4f} ; df={df}; p={df:.4f}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:450: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.set_param_rule( "length", tip_names=["Human", "Chimpanzee"], outgroup_name="Galago", clade=True, is_independent=False, ) lf.set_name("Null Hypothesis") lf.optimise(local=True, show_progress=False) sim_aln = lf.simulate_alignment() sim_aln[:60] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:478: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("HKY85") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(local=True, show_progress=False) kappa_lo, kappa_mle, kappa_hi = lf.get_param_interval("kappa") print(f"lo={kappa_lo:.2f} ; mle={kappa_mle:.2f} ; hi={kappa_hi:.2f}") human_lo, human_mle, human_hi = lf.get_param_interval("length", "Human") print(f"lo={human_lo:.2f} ; mle={human_mle:.2f} ; hi={human_hi:.2f}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model aln = make_aligned_seqs(data=dict(a="ACGG", b="ATAG", c="ATGG")) tree = make_tree(tip_names=aln.names) sm = get_model("F81") lf = sm.make_likelihood_function(tree) lf.set_alignment(aln) json = lf.to_json() json[:60] # just truncating the displayed string /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.deserialise import deserialise_object newlf = deserialise_object(json) newlf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model tree = load_tree("data/primate_brca1.tree") aln = load_aligned_seqs("data/primate_brca1.fasta") sm = get_model("F81") lf = sm.make_likelihood_function(tree, digits=3, space=2) lf.set_alignment(aln) lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:542: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestors = lf.likely_ancestral_seqs() ancestors[:60] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/evo_modelling.rst:549: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ancestral_probs = lf.reconstruct_ancestral_seqs() ancestral_probs["root"][:5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq # create an example sequence seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAA", name="seq1", moltype="dna", ) # Add a feature seq.add_feature(biotype="gene", name="a_gene", spans=[(12, 48)], seqid="seq1") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # Add a feature as a series seq.add_feature( biotype="cpgsite", name="a_cpgsite", spans=[(12, 18), (21, 29), (35, 48)], seqid="seq1", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) # add feature to seq1 aln1.add_feature( seqid="seq1", biotype="exon", name="A", spans=[(3, 8)], on_alignment=False ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # make demo alignment aln1 = make_aligned_seqs( data=[["seq1", "-AAACCCCCA"], ["seq2", "TTTT--TTTT"]], array_align=False ) aln1.add_feature( biotype="exon", name="aligned_exon", spans=[(0, 8)], on_alignment=True, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:108: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq from cogent3.core.annotation_db import BasicAnnotationDb # init empty db and add feature db = BasicAnnotationDb() db.add_feature(seqid="seq1", biotype="exon", name="C", spans=[(45, 48)]) # make demo seq s1 = make_seq( "AAGAAGAAGACCCCCAAAAAAAAAATTTTTTTTTTAAAAAGGGAACCCT", name="seq1", moltype="dna" ) # assign db to sequence s1.annotation_db = db s1.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq %timeit load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:150: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: :hide-code: seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( filename="data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", moltype="dna", ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:189: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:209: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import load_seq loaded_seq = load_seq( "data/C-elegans-chromosome-I.fa", label_to_name=lambda x: x.split()[0], moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:220: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # loaded_seq = < loaded / created the seq> loaded_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff") loaded_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3 import make_seq sub_seq = make_seq( "GCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAATACTAAGCCTAAGCCTAAGACTAAGCCTAAGACTAAGCCTAAGA", name="I", moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: # sub_seq = sub_seq.annotate_from_gff("data/C-elegans-chromosome-I.gff", offset=600) sub_seq.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs brca1_aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) brca1_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:266: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) brca1_aln.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:274: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: brca1_aln.get_seq("Human").annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:296: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") # note we wrap `get_features` in `list` as generator is returned gene = list(seq.get_features(name="WBGene00021661", biotype="gene")) gene /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:312: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) cds[:3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:323: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: cds = list(seq.get_features(biotype="CDS", name="WBGene00021661")) cds /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") region_features = list(seq.get_features(start=10148, stop=26732)) region_features[:3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:345: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: mRNA = list(seq.get_features(start=10148, stop=29322, biotype="mRNA"))[0] mRNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:358: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs # first load alignment and annotate the human seq aln = load_aligned_seqs( "data/primate_brca1.fasta", array_align=False, moltype="dna" ) aln.annotate_from_gff("data/brca1_hsa_shortened.gff", seq_ids=["Human"]) # query alignment providing seqid of interest human_exons = list(aln.get_features(biotype="exon", seqid="Human")) human_exons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:383: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # add a feature to the alignment we created above on difference sequence aln.add_feature(biotype="gene", name="gene:101", spans=[(40, 387)], seqid="Rhesus") any_feature = list(aln.get_features(on_alignment=False)) any_feature /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:405: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs # first we add the feature to the alignment aln.add_feature( biotype="pseudogene", name="pseudogene1", spans=[(420, 666)], on_alignment=True ) # query for features on the alignment aln_features = list(aln.get_features(on_alignment=True)) aln_features /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:426: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln3 = make_aligned_seqs( data=[["x", "C-CCCAAAAA"], ["y", "-T----TTTT"]], array_align=False, moltype="dna", ) exon = aln3.add_feature( seqid="x", biotype="exon", name="ex1", spans=[(0, 4)], on_alignment=False ) exon.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:441: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln_exons = list(aln3.get_features(seqid="x", biotype="exon"))[0] aln_exons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: exon.get_slice(allow_gaps=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) pseudogene = list(seq.get_features(start=10148, stop=26732, biotype="pseudogene"))[0] seq[pseudogene] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:484: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:494: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") subseq = seq[25000:35000] fig = subseq.get_drawable(biotype=("gene", "mRNA", "CDS", "misc_RNA")) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: pseudogene.get_coordinates() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:515: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS"))[0] exon_coords = cds.get_coordinates() exon_coords /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:528: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron_coords = [] for i in range(len(exon_coords) - 1): intron_coords.append((exon_coords[i][1], exon_coords[i + 1][0])) intron_coords /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:540: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intron = seq.add_feature( biotype="intron", name="intron:Y74C9A.3.1", seqid="I", spans=intron_coords ) intron /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:553: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") cds = list(seq.get_features(biotype="CDS")) union_cds = cds[0].union(cds[1:]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:572: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") genes = list(seq.get_features(biotype="gene")) genes = genes[0].union(genes[1:]) genes /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:584: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic = genes.shadow() intergenic /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:592: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: intergenic.get_slice() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:605: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") no_cds = seq.with_masked_annotations("CDS") no_cds[2575800:2575900] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:621: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_aligned_seqs aln = make_aligned_seqs( data=[["x", "C-CCCAAAAAGGGAA"], ["y", "-T----TTTTG-GTT"]], moltype="dna", array_align=False, ) exon = aln.add_feature( seqid="x", biotype="exon", name="exon-be-gone", spans=[(0, 4)], on_alignment=False, ) aln.with_masked_annotations("exon", mask_char="?") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:642: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc = aln.rc() rc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:650: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: rc.with_masked_annotations("exon", mask_char="?") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:664: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_seq seq = load_seq( "data/C-elegans-chromosome-I.fa", annotation_path="data/C-elegans-chromosome-I.gff", label_to_name=lambda x: x.split()[0], moltype="dna", ) gene = list(seq.get_features(name="gene:WBGene00022276", biotype="gene"))[0] children = list(gene.get_children()) children /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:686: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: child = list(seq.get_features(name="transcript:Y74C9A.2a.3", biotype="mRNA"))[0] parent = list(child.get_parent()) parent /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:698: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln2 = make_aligned_seqs( data=[["x", "-AAAAAAAAA"], ["y", "TTTT--TTTT"]], array_align=False, moltype="dna", ) x, y = aln2.get_seq("x"), aln2.get_seq("y") x.annotation_db is y.annotation_db is aln2.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:711: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: seq = make_seq("CCCCCCCCCCCCCCCCCCCC", name="x", moltype="dna") match_exon = seq.add_feature(biotype="exon", name="A", spans=[(3, 8)]) aln2.copy_annotations(seq.annotation_db) aln2.annotation_db /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:721: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: copied = list(aln2.get_features(seqid="x", biotype="exon")) copied /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:732: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: unified = aln_exons.as_one_span() aln3[unified] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:743: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: plus = make_seq("CCCCCAAAAAAAAAATTTTTTTTTTAAAGG", moltype="dna") plus_rpt = plus.add_feature(biotype="blah", name="a", spans=[(5, 15), (25, 28)]) plus[plus_rpt] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:750: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus = plus.rc() minus /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/features.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: minus_rpt = list(minus.get_features(biotype="blah"))[0] minus[minus_rpt] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs data = { "s1": "GCTCATGCCAGCTCTTTACAGCATGAGAACA--AGT", "s2": "ACTCATGCCAACTCATTACAGCATGAGAACAGCAGT", "s3": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s4": "ACTCATGCCAGCTCATTACAGCATGAGAACAGCAGT", "s5": "ACTCATGCCAGCTCAGTACAGCATGAGAACAGCAGT", } nt_seqs = make_aligned_seqs(data=data, moltype="dna") nt_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: nt_seqs.get_translation(gc=1, incomplete_ok=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:50: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") translations = standard_code.sixframes(seq) print(translations) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) seq = make_seq("ATGCTAACATAAA", moltype="dna") stops_frame1 = standard_code.get_stop_indices(seq, start=0) stops_frame1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: stop_index = stops_frame1[0] seq[stop_index : stop_index + 3] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code, make_seq standard_code = get_code(1) standard_code["TTT"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: standard_code["A"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:95: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["TTT"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code["A"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:115: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: targets = ["A", "C"] codons = [standard_code[aa] for aa in targets] codons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: flat_list = sum(codons, []) flat_list /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(1) alphabet = gc.get_alphabet() print(alphabet) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:142: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq my_seq = make_seq("ATGCACTGGTAA", name="my_gene", moltype="dna") codons = my_seq.get_in_motif_size(3) codons /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:155: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = my_seq.get_translation() pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:163: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.core.alphabet import AlphabetError /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import make_seq seq = make_seq("ATGTGATGGTAA", name="s1", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AlphabetError pep = seq.get_translation() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/genetic_code.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pep = seq.get_translation(include_stop=True) pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/mycoplasma-genitalium.fa", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = load_seq("data/brca1-bats.fasta", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna") type(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln.info.source /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/long_testseqs.fasta", moltype="dna") type(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs( "https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/long_testseqs.fasta", moltype="dna", ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/long_testseqs.fasta", moltype="dna", format="fasta") aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:101: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs protein_seqs = {"seq1": "DEKQL-RG", "seq2": "DDK--SRG"} proteins_loaded = make_aligned_seqs(protein_seqs) proteins_loaded.moltype proteins_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: proteins_loaded = make_aligned_seqs(protein_seqs, moltype="protein") proteins_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:133: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs seqs = {"seq1": "AATCG-A", "seq2": "AATCGGA"} seqs_loaded = make_aligned_seqs(seqs) seqs_loaded /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs DNA_seqs = { "sample1 Mus musculus": "AACCTGC--C", "sample2 Gallus gallus": "AAC-TGCAAC", } loaded_seqs = make_aligned_seqs( DNA_seqs, moltype="dna", label_to_name=lambda x: x.split()[0] ) loaded_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_unaligned_seqs seqs = {"seq1": "AATCA", "seq2": "AATCGGA"} seqs = make_unaligned_seqs(data=seqs, moltype="dna") seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import MinimalFastaParser f = open("data/long_testseqs.fasta") seqs = [(name, seq) for name, seq in MinimalFastaParser(f)] seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:197: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser def latin_to_common(latin): return {"Homo sapiens": "human", "Pan troglodtyes": "chimp"}[latin] label_parser = LabelParser( "%(species)s", [[1, "species", latin_to_common]], split_with=":" ) for label in ">abcd:Homo sapiens:misc", ">abcd:Pan troglodtyes:misc": label = label_parser(label) print(label, type(label)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:213: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.fasta import LabelParser, MinimalFastaParser fasta_data = [ ">gi|10047090|ref|NP_055147.1| small muscle protein, X-linked [Homo sapiens]", "MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGAKKLPGPAVNL", "SEIQNIKSELKYVPKAEQ", ">gi|10047092|ref|NP_037391.1| neuronal protein [Homo sapiens]", "MANRGPSYGLSREVQEKIEQKYDADLENKLVDWIILQCAEDIEHPPPGRAHFQKWLMDGTVLCKLINSLY", "PPGQEPIPKISESKMAFKQMEQISQFLKAAETYGVRTTDIFQTVDLWEGKDMAAVQRTLMALGSVAVTKD", ] label_to_name = LabelParser( "%(ref)s", [[1, "gi", str], [3, "ref", str], [4, "description", str]], split_with="|", ) for name, seq in MinimalFastaParser(fasta_data, label_to_name=label_to_name): print(name) print(name.info.gi) print(name.info.description) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_sequences.rst:54: WARNING: TODO entry found: add cross ref for description of Info class /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_moltypes available_moltypes() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_moltype dna = get_moltype("dna") dna /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.ambiguities /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.degenerates /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dna.complement("AGG") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = dna.make_seq("AGGCTT", name="seq1") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rna = get_moltype("rna") rna.is_valid("ACGUACGUACGUACGU") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:87: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.core import moltype as mt DNAgapped = mt.MolType( seq_constructor=mt.DnaSequence, motifset=mt.IUPAC_DNA_chars, ambiguities=mt.IUPAC_DNA_ambiguities, complements=mt.IUPAC_DNA_ambiguities_complements, pairs=mt.DnaStandardPairs, gaps=".", ) seq = DNAgapped.make_seq("ACG.") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/moltypes.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import DNA from cogent3.core.sequence import DnaSequence DnaSequence.moltype = DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq p = make_seq("THISISAPRQTEIN", "myProtein", moltype="protein") type(p) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code standard_code = get_code(1) standard_code.translate("TTTGCAAAC") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_seq nuc = make_seq("TTTGCAAAC", moltype="dna") pep = nuc.get_translation() pep /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/protein_sequences.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs seq = load_aligned_seqs("data/abglobin_aa.phylip", moltype="protein") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.write("data/temp.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") names = tr.get_node_names() names[:4] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: names[4:] names_nodes = tr.get_nodes_dict() names_nodes["Human"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_node_matching_name("Mouse") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tr.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:63: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: hu.name /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:70: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] type(hu) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:88: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() for n in nodes.items(): print(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tr.iter_tips(): print(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:106: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for n in tr.iter_nontips(): print(n.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") edges = tr.get_connecting_edges("edge.1", "Human") for edge in edges: print(edge.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] hu.distance(mu) hu.is_tip() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") nodes = tr.get_nodes_dict() hu = nodes["Human"] mu = nodes["Mouse"] lca = hu.last_common_ancestor(mu) lca /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:154: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: type(lca) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") for a in hu.ancestors(): print(a.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:173: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") node = tr.get_node_matching_name("edge.1") children = list(node.iter_tips()) + list(node.iter_nontips()) for child in children: print(child.name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") dists = tr.get_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: human_dists = [names for names in dists if "Human" in names] for dist in human_dists: print(dist, dists[dist]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.max_tip_tip_distance() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") hu = tr.get_node_matching_name("Human") tips = hu.tips_within_distance(0.2) for t in tips: print(t) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.rooted_at("edge.0").ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.root_at_midpoint().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:254: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:261: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.rooted_with_tip("Mouse").ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:271: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") tr.get_newick() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:278: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.get_newick(with_distances=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:285: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") xml = tr.get_xml() for line in xml.splitlines(): print(line) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:299: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:309: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.preorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:320: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for t in tr.postorder(): print(t.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") for tip in tr.iter_nontips(): tip_names = tip.get_tip_names() print(tip_names) sub_tree = tr.get_sub_tree(tip_names) print(sub_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:348: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.io import remove_files remove_files(["data/temp.tree", "data/temp.pdf"], error_on_missing=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree simple_tree_string = "(B:0.2,(D:0.4)E:0.5)F;" simple_tree = make_tree(simple_tree_string) print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:372: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simple_tree.prune() print(simple_tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:377: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(simple_tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:384: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr1 = load_tree("data/test.tree") print(tr1.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:391: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr2 = tr1.unrooted_deepcopy() print(tr2.get_newick()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:401: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tree_string = "(B:0.2,H:0.2,(C:0.3,D:0.4,E:0.1)F:0.5)G;" tr = make_tree(tree_string) print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.bifurcating().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:422: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree tr = load_tree("data/test.tree") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:429: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tr.balanced().ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:438: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:0.2,(C:0.2,D:0.2)F:0.2)G;") tr2 = make_tree("((C:0.1,D:0.1)F:0.1,B:0.1)G;") tr1.same_topology(tr2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:467: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for rooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,(b,(c,(d,e))));") tr2 = make_tree(treestring="(e,(d,(c,(b,a))));") mc_distance = tr1.tree_distance(tr2, method="matching_cluster") # or method="mc" or method="matching" rooted_rf_distance = tr1.tree_distance(tr2, method="rooted_robinson_foulds") # or method="rrf" or method="rf" print("Matching Cluster Distance:", mc_distance) print("Rooted Robinson Foulds Distance:", rooted_rf_distance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:481: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: # Distance metrics for unrooted trees from cogent3 import make_tree tr1 = make_tree(treestring="(a,b,(c,(d,e)));") tr2 = make_tree(treestring="((a,c),(b,d),e);") lrm_distance = tr1.tree_distance(tr2, method="lin_rajan_moret") # or method="lrm" or method="matching" unrooted_rf_distance = tr1.tree_distance(tr2, method="unrooted_robinson_foulds") # or method="urf" or method="rf" print("Lin-Rajan-Moret Distance:", lrm_distance) print("Unrooted Robinson Foulds Distance:", unrooted_rf_distance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:501: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.set_tip_distances() for t in tr.preorder(): print(t.name, t.TipDistance) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:517: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:0.2,(C:0.3,D:0.4)F:0.5)G;") print(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:524: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tr.scale_branch_lengths() print(tr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:534: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr = make_tree("(B:3,(C:2,D:4)F:5)G;") d, tips = tr.tip_to_tip_distances() for i, t in enumerate(tips): print(t.name, d[i]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/simple_trees.rst:554: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree tr1 = make_tree("(B:2,(C:3,D:4)F:5)G;") tr2 = make_tree("(C:2,(B:3,D:4)F:5)G;") tr1.compare_by_tip_distances(tr2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory cookbook/loading_tabular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table cookbook/loading_tabular.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("https://raw.githubusercontent.com/cogent3/cogent3/develop/doc/data/stats.tsv") cookbook/loading_tabular.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", sep="\t") table cookbook/loading_tabular.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import load_delimited header, rows, title, legend = load_delimited("data/CerebellumDukeDNaseSeq.pk", header=False, sep="\t") rows[:4] cookbook/loading_tabular.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=False, sep="\t") rows = list(reader("data/CerebellumDukeDNaseSeq.pk")) rows[:4] cookbook/loading_tabular.rst:81: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", limit=2) table cookbook/loading_tabular.rst:93: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t" ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:105: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: reader = FilteringParser( lambda line: float(line[2]) <= 10, with_header=True, sep="\t", negate=True ) table = load_table("data/stats.tsv", reader=reader, digits=1) table cookbook/loading_tabular.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=["Locus", "Ratio"], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(columns=[0, -1], with_header=True, sep="\t") table = load_table("data/stats.tsv", reader=reader) table cookbook/loading_tabular.rst:143: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.parse.table import FilteringParser reader = FilteringParser(with_header=True, sep="\t") data = list(reader("data/stats.tsv")) cookbook/loading_tabular.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data[:2] cookbook/loading_tabular.rst:161: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["A", "B", "C"] rows = [range(3), range(3, 6), range(6, 9), range(9, 12)] table = make_table(header=["A", "B", "C"], data=rows) table cookbook/loading_tabular.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(A=[0, 3, 6], B=[1, 4, 7], C=[2, 5, 8]) table = make_table(data=data) table cookbook/loading_tabular.rst:186: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(header=["C", "A", "B"], data=data) table cookbook/loading_tabular.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", index_name="Locus") table["NP_055852"] cookbook/loading_tabular.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table["NP_055852", "Region"] cookbook/loading_tabular.rst:210: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from pandas import DataFrame from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) df = DataFrame(data=data) table = make_table(data_frame=df) table cookbook/loading_tabular.rst:224: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table(header=["a", "b"], data=[[0, "a"], [3, "c"]]) table cookbook/loading_tabular.rst:236: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table cookbook/loading_tabular.rst:247: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table d2D = { "edge.parent": { "NineBande": "root", "edge.1": "root", "DogFaced": "root", "Human": "edge.0", }, "x": { "NineBande": 1.0, "edge.1": 1.0, "DogFaced": 1.0, "Human": 1.0, }, "length": { "NineBande": 4.0, "edge.1": 4.0, "DogFaced": 4.0, "Human": 4.0, }, } table = make_table( data=d2D, ) table cookbook/loading_tabular.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( header=["abcd", "data"], data=[[range(1, 6), "0"], ["x", 5.0], ["y", None]], missing_data="*", digits=1, ) table cookbook/loading_tabular.rst:294: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data, title="Sample title", legend="a legend") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data = dict(a=[0, 3], b=["a", "c"]) table = make_table(data=data) table.title = "My title" table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") for row in table: print(row) break /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:68: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for row in table: print(row["Locus"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table data = dict(a=[0, 3, 5], b=["a", "c", "d"]) table = make_table(data=data) table.shape[0] == 3 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.shape[1] == 2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.columns /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:107: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Region"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:113: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for name in table.columns: print(name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:128: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table[:2, "Region":] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:135: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table[:2, :1] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:145: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") table.format_column("Ratio", "%.1e") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:158: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv", digits=1, space=2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.space = " " table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:175: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table h = ["name", "A/C", "A/G", "A/T", "C/A"] rows = [["tardigrade", 0.0425, 0.1424, 0.0226, 0.0391]] wrap_table = make_table(header=h, data=rows, max_width=30) wrap_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:184: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wrap_table = make_table(header=h, data=rows, max_width=30, index_name="name") wrap_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:192: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data=dict(a=list(range(10)), b=list(range(10)))) table.head() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:199: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.head(2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:214: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.tail(1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(random=3) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.set_repr_policy(head=2, tail=3) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:241: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.header) table = table.with_new_header("Ratio", "Stat") print(table.header) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:251: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table() table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:258: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["a"] = [1, 3, 5] table.columns["b"] = [2, 4, 6] table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:269: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table = table.with_new_column( "LargeCon", lambda r_v: r_v[0] == "Con" and r_v[1] > 10.0, columns=["Region", "Ratio"], ) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:282: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.array /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:292: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") locus = table.to_list("Locus") locus /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:300: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Locus"].tolist() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:311: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") rows = table.to_list(["Region", "Locus"]) rows /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:324: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.to_dict() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:334: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.columns.to_dict() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:342: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") df = table.to_pandas() df /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:350: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: df = table.to_pandas(categories="Region") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:359: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}, index_name="") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:364: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: contingency = table.to_categorical(["Ts", "Tv"]) contingency /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:369: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: g_test = contingency.G_independence() g_test /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:376: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = make_table(data={"Ts": [31, 58], "Tv": [36, 138], "": ["syn", "nsyn"]}) contingency = table.to_categorical(["Ts", "Tv"], index_name="") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:388: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1 = load_table("data/stats.tsv") table2 = load_table("data/stats.tsv") table = table1.appended(None, table2) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:397: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table1.title = "Data1" table2.title = "Data2" table = table1.appended("Data#", table2, title="") table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:409: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.summed("Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:416: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.columns["Ratio"].sum() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:425: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table all_numeric = make_table( header=["A", "B", "C"], data=[range(3), range(3, 6), range(6, 9), range(9, 12)] ) all_numeric /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:436: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:442: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_numeric.summed(col_sum=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:451: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed = make_table( header=["A", "B", "C"], data=[["*", 1, 2], [3, "*", 5], [6, 7, "*"]] ) mixed /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:460: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(strict=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:466: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mixed.summed(col_sum=False, strict=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:475: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") sub_table = table.filtered(lambda x: x < 10.0, columns="Ratio") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:483: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:490: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sub_table = table.filtered("Ratio < 10.0 and Region == 'NonCon'") sub_table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:500: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: big_numeric = all_numeric.filtered_by_column(lambda x: sum(x) > 20) big_numeric /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:508: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.sorted(columns="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:516: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns="Ratio", reverse="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:523: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.sorted(columns=["Region", "Ratio"], reverse="Ratio") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:530: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list("Region") raw /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:539: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") raw = table.to_list(["Locus", "Region"]) raw /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:548: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.distinct_values("Region") == set(["NonCon", "Con"]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:556: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") assert table.count("Region == 'NonCon' and Ratio > 1") == 1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:566: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table table = make_table( data=dict(A=["a", "b", "b", "b", "a"], B=["c", "c", "c", "c", "d"]) ) unique = table.count_unique("A") type(unique) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:576: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:582: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unique = table.count_unique(["A", "B"]) unique /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:587: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: r = unique.to_table() r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:597: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rows = [ ["NP_004893", True], ["NP_005079", True], ["NP_005500", False], ["NP_055852", False], ] region_type = make_table(header=["Locus", "LargeCon"], data=rows) stats_table = load_table("data/stats.tsv") new = stats_table.joined(region_type, columns_self="Locus") new /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:617: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_table header = ["#OTU ID", "14SK041", "14SK802"] rows = [ [-2920, "332", 294], [-1606, "302", 229], [-393, 141, 125], [-2109, 138, 120], ] table = make_table(header=header, rows=rows) table /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:633: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tp = table.transposed(new_column_name="sample", select_as_header="#OTU ID") tp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:643: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="md") print(table) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:655: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv", format="tex") print(table) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:667: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_markdown(justify="ccr")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:675: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_latex(justify="ccr", label="tab:table1")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:685: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst(csv_table=True)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:695: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table( "data/stats.tsv", title="Some stats.", legend="Derived from something." ) print(table.to_rst()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:707: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") print(table.to_string(format="latex")) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:717: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: rows = [ ["1", 100, 101, 1.123], ["1", 101, 102, 1.123], ["1", 102, 103, 1.123], ["1", 103, 104, 1.123], ["1", 104, 105, 1.123], ["1", 105, 106, 1.123], ["1", 106, 107, 1.123], ["1", 107, 108, 1.123], ["1", 108, 109, 1], ["1", 109, 110, 1], ["1", 110, 111, 1], ["1", 111, 112, 1], ["1", 112, 113, 1], ["1", 113, 114, 1], ["1", 114, 115, 1], ["1", 115, 116, 1], ["1", 116, 117, 1], ["1", 117, 118, 1], ["1", 118, 119, 2], ["1", 119, 120, 2], ["1", 120, 121, 2], ["1", 150, 151, 2], ["1", 151, 152, 2], ["1", 152, 153, 2], ["1", 153, 154, 2], ["1", 154, 155, 2], ["1", 155, 156, 2], ["1", 156, 157, 2], ["1", 157, 158, 2], ["1", 158, 159, 2], ["1", 159, 160, 2], ["1", 160, 161, 2], ] bgraph = make_table(header=["chrom", "start", "end", "value"], rows=rows) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:756: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bgraph.head() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:762: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print( bgraph.to_string( format="bedgraph", name="test track", description="test of bedgraph", color=(255, 0, 0), digits=0, ) ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:777: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_table table = load_table("data/stats.tsv") straight_html = table.to_html() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:789: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.format.table import known_formats known_formats /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:798: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table.write("stats_tab.tex", justify="ccr", label="tab:table1") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:807: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: table = load_table("data/stats.tsv") table.write("stats_tab.txt", sep="\t") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/tables.rst:814: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pathlib for name in ("stats_tab.txt", "stats_tab.tex"): p = pathlib.Path(name) if p.exists(): p.unlink() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k cookbook/union_dict.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.a cookbook/union_dict.rst:20: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data["a"] cookbook/union_dict.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.d cookbook/union_dict.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data.b |= {"d": 25} data.b cookbook/union_dict.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b.union({"d": [25]}) cookbook/union_dict.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: data.b {"c": 24, "d": [25]} cookbook/union_dict.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: KeyError from cogent3.util.union_dict import UnionDict data = UnionDict(a=2, b={"c": 24, "d": [25]}) data["k"] cookbook/union_dict.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: AttributeError data.k /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy def DiffOmega(omega): def omega_from_S(S): omega_est = S / (1 - numpy.e ** (-1 * S)) return abs(omega - omega_est) ** 2 return omega_from_S omega = 0.1 f = DiffOmega(omega) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.optimisers import maximise, minimise S = minimise( f, # the function xinit=1.0, # the initial value bounds=(-100, 100), # [lower,upper] bounds for the parameter local=True, # just local optimisation, not Simulated Annealing show_progress=False, ) assert 0.0 <= f(S) < 1e-6 print("S=%.4f" % S) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: TypeError from cogent3.util.misc import iterable my_var = 10 for i in my_var: print("will not work") for i in iterable(my_var): print(i) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:75: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import curry def foo(x, y): """Some function""" return x + y bar = curry(foo, 5) print(bar.__doc__) bar(10) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_iterable can_iter = [1, 2, 3, 4] cannot_iter = 1.234 is_iterable(can_iter) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:100: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_iterable(cannot_iter) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import is_char class foo: pass is_char("a") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:118: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char("ab") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:122: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: is_char(foo()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:131: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import recursive_flatten l = [[[[1, 2], "abcde"], [5, 6]], [7, 8], [9, 10]] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: recursive_flatten(l) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:146: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import not_list_tuple not_list_tuple(1) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:152: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple([1]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: not_list_tuple("ab") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import add_lowercase d = {"A": 5, "B": 6, "C": 7, "foo": 8, 42: "life"} add_lowercase(d) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:177: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from numpy import array from cogent3.util.misc import DistanceFromMatrix m = array([[1, 2, 3], [4, 5, 6], [7, 8, 9]]) f = DistanceFromMatrix(m) f(0, 0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:187: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(1, 2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:196: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ClassChecker class not_okay(object): pass no = not_okay() class okay(object): pass o = okay() class my_dict(dict): pass md = my_dict() cc = ClassChecker(str, okay, dict) o in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:217: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: no in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:221: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: 5 in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:225: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: {"a": 5} in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:229: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: "asasas" in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:233: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: md in cc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:242: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import Delegator class ListAndString(list, Delegator): def __init__(self, items, string): Delegator.__init__(self, string) for i in items: self.append(i) ls = ListAndString([1, 2, 3], "ab_cd") len(ls) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:255: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls[0] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:259: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.upper() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:263: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.split("_") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:272: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import FunctionWrapper f = FunctionWrapper(str) f /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:279: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: f(123) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:290: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from cogent3.util.misc import ConstraintError /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:295: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.util.misc import ConstrainedDict d = ConstrainedDict({"a": 1, "b": 2, "c": 3}, constraint="abc") d /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/useful_utilities.rst:302: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: ConstraintError d["d"] = 5 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst:4: WARNING: duplicate label union_dict, other instance in /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/union_dict.rst /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:10: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import available_codes available_codes() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/cookbook/what_codes.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_code gc = get_code(4) gc /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:18: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") aln = aln.no_degenerates(motif_length=3) aln = aln.get_translation() aln = aln[:100] # for compute speed in testing the documentation coevo = aln.coevolution(show_progress=False, drawable="heatmap") coevo.drawable.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png" coevo.drawable.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="violin") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: coevo = aln.coevolution(show_progress=False, drawable="box") coevo.drawable.show(width=300) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-coevolution.rst:11: WARNING: TODO entry found: add citation for NMI /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_unaligned_seqs seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna") draw = seqs.dotplot() draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png" draw.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:57: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400) draw.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-1.rst:11: WARNING: TODO entry found: Change dotplot ref to a citation /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import get_app loader = get_app("load_json") seqs = loader("data/tp53.json") dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600) dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png" dp.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: help(dp.remove_track) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-2.rst:41: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: dp.remove_track(left_track=True) dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: from cogent3 import load_aligned_seqs, get_app seqs = load_aligned_seqs("data/brca1.fasta", moltype="dna").degap() seqs = seqs.take_seqs( ["LeafNose", "FalseVamp", "RoundEare", "Sloth", "Anteater", "HairyArma"] ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide", indel_rate=1e-2, indel_length=1e-9) aln = aligner(seqs) dp = aln[2200:2500].dotplot("HairyArma", "RoundEare") dp.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:38: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-3.png" dp.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aligner = get_app("progressive_align", "nucleotide") aln = aligner(seqs) aln[2200:2500].dotplot("HairyArma", "RoundEare").show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-dotplot-3.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :raises: aln[2300:2500] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs aln = load_aligned_seqs("data/brca1.fasta", moltype="dna") counts = aln.count_gaps_per_seq(unique=True) counts[10: 20] # limiting the width of the displayed output /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="bar") counts.drawable.show(width=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-gaps-per-seq.png" counts.drawable.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="violin") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-gaps-per-seq.rst:51: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: counts = aln.count_gaps_per_seq(unique=True, drawable="box") counts.drawable.show(width=300, height=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_aligned_seqs, make_seq s1 = make_seq("TGATGTAAGGTAGTT", name="s1", moltype="dna") s2 = make_seq("--CTGGAAGGGT---", name="s2", moltype="dna") seqs = make_aligned_seqs(data=[s1, s2], array_align=False, moltype="dna") draw = seqs.information_plot(window=2, include_gap=True) draw.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1.fasta", moltype="protein") fig = aln.information_plot(stat="median") fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-info-plot.rst:37: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-info-plot.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.parse import jaspar _, pwm = jaspar.read("data/tbp.jaspar") freqarr = pwm.to_freq_array() freqarr[:5] # illustrating the contents of the MotifFreqsArray /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: logo = freqarr.logo() logo.show(height=250, width=500) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:30: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-seqlogo.png" logo.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna") l = aln[:311].seqlogo(height=300, width=500, wrap=60, vspace=0.05) l.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_aln-seqlogo.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aa = aln.get_translation(incomplete_ok=True)[:120] logo = aa.seqlogo(width=500, height=300, wrap=50, vspace=0.1) logo.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:16: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_seq seq = load_seq("data/C-elegans-chromosome-I.gb", moltype="dna") seq /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:25: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seq = seq[25000:35000] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:31: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable() fig.show(height=400, width=700) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:43: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig = seq.get_drawable(biotype=("gene", "CDS", "mRNA")) fig.show(height=300, width=650) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/aln/plot_seq-features.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_seq-features.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(style="angular", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-angular.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-angular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("circular", width=600, height=600) fig.scale_bar = "top right" fig.label_pad = 0.1 fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta", width=2), ) fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:39: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.3 fig.show(width=650, height=600) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-circular.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-circular.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:9: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure("radial", width=600, height=600) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:19: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-radial.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-radial.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.label_pad = 0.23 fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() ens_tree = reader("data/GN-tree.json") fig = ens_tree.get_figure(width=600, height=600) fig.scale_bar = "top right" fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:24: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-square.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.style_edges( "AfricanEl", tip2="Manatee", legendgroup="Afrotheria", line=dict(color="magenta"), ) fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-square.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.contemporaneous = True fig.show() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:11: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.app import io reader = io.load_json() tree = reader("data/tree-with-support.json") fig = tree.get_figure(show_support=True, threshold=0.8) fig.scale_bar = None fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: fig.support_xshift = 15 fig.support_yshift = 0 fig.show(width=500, height=400) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/draw/tree/plot_tree-support.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: outpath = set_working_directory.get_thumbnail_dir() / "plot_tree-support.png" fig.write(outpath) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_aligned_seqs, make_unaligned_seqs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:14: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: seqs = { "hum": "AAGCAGATCCAGGAAAGCAGCGAGAATGGCAGCCTGGCCGCGCGCCAGGAGAGGCAGGCCCAGGTCAACCTCACT", "mus": "AAGCAGATCCAGGAGAGCGGCGAGAGCGGCAGCCTGGCCGCGCGGCAGGAGAGGCAGGCCCAAGTCAACCTCACG", "rat": "CTGAACAAGCAGCCACTTTCAAACAAGAAA", } unaligned_DNA = make_unaligned_seqs(seqs, moltype="dna") unaligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: unaligned_aa = unaligned_DNA.get_translation() unaligned_aa /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/align_codons_to_protein.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aligned_aa_seqs = { "hum": "KQIQESSENGSLAARQERQAQVNLT", "mus": "KQIQESGESGSLAARQERQAQVNLT", "rat": "LNKQ------PLS---------NKK", } aligned_aa = make_aligned_seqs(aligned_aa_seqs, moltype="protein") aligned_DNA = aligned_aa.replace_seqs(unaligned_DNA) aligned_DNA /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.cluster.UPGMA import upgma from cogent3.evolve import distance /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:29: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/test.paml") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster = upgma(d.get_pairwise_distances()) print(mycluster.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mycluster.write("test_upgma.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_UPGMA_cluster.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_upgma.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.phylo import nj /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=get_model("HKY85")) d.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree = nj.nj(d.get_pairwise_distances(), show_progress=False) print(mytree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:47: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: mytree.write("test_nj.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_neigbourjoining_tree.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("test_nj.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs from cogent3.evolve import distance /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) d.get_pairwise_distances() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:44: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: d.write("dists_for_phylo.phylip", format="phylip") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:61: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os for file_name in "dists_for_phylo.phylip", "dists_for_phylo.pickle": os.remove(file_name) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/calculate_pairwise_distances.rst:48: WARNING: TODO entry found: write out in json format /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:42: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: tf = get_model("GY94") nf = get_model("MG94GTR") cnf = get_model("CNFGTR") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree aln = load_aligned_seqs("data/primate_brca1.fasta", moltype="dna") tree = load_tree("data/primate_brca1.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:64: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_param_rule("omega", is_constant=True, value=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: optimiser_args = dict( local=True, max_restarts=5, tolerance=1e-8, show_progress=False ) lf.set_alignment(aln) lf.optimise(**optimiser_args) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:92: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: neutral_lnL = lf.get_log_likelihood() neutral_nfp = lf.get_num_free_params() lf.set_param_rule("omega", is_constant=False) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:104: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from scipy.stats.distributions import chi2 LR = 2 * (non_neutral_lnL - neutral_lnL) df = non_neutral_nfp - neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:114: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Chimpanzee", "Human"], outgroup_name="Galago", clade=True ) lf.optimise(**optimiser_args) lf chimp_human_clade_lnL = lf.get_log_likelihood() chimp_human_clade_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:124: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (chimp_human_clade_lnL - non_neutral_lnL) df = chimp_human_clade_nfp - non_neutral_nfp print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:137: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = cnf.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) lf.optimise(**optimiser_args) non_neutral_lnL = lf.get_log_likelihood() non_neutral_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:149: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: annot_tree = lf.get_annotated_tree() omega_mle = lf.get_param_value("omega") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:156: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf = cnf.make_likelihood_function( annot_tree, bins=["neutral", "adaptive"], digits=2, space=3 ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:164: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: epsilon = 1e-6 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:170: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("omega", bin="neutral", upper=1, init=omega_mle) rate_lf.set_param_rule( "omega", bin="adaptive", lower=1 + epsilon, upper=100, init=1 + 2 * epsilon ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:179: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_param_rule("bprobs", init=[1 - epsilon, epsilon]) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:185: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: rate_lf.set_alignment(aln) rate_lf.optimise(**optimiser_args) rate_lnL = rate_lf.get_log_likelihood() rate_nfp = rate_lf.get_num_free_params() LR = 2 * (rate_lnL - non_neutral_lnL) df = rate_nfp - non_neutral_nfp rate_lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:195: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(chi2.sf(LR, df)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:201: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pp = rate_lf.get_bin_probs() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/codon_models.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: from IPython.core.display import HTML from numpy import array from cogent3 import make_table header = ["Site Class", "Proportion", "Background Edges", "Foreground Edges"] data = { "Site Class": array(["0", "1", "2a", "2b"], dtype=" 1", "0 < omega0 < 1"], dtype=" 1.8: tips_to_delete.append(n) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:121: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: for n in tips_to_delete: n.parent.remove(n) complex_tree.prune() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/manipulating_tree_nodes.rst:129: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(complex_tree.ascii_art(show_internal=False)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: al = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("MG94GTR") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=2) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(al) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(global_tolerance=1.0, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:71: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(local=True, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:77: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:83: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: at = lf.get_annotated_tree() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/neutral_test.rst:97: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(f"Likelihood ratio statistic = {LR}") print(f"degrees-of-freedom = {df}") print(f"probability = {P}") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve import bootstrap from cogent3.evolve.models import HKY85 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_alt_function(): t = load_tree("data/test.tree") sm = HKY85() return sm.make_likelihood_function(t) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: def create_null_function(): lf = create_alt_function() # set the local clock for humans & howler monkey lf.set_local_clock("Human", "HowlerMon") return lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP = bootstrap.EstimateProbability( create_null_function(), create_alt_function(), aln ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:60: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.set_num_replicates(5) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:66: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: estimateP.run(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: p = estimateP.get_estimated_prob() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/parametric_bootstrap.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("%.2f, %.2f" % estimateP.get_observed_lnL()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:26: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import numpy numpy.random.seed(11) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import numpy t = numpy.arange(0, 10, 0.1) n = numpy.random.randn(len(t)) nse = numpy.convolve(n, numpy.exp(-t / 0.05)) * 0.1 nse = nse[: len(t)] sig = numpy.sin(2 * numpy.pi * t) + nse /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:48: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import dft pwr, period = dft(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: pwr = abs(pwr) max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:69: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr pwr, period = auto_corr(sig) print(period) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: max_pwr, max_period = sorted(zip(pwr, period))[-1] print(max_pwr, max_period) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:89: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: s = ( "ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG" "GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT" "AATTTTTAACCGCGGAATTGCGTC" ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"]) symbols = seq_to_symbols(s) len(symbols) == len(s) symbols /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:110: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import ipdft powers, periods = ipdft(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:117: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:123: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import auto_corr, hybrid powers, periods = auto_corr(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:134: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = hybrid(symbols) powers /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:139: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: periods /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:151: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel pwr = goertzel(sig, 10) print(pwr) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers, periods = auto_corr(symbols) llim = 2 period5 = 5 - llim periods[period5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:172: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: powers[period5] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:178: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import goertzel period = 4 power = goertzel(symbols, period) ipdft_powers, periods = ipdft(symbols) ipdft_power = abs(ipdft_powers[period - llim]) round(power, 6) == round(ipdft_power, 6) power /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:191: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: power = hybrid(symbols, period=period) power /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:204: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Goertzel goertzel_calc = Goertzel(len(sig), period=10) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:212: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap obs_stat, p = blockwise_bootstrap( sig, calc=goertzel_calc, block_size=10, num_reps=1000 ) print(obs_stat) print(p) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:230: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.period import Hybrid hybrid_calculator = Hybrid(len(s), period=4) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:240: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import SeqToSymbols seq_to_symbols = SeqToSymbols(["AA", "TT", "AT"], length=len(s)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/period_estimation.rst:248: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3.maths.stats.period import blockwise_bootstrap stat, p = blockwise_bootstrap( s, calc=hybrid_calculator, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbols, ) print(stat) p < 0.1 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import pickle from cogent3 import load_aligned_seqs from cogent3.evolve import distance from cogent3.evolve.fast_distance import DistanceMatrix from cogent3.evolve.models import HKY85 al = load_aligned_seqs("data/long_testseqs.fasta") d = distance.EstimateDistances(al, submodel=HKY85()) d.run(show_progress=False) with open("dists_for_phylo.pickle", "wb") as f: pickle.dump(d.get_pairwise_distances(), f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:32: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import pickle from cogent3.phylo import least_squares /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: with open("dists_for_phylo.pickle", "rb") as f: dists = pickle.load(f) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:49: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls = least_squares.WLS(dists) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:55: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls_distance_matrix = least_squares.WLS(DistanceMatrix(dists)) ls_pairwise_matrix = least_squares.WLS(dists.to_dict()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:67: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: score, tree = ls.trex(a=5, k=1, show_progress=False) assert score < 1e-4 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:79: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: trees = ls.trex(a=5, k=5, return_all=True, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:85: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(len(trees)) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls_stats = [tree[0] for tree in trees] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:103: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t1 = trees[0][1].balanced() t2 = trees[1][1].balanced() print(t1.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:109: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(t2.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:120: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import make_tree query_tree = make_tree( "((Human:.2,DogFaced:.2):.3,(NineBande:.1, Mouse:.5):.2,HowlerMon:.1)" ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:130: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: ls.evaluate_tree(query_tree) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:136: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: wls, t = ls.evaluate_topology(query_tree) assert "%.4f" % wls == "0.0084" /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/phylo_by_ls.rst:148: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import os os.remove("dists_for_phylo.pickle") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:15: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_tree from cogent3.evolve.substitution_model import TimeReversibleNucleotide /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:22: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide(equal_motif_probs=True) tree = load_tree("data/test.tree") lf = model.make_likelihood_function(tree) lf.set_param_rule("length", value=0.6, is_constant=True) aln1 = lf.simulate_alignment(sequence_length=10000) lf.set_param_rule("length", value=0.2, is_constant=True) aln2 = lf.simulate_alignment(sequence_length=10000) aln3 = aln1 + aln2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="free" ) lf = model.make_likelihood_function(tree, bins=2, digits=2, space=3) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: bprobs = [t for t in lf.get_statistics() if "bin" in t.title][0] bprobs /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/rate_heterogeneity.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: model = TimeReversibleNucleotide( equal_motif_probs=True, ordered_param="rate", distribution="gamma" ) lf = model.make_likelihood_function(tree, bins=4) lf.set_param_rule("bprobs", is_constant=True) lf.set_alignment(aln3) lf.optimise(local=True, max_restarts=2, show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import get_model from scipy.stats.distributions import chi2 /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:21: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: aln = load_aligned_seqs("data/long_testseqs.fasta") t = load_tree(filename="data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:28: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("HKY85") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:34: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = sm.make_likelihood_function(t, digits=2, space=3) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:40: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_local_clock("Human", "HowlerMon") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:46: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:52: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:58: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("clock") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:65: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: null_lnL = lf.get_log_likelihood() null_nfp = lf.get_num_free_params() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:72: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("length", is_independent=True) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:78: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.optimise(show_progress=False) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:84: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_name("non clock") lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: LR = 2 * (lf.get_log_likelihood() - null_lnL) df = lf.get_num_free_params() - null_nfp P = chi2.sf(LR, df) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/relative_rate.rst:99: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print("Likelihood ratio statistic = ", LR) print("degrees-of-freedom = ", df) print("probability = ", P) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, load_tree from cogent3.evolve.models import MG94HKY aln = load_aligned_seqs("data/long_testseqs.fasta") tree = load_tree("data/test.tree") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = MG94HKY() lf = sm.make_likelihood_function(tree, digits=2, space=3) lf.set_alignment(aln) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:35: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: print(tree.ascii_art()) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["DogFaced", "Mouse"], outgroup_name="Human", init=2.0, clade=True, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:73: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", init=1.0) lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=False, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:91: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:96: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", init=2.0, stem=True, clade=True, ) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:160: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: lf.set_param_rule("omega", init=1.0) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:165: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, value=1.0, is_constant=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:180: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_constant=False, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:194: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule( "omega", tip_names=["Human", "HowlerMon"], outgroup_name="Mouse", clade=True, is_independent=True, ) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/scope_model_params_on_trees.rst:208: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf.set_param_rule("omega", is_independent=True) lf.optimise(local=True, show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simple.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_tree from cogent3.evolve.models import get_model model = get_model("HKY85") aln = load_aligned_seqs("data/primate_cdx2_promoter.fasta") tree = make_tree(tip_names=aln.names) lf = model.make_likelihood_function(tree) lf.set_alignment(aln) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:8: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: import sys from cogent3 import make_tree from cogent3.evolve.models import get_model /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:17: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: t = make_tree("(a:0.4,b:0.3,(c:0.15,d:0.2)edge.0:0.1);") /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:23: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: sm = get_model("F81") lf = sm.make_likelihood_function(t) lf.set_constant_lengths() lf.set_motif_probs(dict(A=0.1, C=0.2, G=0.3, T=0.4)) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/simulate_alignment.rst:33: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: simulated = lf.simulate_alignment(sequence_length=1000) simulated /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:1: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: :hide-code: import set_working_directory /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:13: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: from cogent3 import load_aligned_seqs, make_table, make_tree from cogent3.evolve.models import HKY85 from scipy.stats.distributions import chi2 from cogent3.recalculation.scope import ALL, EACH aln = load_aligned_seqs("data/long_testseqs.fasta") half = len(aln) // 2 aln1 = aln[:half] aln2 = aln[half:] /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:27: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: loci_names = ["1st-half", "2nd-half"] loci = [aln1, aln2] tree = make_tree(tip_names=aln.names) mod = HKY85() /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:36: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: lf = mod.make_likelihood_function(tree, loci=loci_names, digits=2, space=3) lf.set_param_rule("length", is_independent=False) lf.set_param_rule("kappa", loci=ALL) lf.set_alignment(loci) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:45: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: all_lnL = lf.lnL all_nfp = lf.nfp lf.set_param_rule("kappa", loci=EACH) lf.optimise(show_progress=False) lf /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:53: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: each_lnL = lf.lnL each_nfp = lf.nfp LR = 2 * (each_lnL - all_lnL) df = each_nfp - all_nfp /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/examples/testing_multi_loci.rst:62: ERROR: Unknown directive type "jupyter-execute". .. jupyter-execute:: make_table( header=["LR", "df", "p"], rows=[[LR, df, chi2.sf(LR, df)]], digits=2, space=3, ) /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/templates/class.rst:3: ERROR: Error in "currentmodule" directive: maximum 1 argument(s) allowed, 3 supplied. .. currentmodule:: {{ module }} WARNING: invalid signature for autoclass ('{{ name }}') WARNING: don't know which module to import for autodocumenting '{{ name }}' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name) looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.Alignment.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.ArrayAlignment.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alignment/classes/cogent3.core.alignment.SequenceCollection.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/alphabet/classes/cogent3.core.alphabet.Alphabet.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation/classes/cogent3.core.annotation.Feature.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.BasicAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.GenbankAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/annotation_db/classes/cogent3.core.annotation_db.GffAnnotationDb.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/genetic_code/classes/cogent3.core.genetic_code.GeneticCode.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/moltype/classes/cogent3.core.moltype.MolType.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.DnaSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.ProteinSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/sequence/classes/cogent3.core.sequence.RnaSequence.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.parse.table.FilteringParser.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.util.table.Columns.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/table/classes/cogent3.util.table.Table.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/api/tree/classes/cogent3.core.tree.PhyloNode.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/app_cookbook/sample-trim-stops.rst: WARNING: document isn't included in any toctree /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/doc/app/index-help.rst: WARNING: document isn't included in any toctree 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg/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/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp -r /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/tests/data /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build I: pybuild base:311: cd /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip' ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build configfile: pyproject.toml plugins: cov-5.0.0, typeguard-4.4.1, anyio-4.6.0, xdist-3.6.1 collected 11030 items / 4 deselected / 11026 selected tests/test_align/test_align.py ...............................X... 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[ 93%] tests/test_maths/test_util.py ....... [ 93%] tests/test_parse/test_blast.py .............. [ 93%] tests/test_parse/test_blast_xml.py ............... [ 93%] tests/test_parse/test_cigar.py ..... [ 93%] tests/test_parse/test_clustal.py ......... [ 93%] tests/test_parse/test_dialign.py ... [ 93%] tests/test_parse/test_ebi.py ........................................... [ 94%] ............ [ 94%] tests/test_parse/test_fasta.py ............................... [ 94%] tests/test_parse/test_gbseq.py . [ 94%] tests/test_parse/test_genbank.py ....................... [ 94%] tests/test_parse/test_gff.py ............ [ 94%] tests/test_parse/test_greengenes.py .... [ 94%] tests/test_parse/test_locuslink.py ............. [ 94%] tests/test_parse/test_ncbi_taxonomy.py .................. [ 95%] tests/test_parse/test_nexus.py ............... [ 95%] tests/test_parse/test_pamlmatrix.py . [ 95%] tests/test_parse/test_phylip.py ... [ 95%] tests/test_parse/test_psl.py ... [ 95%] tests/test_parse/test_pwm_parsers.py .. [ 95%] tests/test_parse/test_rdb.py .................. [ 95%] tests/test_parse/test_record.py ........................................ [ 95%] .. [ 95%] tests/test_parse/test_record_finder.py ................. [ 96%] tests/test_parse/test_tinyseq.py . [ 96%] tests/test_parse/test_tree.py ................... [ 96%] tests/test_parse/test_unigene.py .... [ 96%] tests/test_phylo.py .................. [ 96%] tests/test_recalculation.py . [ 96%] tests/test_tree_distance.py ............................... [ 96%] tests/test_util/test_deserialise.py .................................... [ 97%] .. [ 97%] tests/test_util/test_dictarray.py ............................... [ 97%] tests/test_util/test_io.py ...................................ssss.sss [ 97%] tests/test_util/test_misc.py ........................................... [ 98%] ............................................ [ 98%] tests/test_util/test_parallel.py ... [ 98%] tests/test_util/test_recode_alignment.py ............... [ 98%] tests/test_util/test_table.py .......................................... [ 99%] ............................................................... [ 99%] tests/test_util/test_transform.py ..... [ 99%] tests/test_util/test_union_dict.py ........... [ 99%] tests/test_util/test_warning.py ......................... [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated tests/test_util/test_deserialise.py::test_deser_annotated_aln /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/.pybuild/cpython3_3.12_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning: class Map is discontinued and will be removed in version 2024.6 reason='Replaced by IndelMap and FeatureMap' -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html = 11014 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 8 warnings in 305.87s (0:05:05) = create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild debian/rules execute_after_dh_installdocs make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' 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/reproducible-path/python-cogent-2024.5.7a1+dfsg' debian/rules override_dh_sphinxdoc-indep make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_sphinxdoc -i dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/_static/design-tabs.js sed -i 's%https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js%file:///usr/share/javascript/requirejs/require.min.js%' `find /build/reproducible-path/python-cogent-2024.5.7a1+dfsg/debian/python-cogent-doc/usr/share/doc/python-cogent-doc/html/ -type f -name "*.html"` make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_sphinxdoc -O--buildsystem=pybuild -Npython-cogent-doc dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_python3 --shebang=/usr/bin/python3 I: dh_python3 pydist:339: Ignoring complex environment marker: numba>0.53; python_version>='3.9' and python_version <'3.12' I: dh_python3 pydist:339: Ignoring complex environment marker: numba>0.54; python_version>='3.10' and python_version <'3.12' make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -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/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild debian/rules execute_after_dh_shlibdeps make[1]: Entering directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_numpy3 make[1]: Leaving directory '/build/reproducible-path/python-cogent-2024.5.7a1+dfsg' dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-cogent3: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package python-cogent-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-cogent3' in '../python3-cogent3_2024.5.7a1+dfsg-3_amd64.deb'. dpkg-deb: building package 'python-cogent-doc' in '../python-cogent-doc_2024.5.7a1+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../python-cogent_2024.5.7a1+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../python-cogent_2024.5.7a1+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1098549/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1098549/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/1098549 and its subdirectories I: Current time: Sun Dec 14 04:19:14 +14 2025 I: pbuilder-time-stamp: 1765635554