Fri May 17 21:30:23 UTC 2024 I: starting to build python-cooler/trixie/amd64 on jenkins on '2024-05-17 21:30' Fri May 17 21:30:23 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/6148/console.log Fri May 17 21:30:23 UTC 2024 I: Downloading source for trixie/python-cooler=0.9.3-1 --2024-05-17 21:30:23-- http://deb.debian.org/debian/pool/main/p/python-cooler/python-cooler_0.9.3-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2825 (2.8K) [text/prs.lines.tag] Saving to: ‘python-cooler_0.9.3-1.dsc’ 0K .. 100% 403M=0s 2024-05-17 21:30:23 (403 MB/s) - ‘python-cooler_0.9.3-1.dsc’ saved [2825/2825] Fri May 17 21:30:23 UTC 2024 I: python-cooler_0.9.3-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-cooler Binary: python3-cooler, python3-cooler-examples Architecture: any-amd64 arm64 loong64 mips64el ppc64el ia64 ppc64 riscv64 sparc64 alpha all Version: 0.9.3-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/mirnylab/cooler Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/python-cooler Vcs-Git: https://salsa.debian.org/med-team/python-cooler.git Testsuite: autopkgtest Testsuite-Triggers: python3-dask, python3-mock, python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, python3-all, python3-hatchling, python3-hatch-vcs, python3-simplejson , python3-pandas (>= 2.1) , python3-scipy (>= 1.10~) , python3-h5py , python3-asciitree , python3-multiprocess , python3-click , python3-cytoolz , python3-pytest , python3-biopython , python3-pyfaidx , python3-pysam , python3-pairix , python3-yaml , python3-dask Package-List: python3-cooler deb python optional arch=any-amd64,arm64,loong64,mips64el,ppc64el,ia64,ppc64,riscv64,sparc64,alpha python3-cooler-examples deb python optional arch=all Checksums-Sha1: 0c366e6f4af1f4c804981016966dd89f97e1ab20 11357608 python-cooler_0.9.3.orig.tar.gz 98f9d1927283377977b9ef4fc03ea0b9ae2454bc 7460 python-cooler_0.9.3-1.debian.tar.xz Checksums-Sha256: ee4e4ad75f8d7a84f69fd56e174002991a56f6e434a728560cef22ac2b9983c4 11357608 python-cooler_0.9.3.orig.tar.gz 0b6db74add8bc39ec66876f20c56bdd11b0564b8add8ab2b5fe33e35e4ca5584 7460 python-cooler_0.9.3-1.debian.tar.xz Files: 1a4cc67272f996cfc8473a2599ac9e45 11357608 python-cooler_0.9.3.orig.tar.gz 721176874fefd9d8840add50fe95b393 7460 python-cooler_0.9.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCgAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW/4cIOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtGJ6A//fG0qiLncw7p5cH4Fk/bj7K20ewW7euKN224E 96RjBlP/j3spIr2H5bGA3bY/GP2rJ+0mghPwMrWfPftFr+5EuiL9XL7GF0O72UW/ VblfzwJyx2u2MZKKCGSIm3TlnF4iq+icUx/hUT9g7KkiSjdK+4G/dpPji3VetDvt gaM/P7M7wRKDhw0tAo2jTCG5/TFN8FyzTGe5ALRNNo8AAEAVgRTNOFaqy0QCH8Ue aOCDo9hiWo1ANanwjct2Npl5qgA3Q3b94/g6i1J7zG/ZVVfxMZKeiGUgmYN2QpOt M9UPFBNtJCgJNR3QqkvC63NUpsz8OxbToXix+KDKquUULnz0IslWTBwmqCv1bXgC RjzjUjO3kwklYd/lM/OlC8HqZgiVXs1U6FbpXJzYO6eF+rSH4fuzjr40rSGJKbYt a/42VDnifqrp3R/kF4lQelEMcaw64l7asib+pJJFWHi9fXsf7Lag07k/Pqza2jNF GUyPsVOfPvPrUDElTgfLOgPGtY/TCbJbRYjgOXldZqlL9jZyaz2El3lbI3vItE+O wRLbyj6XkhVhNdY6mX7WS1XbbtELu14KSF0UcOez0sznL5LXV6fcmbdj6p3AuycM YbWOg6L1QoH5mDK0aFDyIoYTvmLLmbHrVTLgfa101zPaZhP5hNDlMKDXrDccOXzP 3k1d7gc= =a2rI -----END PGP SIGNATURE----- Fri May 17 21:30:23 UTC 2024 I: Checking whether the package is not for us Fri May 17 21:30:23 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Fri May 17 21:30:23 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Fri May 17 21:47:06 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 17 09:30:26 -12 2024 I: pbuilder-time-stamp: 1715981427 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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-cooler_0.9.3-1.dsc] I: copying [./python-cooler_0.9.3.orig.tar.gz] I: copying [./python-cooler_0.9.3-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Feb 4 19:13:06 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-cooler_0.9.3-1.dsc: no acceptable signature found dpkg-source: info: extracting python-cooler in python-cooler-0.9.3 dpkg-source: info: unpacking python-cooler_0.9.3.orig.tar.gz dpkg-source: info: unpacking python-cooler_0.9.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying exclude_tests_in_need_of_ipytree.patch dpkg-source: info: applying skip-http-connection.patch dpkg-source: info: applying pytest-coverage.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3598938/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='85623037200b4f69ac96ee4d04e7f33c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='3598938' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AfJycBBk/pbuilderrc_hEiK --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AfJycBBk/b1 --logfile b1/build.log python-cooler_0.9.3-1.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 17 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3598938/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: debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, python3-all, python3-hatchling, python3-hatch-vcs, python3-simplejson, python3-pandas (>= 2.1), python3-scipy (>= 1.10~), python3-h5py, python3-asciitree, python3-multiprocess, python3-click, python3-cytoolz, python3-pytest, python3-biopython, python3-pyfaidx, python3-pysam, python3-pairix, python3-yaml, python3-dask dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python 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; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-hatchling; however: Package python3-hatchling is not installed. pbuilder-satisfydepends-dummy depends on python3-hatch-vcs; however: Package python3-hatch-vcs is not installed. pbuilder-satisfydepends-dummy depends on python3-simplejson; however: Package python3-simplejson is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas (>= 2.1); however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy (>= 1.10~); however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-h5py; however: Package python3-h5py is not installed. pbuilder-satisfydepends-dummy depends on python3-asciitree; however: Package python3-asciitree is not installed. pbuilder-satisfydepends-dummy depends on python3-multiprocess; however: Package python3-multiprocess is not installed. pbuilder-satisfydepends-dummy depends on python3-click; however: Package python3-click is not installed. pbuilder-satisfydepends-dummy depends on python3-cytoolz; however: Package python3-cytoolz is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pairix; however: Package python3-pairix is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-dask; however: Package python3-dask 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhdf5-103-1t64{a} libhdf5-hl-100t64{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libsub-override-perl{a} libsz2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} pybuild-plugin-pyproject{a} python3{a} python3-all{a} python3-asciitree{a} python3-biopython{a} python3-build{a} python3-cairo{a} python3-chardet{a} python3-click{a} python3-cloudpickle{a} python3-colorama{a} python3-cytoolz{a} python3-dask{a} python3-dateutil{a} python3-decorator{a} python3-dill{a} python3-distutils{a} python3-freetype{a} python3-fsspec{a} python3-h5py{a} python3-h5py-serial{a} python3-hatch-vcs{a} python3-hatchling{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-installer{a} python3-lib2to3{a} python3-locket{a} python3-minimal{a} python3-more-itertools{a} python3-multiprocess{a} python3-numpy{a} python3-packaging{a} python3-pairix{a} python3-pandas{a} python3-pandas-lib{a} python3-partd{a} python3-pathspec{a} python3-pil{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyfaidx{a} python3-pyproject-hooks{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-setuptools-scm{a} python3-simplejson{a} python3-six{a} python3-toml{a} python3-toolz{a} python3-trove-classifiers{a} python3-typing-extensions{a} python3-tz{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra git krb5-locales libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-blosc python3-bottleneck python3-bs4 python3-distributed python3-dropbox python3-fusepy python3-html5lib python3-jinja2 python3-libarchive-c python3-lxml python3-matplotlib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-paramiko python3-pygit2 python3-pygments python3-requests python3-tables python3-zmq shared-mime-info wget xdg-user-dirs 0 packages upgraded, 177 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After unpacking 485 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.3-1 [809 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.3-1 [2139 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240422 [107 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 62 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 82 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-5 [433 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get: 100 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b1 [35.3 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b1 [10.4 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.3-1 [1951 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [110 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b1 [52.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get: 124 http://deb.debian.org/debian trixie/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 python3-build all 1.2.1-1 [34.1 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.3-1 [659 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.11.8-1 [1056 B] Get: 134 http://deb.debian.org/debian trixie/main amd64 python3-asciitree all 0.3.3-4 [5612 B] Get: 135 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-8 [5466 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 141 http://deb.debian.org/debian trixie/main amd64 python3-reportlab all 4.2.0-2 [1149 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 python3-click all 8.1.7-1 [94.0 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 python3-cloudpickle all 3.0.0-2 [25.4 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 python3-toolz all 0.12.1-1 [43.9 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 python3-cytoolz amd64 0.12.2-2 [451 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 python3-fsspec all 2024.3.1-1 [115 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 python3-locket all 1.0.0-2 [5820 B] Get: 152 http://deb.debian.org/debian trixie/main amd64 python3-partd all 1.4.1-1 [15.2 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 python3-dask all 2024.1.1+dfsg-1 [930 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python3-dill all 0.3.8-1 [81.7 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.10.0-1+b3 [1400 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-trove-classifiers all 2024.1.31-1 [9968 B] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-hatchling all 1.24.2-1 [53.2 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-multiprocess all 0.70.16-2 [105 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-pairix amd64 0.3.7-7 [46.0 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [7882 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.1.4+dfsg-8 [3015 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-1 [4654 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 7.4.4-3 [239 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-simplejson amd64 3.19.2-1+b1 [69.4 kB] Fetched 111 MB in 15s (7557 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_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 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-cooler-0.9.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-cooler_0.9.3-1_source.changes dpkg-buildpackage: info: source package python-cooler dpkg-buildpackage: info: source version 0.9.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --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-cooler-0.9.3/.pybuild/cpython3_3.12_cooler * Building wheel... Successfully built cooler-0.9.3-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler * Building wheel... Successfully built cooler-0.9.3-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.11 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.3, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build configfile: pyproject.toml collected 136 items tests/test_api.py .......... [ 7%] tests/test_balance.py .... [ 10%] tests/test_cli.py .s..s..... [ 17%] tests/test_cli_export.py .Fs [ 19%] tests/test_cli_fileops.py .... [ 22%] tests/test_cli_ingest.py FFFFFFFFFFF [ 30%] tests/test_cli_ops.py FFF. [ 33%] tests/test_core.py ........... [ 41%] tests/test_create.py Fs.F..FFF [ 48%] tests/test_create_ingest.py FFFFFFFFFFF.FFF [ 59%] tests/test_create_sanitize.py ........ [ 65%] tests/test_fileops.py ........s.. [ 73%] tests/test_parallel.py ... [ 75%] tests/test_reduce.py FFFFFFFFFF [ 83%] tests/test_util.py .........s............. [100%] =================================== FAILURES =================================== __________________________________ test_dump ___________________________________ def test_dump(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke(dump, [f_in]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-t", "chroms", "--columns", "length"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-t", "bins", "--columns", "chrom,start"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1:0-16", "-r2", "chr1:10-25"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1:10-25", "-r2", "chr1:0-5"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join", "--one-based-ids"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join", "--one-based-starts"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--annotate", "chrom", "--one-based-starts"]) assert result.exit_code == 0 # unbalanced file result = runner.invoke(dump, [f_in, "-b"]) assert result.exit_code == 1 # roundtrip symm-upper data result = runner.invoke(dump, [f_in, "-H", "-t", "bins"]) bins = pd.read_csv(StringIO(result.output), sep="\t") result = runner.invoke(dump, [f_in, "-H"]) pixels = pd.read_csv(StringIO(result.output), sep="\t") > cooler.create_cooler("out.cool", bins, pixels, symmetric_upper=True) tests/test_cli_export.py:74: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ________________ test_cload_symm_asymm[symm.upper-extra_args0] _________________ ref = 'symm.upper', extra_args = [] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError ________________ test_cload_symm_asymm[symm.upper-extra_args1] _________________ ref = 'symm.upper', extra_args = ['--input-copy-status', 'unique'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError ___________________ test_cload_symm_asymm[asymm-extra_args2] ___________________ ref = 'asymm', extra_args = ['--no-symmetric-upper'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError _________________ test_cload_mergepass[symm.upper-extra_args0] _________________ ref = 'symm.upper', extra_args = ['--temp-dir', '.', '--no-delete-temp'] @pytest.mark.parametrize( "ref,extra_args", [("symm.upper", ["--temp-dir", ".", "--no-delete-temp"])] ) def test_cload_mergepass(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:86: AssertionError _______________________________ test_cload_field _______________________________ def test_cload_field(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--field", "score=8"] result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:98: AssertionError ___________________________ test_cload_other_options ___________________________ def test_cload_other_options(): runner = CliRunner() with runner.isolated_filesystem(): meta = {"foo": "bar", "number": 42} with open("meta.json", "w") as f: json.dump(meta, f) extra_args = [ "--metadata", "meta.json", "--zero-based", "--storage-options", "shuffle=True,fletcher32=True,compression=lzf", ] result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:161: AssertionError _________________ test_load_symm_asymm[symm.upper-extra_args0] _________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.bg2' extra_args = [] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError _________________ test_load_symm_asymm[symm.upper-extra_args1] _________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.bg2' extra_args = ['--one-based', '--input-copy-status', 'unique'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError ___________________ test_load_symm_asymm[asymm-extra_args2] ____________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.bg2' extra_args = ['--one-based', '--no-symmetric-upper'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError _______________________________ test_load_field ________________________________ def test_load_field(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--field", "count=7:dtype=float"] result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:211: AssertionError _______________________________ test_load_field2 _______________________________ def test_load_field2(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--count-as-float"] result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:225: AssertionError __________________________________ test_merge __________________________________ def test_merge(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( merge, ["toy.2.double.cool", f_in, f_in, "--field", "count:dtype=int"] ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:31: AssertionError _________________________________ test_coarsen _________________________________ def test_coarsen(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") f_ref = op.join(datadir, "toy.symm.upper.4.cool") result = runner.invoke( coarsen, [ f_in, "--factor", "2", "--nproc", "2", "-o", "toy.2.coarsen_2.cool" ], ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:50: AssertionError _________________________________ test_zoomify _________________________________ def test_zoomify(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [f_in, "--balance", "--legacy", "-o", "toy.2.mcool"] ) assert result.exit_code == 0 f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [ f_in, "--balance", "--nproc", "2", "-o", "toy.2.mcool" ] ) assert result.exit_code == 0 f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [ f_in, "--balance", "--resolutions", "2,4,8", "-o", "toy.2.mcool" ] ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:98: AssertionError _ test_create_append[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ fp = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")] ) def test_create_append(fp): > import dask.dataframe as dd tests/test_create.py:24: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ___________________________ test_create_custom_cols ____________________________ def test_create_custom_cols(): with isolated_filesystem(): df = pd.DataFrame( { "bin1_id": [0, 1, 1, 1, 2, 2, 3, 4, 5], "bin2_id": [1, 1, 3, 4, 5, 6, 7, 8, 9], "foo": [1, 1, 1, 1, 1, 2, 2, 2, 2], "bar": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9], }, columns=["bin1_id", "bin2_id", "foo", "bar"], ) bins = pd.DataFrame( { "chrom": ["chr1"] * 5 + ["chr2"] * 5, "start": list(range(5)) * 2, "end": list(range(1, 6)) * 2, } ) # works in unordered mode > cooler.create_cooler("test.cool", bins, df, columns=["foo", "bar"]) tests/test_create.py:159: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ______________________________ test_create_cooler ______________________________ def test_create_cooler(): chromsizes = cooler.util.read_chromsizes( op.join(datadir, "toy.chrom.sizes") ) bins = cooler.util.binnify(chromsizes, 1) pixels = pd.read_csv( op.join(datadir, "toy.symm.upper.1.zb.coo"), sep='\t', names=['bin1_id', 'bin2_id', 'count'] ) pixels['foo'] = 42.0 with isolated_filesystem(): > cooler.create.create_cooler( "test.cool", bins, pixels, assembly='toy', metadata={'hello': 'world', 'list': [1, 2, 3]}, ) tests/test_create.py:304: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _________________________ test_create_cooler_from_dask _________________________ def test_create_cooler_from_dask(): > dd = pytest.importorskip("dask.dataframe") tests/test_create.py:405: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_create_scool[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ fp = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")] ) def test_create_scool(fp): c = cooler.Cooler(fp) # chromsizes = c.chromsizes bins = c.bins()[:] pixels = c.pixels()[:] # random and different content to prove only chrom, start, end is linked and the rest is independent for each cell from copy import deepcopy bins_cell1 = deepcopy(bins) bins_cell2 = deepcopy(bins) bins_cell3 = deepcopy(bins) bins_cell1['weight'] = np.array([0] * len(bins_cell1["start"])) bins_cell2['weight'] = np.array([1] * len(bins_cell1["start"])) bins_cell3['weight'] = np.array([2] * len(bins_cell1["start"])) bins_cell1['KR'] = np.array([3] * len(bins_cell1["start"])) bins_cell2['KR'] = np.array([4] * len(bins_cell1["start"])) bins_cell3['KR'] = np.array([5] * len(bins_cell1["start"])) name_pixel_dict = {'cell1': pixels, 'cell2': pixels, 'cell3': pixels} name_bins_dict = {'cell1': bins_cell1, 'cell2': bins_cell2, 'cell3': bins_cell3} with isolated_filesystem(): > cooler.create_scool('outfile_test.scool', name_bins_dict, name_pixel_dict) tests/test_create.py:461: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1237: in create_scool create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _____________________________ test_from_hdf5_pairs _____________________________ def test_from_hdf5_pairs(): def should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs): # try different chunk sizes binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc1 = h5["indexes"]["chrom_offset"][:] ob1 = h5["indexes"]["bin1_offset"][:] p1 = cooler.api.pixels(h5, join=False) binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=666 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc2 = h5["indexes"]["chrom_offset"][:] ob2 = h5["indexes"]["bin1_offset"][:] p2 = cooler.api.pixels(h5, join=False) assert np.all(oc1 == oc2) assert np.all(ob1 == ob2) assert np.all(p1.values == p2.values) def should_raise_if_input_not_sorted(chromsizes, bintable, mock_pairs): # not sorted by chrm1 # with h5py.File(testcool_path, 'w') as h5: bad_reads = { "chrms1": mock_pairs["chrms2"], "cuts1": mock_pairs["cuts2"], "chrms2": mock_pairs["chrms1"], "cuts2": mock_pairs["cuts1"], } with pytest.raises(ValueError): cooler.create.HDF5Aggregator(bad_reads, chromsizes, bintable, chunksize=66) # not triu bad_reads = { "chrms1": mock_pairs["chrms1"].copy(), "cuts1": mock_pairs["cuts1"].copy(), "chrms2": mock_pairs["chrms2"].copy(), "cuts2": mock_pairs["cuts2"].copy(), } bad_reads["chrms1"][0] = 0 bad_reads["chrms2"][0] = 0 bad_reads["cuts1"][0] = 10 bad_reads["cuts2"][0] = 9 binner = cooler.create.HDF5Aggregator( bad_reads, chromsizes, bintable, chunksize=66 ) with pytest.raises(ValueError): cooler.create.create(testcool_path, bintable, binner) def should_work_with_int32_cols(chromsizes, bintable, mock_pairs): # int64 binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc1 = h5["indexes"]["chrom_offset"][:] ob1 = h5["indexes"]["bin1_offset"][:] p1 = cooler.api.pixels(h5, join=False) # int32 mock_pairs32 = { "chrms1": mock_pairs["chrms1"].astype(np.int32), "cuts1": mock_pairs["cuts1"].astype(np.int32), "chrms2": mock_pairs["chrms2"].astype(np.int32), "cuts2": mock_pairs["cuts2"].astype(np.int32), } binner = cooler.create.HDF5Aggregator( mock_pairs32, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc2 = h5["indexes"]["chrom_offset"][:] ob2 = h5["indexes"]["bin1_offset"][:] p2 = cooler.api.pixels(h5, join=False) assert np.all(oc1 == oc2) assert np.all(ob1 == ob2) assert np.all(p1.values == p2.values) def _mock_hdf5_pairs(): np.random.seed(1) chrms = np.random.randint(0, n_chroms, n_records * 2) cuts = np.random.randint(0, clen, n_records * 2) abs_cuts = np.array([clen * chrm + cut for chrm, cut in zip(chrms, cuts)]) abs_cuts1, abs_cuts2 = abs_cuts[:n_records], abs_cuts[n_records:] mock_pairs = { "chrms1": chrms[:n_records], "cuts1": cuts[:n_records], "chrms2": chrms[n_records:], "cuts2": cuts[n_records:], } # Triu-sort mask = abs_cuts1 > abs_cuts2 mock_pairs["chrms1"][mask], mock_pairs["chrms2"][mask] = ( mock_pairs["chrms2"][mask], mock_pairs["chrms1"][mask], ) mock_pairs["cuts1"][mask], mock_pairs["cuts2"][mask] = ( mock_pairs["cuts2"][mask], mock_pairs["cuts1"][mask], ) abs_cuts1[mask], abs_cuts2[mask] = abs_cuts2[mask], abs_cuts1[mask] idx = np.lexsort([abs_cuts2, abs_cuts1]) for key in mock_pairs: mock_pairs[key] = mock_pairs[key][idx] return mock_pairs n_chroms = 2 clen = 2000 n_records = 3000 chromsizes = pd.Series(index=["chr1", "chr2"], data=[clen, clen]) mock_pairs = _mock_hdf5_pairs() # uniform bins bintable = cooler.binnify(chromsizes, 100) > should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs) tests/test_create_ingest.py:167: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_create_ingest.py:52: in should_not_depend_on_chunksize cooler.create.create(testcool_path, bintable, binner) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_tabix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.filterwarnings("ignore") @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"), ) ], ) def test_cload_tabix(bins_path, pairs_path, ref_path): > cload_tabix.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="hg19", nproc=8, zero_based=False, max_split=2, ) tests/test_create_ingest.py:190: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:240: in tabix create_cooler( cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_pairix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"), ) ], ) def test_cload_pairix(bins_path, pairs_path, ref_path): > cload_pairix.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="hg19", nproc=8, zero_based=False, max_split=2, ) tests/test_create_ingest.py:221: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:308: in pairix create_cooler( cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_field[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs' @pytest.mark.parametrize( "bins_path,pairs_path", [ ( op.join(testdir, "data", "toy.chrom.sizes") + ":2", op.join(testdir, "data", "toy.pairs"), ) ], ) def test_cload_field(bins_path, pairs_path): kwargs = dict( metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback( bins_path, pairs_path, testcool_path, field=("score=8:dtype=float",), **kwargs ) tests/test_create_ingest.py:326: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_cload_custom_tempdir[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs' @pytest.mark.parametrize( "bins_path,pairs_path", [ ( op.join(testdir, "data", "toy.chrom.sizes") + ":2", op.join(testdir, "data", "toy.pairs"), ) ], ) def test_cload_custom_tempdir(bins_path, pairs_path): for temp_dir in [op.join(testdir, "data"), "-"]: > cload_pairs.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=temp_dir, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) tests/test_create_ingest.py:345: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _____________________________ test_load_bg2_vs_coo _____________________________ def test_load_bg2_vs_coo(): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) out_path1 = op.join(tmp, "test1.cool") out_path2 = op.join(tmp, "test2.cool") > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.bg2.gz"), out_path1, format="bg2", **kwargs ) tests/test_create_ingest.py:394: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _________________________ test_load_zero_one_based_bg2 _________________________ def test_load_zero_one_based_bg2(): kwargs = dict( format="bg2", metadata=None, assembly="toy", chunksize=10, field=(), count_as_float=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) # 1-based-start BG2 input ref = "toy.symm.upper.1.ob.bg2" bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1" pixels_path = op.join(testdir, "data", ref) > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs) tests/test_create_ingest.py:441: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _________________________ test_load_zero_one_based_coo _________________________ def test_load_zero_one_based_coo(): kwargs = dict( format="coo", metadata=None, assembly="toy", chunksize=10, field=(), count_as_float=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) # 1-based-start COO input ref = "toy.symm.upper.1.ob.coo" bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1" pixels_path = op.join(testdir, "data", ref) > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs) tests/test_create_ingest.py:490: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ____________________________ test_cload_append_mode ____________________________ def test_cload_append_mode(): for append in (True, False): out_path = op.join(tmp, "test.cool") with h5py.File(out_path, "w") as f: f.attrs["xxxx"] = True kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=append, ) > cload_pairs.callback( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), out_path, **kwargs ) tests/test_create_ingest.py:551: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ____________________________ test_load_append_mode _____________________________ def test_load_append_mode(): for append in (True, False): out_path = op.join(tmp, "test.cool") with h5py.File(out_path, "w") as f: f.attrs["xxxx"] = True kwargs = dict( metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=append, ) > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"), out_path, format="coo", **kwargs ) tests/test_create_ingest.py:588: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ___________________________ test_load_custom_tempdir ___________________________ def test_load_custom_tempdir(): for temp_dir in [op.join(testdir, "data"), "-"]: > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"), testcool_path, format="coo", metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=temp_dir, no_delete_temp=False, storage_options=None, append=False, ) tests/test_create_ingest.py:608: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ path1 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' path2 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "path1,path2", [ ( op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), op.join(datadir, "toy.asymm.2.cool") ) ], ) def test_merge(path1, path2): with isolated_filesystem(): > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6)) tests/test_reduce.py:30: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool] _ path1 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool' path2 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool' @pytest.mark.parametrize( "path1,path2", [ ( op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), op.join(datadir, "toy.asymm.2.cool") ) ], ) def test_merge(path1, path2): with isolated_filesystem(): > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6)) tests/test_reduce.py:30: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _________________________________ test_merge2 __________________________________ def test_merge2(): with isolated_filesystem(): path1 = op.join(datadir, "toy.symm.upper.2.cool") path2 = op.join(datadir, "toy.symm.upper.2.cool") > merge_coolers( "test.cool", [path1, path2], mergebuf=3, agg={'count': 'mean'} ) tests/test_reduce.py:42: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError ______________________ test_coarsen_partitions_correctly _______________________ def test_coarsen_partitions_correctly(): kwargs = dict(nproc=1, columns=None, dtypes=None, agg=None) with isolated_filesystem(): f_ref = op.join(datadir, "odd.4.cool") f_in = op.join(datadir, "odd.1.cool") > coarsen_cooler(f_in, "odd.1.coarsen_4.cool", factor=4, chunksize=2, **kwargs) tests/test_reduce.py:145: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _________________________________ test_zoomify _________________________________ def test_zoomify(): kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None) with isolated_filesystem(): > zoomify_cooler( op.join(datadir, "toy.asymm.2.cool"), "test.2.mcool", resolutions=[4, 8, 16, 32], **kwargs ) tests/test_reduce.py:156: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:832: in zoomify_cooler coarsen_cooler( cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _____________________________ test_legacy_zoomify ______________________________ def test_legacy_zoomify(): infile = op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool") chunksize = int(10e6) # n_zooms = 2 n_cpus = 1 with isolated_filesystem(): > legacy_zoomify(infile, "test.multires.cool", n_cpus, chunksize) tests/test_reduce.py:197: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:900: in legacy_zoomify coarsen_cooler( cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError _______________________________ test_append_mode _______________________________ def test_append_mode(): # merge path1 = path2 = op.join(datadir, "toy.asymm.2.cool") out_path = "test.cool" for append in (True, False): with isolated_filesystem(): with h5py.File("test.cool", "w") as f: f.attrs["xxxx"] = True > merge_coolers( out_path, [path1, path2], mergebuf=int(15e6), mode="a" if append else "w" ) tests/test_reduce.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.12/inspect.py:3310: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.12/inspect.py:3054: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.12/inspect.py:2642: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.12/inspect.py:2467: TypeError =============================== warnings summary =============================== tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:44: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:47: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_api.py:51: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(chroms.dtype) tests/test_balance.py::test_balancing_other_options[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-0.01] tests/test_cli_ops.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/balance.py:112: RuntimeWarning: Mean of empty slice. scale = nzmarg.mean() tests/test_balance.py::test_balancing_other_options[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-0.01] tests/test_cli_ops.py::test_zoomify /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) tests/test_cli.py::test_makebins /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/cli/makebins.py:55: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. bins["id"] = bins.groupby("chrom").cumcount() tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 2 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:730: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead is_cat = pd.api.types.is_categorical_dtype(bins["chrom"]) tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 1 warning /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:771: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. self._bins_grouped = bins.groupby("chrom", sort=False) tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 2 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/util.py:395: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _chrom, group in bins.groupby("chrom"): tests/test_cli_ingest.py: 11 warnings tests/test_create_ingest.py: 8 warnings tests/test_create_sanitize.py: 9 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/create/_ingest.py:133: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` chromsizes1 = gs.chromsizes[chrom1_ids].values tests/test_cli_ingest.py: 11 warnings tests/test_create_ingest.py: 8 warnings tests/test_create_sanitize.py: 9 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/create/_ingest.py:134: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` chromsizes2 = gs.chromsizes[chrom2_ids].values tests/test_cli_ops.py::test_coarsen tests/test_cli_ops.py::test_zoomify tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool] tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool] tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool] tests/test_reduce.py::test_coarsen_partitions_correctly tests/test_reduce.py::test_zoomify tests/test_reduce.py::test_legacy_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:548: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return old_bins.groupby("chrom").apply(_each).reset_index(drop=True) tests/test_cli_ops.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/cli/zoomify.py:198: UserWarning: Map is already < 256 x 256. Provide resolutions explicitly if you want to coarsen more. warnings.warn( tests/test_cli_ops.py::test_zoomify tests/test_cli_ops.py::test_zoomify tests/test_reduce.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:792: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. n_bins_longest_chrom[base_binsize] = clr.bins()[:].groupby("chrom").size().max() tests/test_cli_ops.py::test_balance tests/test_cli_ops.py::test_balance tests/test_cli_ops.py::test_balance /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/balance.py:108: ConvergenceWarning: Iteration limit reached without convergence. warnings.warn( tests/test_cli_ops.py::test_balance /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/cli/balance.py:183: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. bins_grouped = clr.bins()[:].groupby('chrom') tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_create.py::test_write tests/test_create.py::test_write /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/core/_tableops.py:120: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead elif is_categorical_dtype(data): tests/test_core.py::test_put /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_core.py:94: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(out['chrom_enum'].dtype) tests/test_core.py::test_put /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_core.py:104: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert not pd.api.types.is_categorical_dtype(out['chrom_string'].dtype) tests/test_create.py::test_rename_chroms tests/test_create.py::test_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/create/_create.py:349: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead if is_categorical_dtype(bins["chrom"]): tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool] tests/test_reduce.py::test_merge2 tests/test_reduce.py::test_append_mode /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/cooler/reduce.py:247: DeprecationWarning: np.find_common_type is deprecated. Please use `np.result_type` or `np.promote_types`. See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information. (Deprecated NumPy 1.25) dtypes[col] = np.find_common_type(dtype_map[col], []) tests/test_util.py::test_bedslice /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_util.py:234: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. grouped = bins.groupby('chrom') tests/test_util.py::test_check_bins /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/test_util.py:312: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"]) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_cli_export.py::test_dump - TypeError: descriptor '__call__'... FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args1] FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[asymm-extra_args2] - a... FAILED tests/test_cli_ingest.py::test_cload_mergepass[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_cload_field - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_cload_other_options - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args1] FAILED tests/test_cli_ingest.py::test_load_symm_asymm[asymm-extra_args2] - as... FAILED tests/test_cli_ingest.py::test_load_field - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_load_field2 - assert 1 == 0 FAILED tests/test_cli_ops.py::test_merge - assert 1 == 0 FAILED tests/test_cli_ops.py::test_coarsen - assert 1 == 0 FAILED tests/test_cli_ops.py::test_zoomify - assert 1 == 0 FAILED tests/test_create.py::test_create_append[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create.py::test_create_custom_cols - TypeError: descriptor ... FAILED tests/test_create.py::test_create_cooler - TypeError: descriptor '__ca... FAILED tests/test_create.py::test_create_cooler_from_dask - TypeError: descri... FAILED tests/test_create.py::test_create_scool[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_from_hdf5_pairs - TypeError: descrip... FAILED tests/test_create_ingest.py::test_cload_tabix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_cload_pairix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy_hash.pairs.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_field[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] FAILED tests/test_create_ingest.py::test_cload_custom_tempdir[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.pairs] FAILED tests/test_create_ingest.py::test_load_bg2_vs_coo - TypeError: descrip... FAILED tests/test_create_ingest.py::test_load_zero_one_based_bg2 - TypeError:... FAILED tests/test_create_ingest.py::test_load_zero_one_based_coo - TypeError:... FAILED tests/test_create_ingest.py::test_cload_append_mode - TypeError: descr... FAILED tests/test_create_ingest.py::test_load_append_mode - TypeError: descri... FAILED tests/test_create_ingest.py::test_load_custom_tempdir - TypeError: des... FAILED tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool] FAILED tests/test_reduce.py::test_merge2 - TypeError: descriptor '__call__' f... FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.4.cool] FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.asymm.4.cool] FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build/tests/data/toy.symm.upper.var2x.cool] FAILED tests/test_reduce.py::test_coarsen_partitions_correctly - TypeError: d... FAILED tests/test_reduce.py::test_zoomify - TypeError: descriptor '__call__' ... FAILED tests/test_reduce.py::test_legacy_zoomify - TypeError: descriptor '__c... FAILED tests/test_reduce.py::test_append_mode - TypeError: descriptor '__call... ====== 44 failed, 86 passed, 6 skipped, 253 warnings in 136.89s (0:02:16) ====== E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.12_cooler/build; python3.12 -m pytest tests I: pybuild base:311: cd /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build configfile: pyproject.toml collected 136 items tests/test_api.py .......... [ 7%] tests/test_balance.py .... [ 10%] tests/test_cli.py .s..s..... [ 17%] tests/test_cli_export.py .Fs [ 19%] tests/test_cli_fileops.py .... [ 22%] tests/test_cli_ingest.py FException ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp9n18knvf/tmptnl1maeo.multi.cool' FFFFFException ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpgmr3ss20/tmpekcefaqn.multi.cool' Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpica4z3op/tmprema44tj.multi.cool' FFFFF [ 30%] tests/test_cli_ops.py FFF. [ 33%] tests/test_core.py ........... [ 41%] tests/test_create.py Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmphvqt_o24/tmpkf451rc8.multi.cool' Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpo_fwr_nd/tmpgtgk0lfj.multi.cool' Fs.F..FFF [ 48%] tests/test_create_ingest.py FFFFFFFFFFF.FFF [ 59%] tests/test_create_sanitize.py ........ [ 65%] tests/test_fileops.py ........s.. [ 73%] tests/test_parallel.py ... [ 75%] tests/test_reduce.py FFFFFFFFFF [ 83%] tests/test_util.py .........s............. [100%] =================================== FAILURES =================================== __________________________________ test_dump ___________________________________ def test_dump(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke(dump, [f_in]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-t", "chroms", "--columns", "length"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-t", "bins", "--columns", "chrom,start"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1:0-16", "-r2", "chr1:10-25"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "-r", "chr1:10-25", "-r2", "chr1:0-5"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join", "--one-based-ids"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--join", "--one-based-starts"]) assert result.exit_code == 0 result = runner.invoke(dump, [f_in, "--annotate", "chrom", "--one-based-starts"]) assert result.exit_code == 0 # unbalanced file result = runner.invoke(dump, [f_in, "-b"]) assert result.exit_code == 1 # roundtrip symm-upper data result = runner.invoke(dump, [f_in, "-H", "-t", "bins"]) bins = pd.read_csv(StringIO(result.output), sep="\t") result = runner.invoke(dump, [f_in, "-H"]) pixels = pd.read_csv(StringIO(result.output), sep="\t") > cooler.create_cooler("out.cool", bins, pixels, symmetric_upper=True) tests/test_cli_export.py:74: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ________________ test_cload_symm_asymm[symm.upper-extra_args0] _________________ ref = 'symm.upper', extra_args = [] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError ________________ test_cload_symm_asymm[symm.upper-extra_args1] _________________ ref = 'symm.upper', extra_args = ['--input-copy-status', 'unique'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError ___________________ test_cload_symm_asymm[asymm-extra_args2] ___________________ ref = 'asymm', extra_args = ['--no-symmetric-upper'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect triu pairs ("symm.upper", ["--input-copy-status", "unique"]), # reflect triu pairs ("asymm", ["--no-symmetric-upper"]), ], ) def test_cload_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:72: AssertionError _________________ test_cload_mergepass[symm.upper-extra_args0] _________________ ref = 'symm.upper', extra_args = ['--temp-dir', '.', '--no-delete-temp'] @pytest.mark.parametrize( "ref,extra_args", [("symm.upper", ["--temp-dir", ".", "--no-delete-temp"])] ) def test_cload_mergepass(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:86: AssertionError _______________________________ test_cload_field _______________________________ def test_cload_field(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--field", "score=8"] result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:98: AssertionError ___________________________ test_cload_other_options ___________________________ def test_cload_other_options(): runner = CliRunner() with runner.isolated_filesystem(): meta = {"foo": "bar", "number": 42} with open("meta.json", "w") as f: json.dump(meta, f) extra_args = [ "--metadata", "meta.json", "--zero-based", "--storage-options", "shuffle=True,fletcher32=True,compression=lzf", ] result = _run_cload_pairs(runner, 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:161: AssertionError _________________ test_load_symm_asymm[symm.upper-extra_args0] _________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.bg2' extra_args = [] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError _________________ test_load_symm_asymm[symm.upper-extra_args1] _________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.bg2' extra_args = ['--one-based', '--input-copy-status', 'unique'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError ___________________ test_load_symm_asymm[asymm-extra_args2] ____________________ ref = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.bg2' extra_args = ['--one-based', '--no-symmetric-upper'] @pytest.mark.parametrize( "ref,extra_args", [ ("symm.upper", []), # reflect tril pairs ("symm.upper", ["--one-based", "--input-copy-status", "unique"]), # reflect tril pairs ("asymm", ["--one-based", "--no-symmetric-upper"]), ], ) def test_load_symm_asymm(ref, extra_args): runner = CliRunner() with runner.isolated_filesystem(): ref = op.join(datadir, f"toy.{ref}.2.bg2") result = _run_load(runner, ref, "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:201: AssertionError _______________________________ test_load_field ________________________________ def test_load_field(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--field", "count=7:dtype=float"] result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:211: AssertionError _______________________________ test_load_field2 _______________________________ def test_load_field2(): runner = CliRunner() with runner.isolated_filesystem(): extra_args = ["--count-as-float"] result = _run_load(runner, "toy.symm.upper.2.bg2", "bg2", 2, extra_args) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ingest.py:225: AssertionError __________________________________ test_merge __________________________________ def test_merge(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( merge, ["toy.2.double.cool", f_in, f_in, "--field", "count:dtype=int"] ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:31: AssertionError _________________________________ test_coarsen _________________________________ def test_coarsen(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") f_ref = op.join(datadir, "toy.symm.upper.4.cool") result = runner.invoke( coarsen, [ f_in, "--factor", "2", "--nproc", "2", "-o", "toy.2.coarsen_2.cool" ], ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:50: AssertionError _________________________________ test_zoomify _________________________________ def test_zoomify(): runner = CliRunner() with runner.isolated_filesystem(): f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [f_in, "--balance", "--legacy", "-o", "toy.2.mcool"] ) assert result.exit_code == 0 f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [ f_in, "--balance", "--nproc", "2", "-o", "toy.2.mcool" ] ) assert result.exit_code == 0 f_in = op.join(datadir, "toy.symm.upper.2.cool") result = runner.invoke( zoomify, [ f_in, "--balance", "--resolutions", "2,4,8", "-o", "toy.2.mcool" ] ) > assert result.exit_code == 0 E assert 1 == 0 E + where 1 = .exit_code tests/test_cli_ops.py:98: AssertionError _ test_create_append[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ fp = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")] ) def test_create_append(fp): > import dask.dataframe as dd tests/test_create.py:24: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ___________________________ test_create_custom_cols ____________________________ def test_create_custom_cols(): with isolated_filesystem(): df = pd.DataFrame( { "bin1_id": [0, 1, 1, 1, 2, 2, 3, 4, 5], "bin2_id": [1, 1, 3, 4, 5, 6, 7, 8, 9], "foo": [1, 1, 1, 1, 1, 2, 2, 2, 2], "bar": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9], }, columns=["bin1_id", "bin2_id", "foo", "bar"], ) bins = pd.DataFrame( { "chrom": ["chr1"] * 5 + ["chr2"] * 5, "start": list(range(5)) * 2, "end": list(range(1, 6)) * 2, } ) # works in unordered mode > cooler.create_cooler("test.cool", bins, df, columns=["foo", "bar"]) tests/test_create.py:159: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ______________________________ test_create_cooler ______________________________ def test_create_cooler(): chromsizes = cooler.util.read_chromsizes( op.join(datadir, "toy.chrom.sizes") ) bins = cooler.util.binnify(chromsizes, 1) pixels = pd.read_csv( op.join(datadir, "toy.symm.upper.1.zb.coo"), sep='\t', names=['bin1_id', 'bin2_id', 'count'] ) pixels['foo'] = 42.0 with isolated_filesystem(): > cooler.create.create_cooler( "test.cool", bins, pixels, assembly='toy', metadata={'hello': 'world', 'list': [1, 2, 3]}, ) tests/test_create.py:304: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _________________________ test_create_cooler_from_dask _________________________ def test_create_cooler_from_dask(): > dd = pytest.importorskip("dask.dataframe") tests/test_create.py:405: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_create_scool[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ fp = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "fp", [op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool")] ) def test_create_scool(fp): c = cooler.Cooler(fp) # chromsizes = c.chromsizes bins = c.bins()[:] pixels = c.pixels()[:] # random and different content to prove only chrom, start, end is linked and the rest is independent for each cell from copy import deepcopy bins_cell1 = deepcopy(bins) bins_cell2 = deepcopy(bins) bins_cell3 = deepcopy(bins) bins_cell1['weight'] = np.array([0] * len(bins_cell1["start"])) bins_cell2['weight'] = np.array([1] * len(bins_cell1["start"])) bins_cell3['weight'] = np.array([2] * len(bins_cell1["start"])) bins_cell1['KR'] = np.array([3] * len(bins_cell1["start"])) bins_cell2['KR'] = np.array([4] * len(bins_cell1["start"])) bins_cell3['KR'] = np.array([5] * len(bins_cell1["start"])) name_pixel_dict = {'cell1': pixels, 'cell2': pixels, 'cell3': pixels} name_bins_dict = {'cell1': bins_cell1, 'cell2': bins_cell2, 'cell3': bins_cell3} with isolated_filesystem(): > cooler.create_scool('outfile_test.scool', name_bins_dict, name_pixel_dict) tests/test_create.py:461: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/create/_create.py:1237: in create_scool create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _____________________________ test_from_hdf5_pairs _____________________________ def test_from_hdf5_pairs(): def should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs): # try different chunk sizes binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc1 = h5["indexes"]["chrom_offset"][:] ob1 = h5["indexes"]["bin1_offset"][:] p1 = cooler.api.pixels(h5, join=False) binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=666 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc2 = h5["indexes"]["chrom_offset"][:] ob2 = h5["indexes"]["bin1_offset"][:] p2 = cooler.api.pixels(h5, join=False) assert np.all(oc1 == oc2) assert np.all(ob1 == ob2) assert np.all(p1.values == p2.values) def should_raise_if_input_not_sorted(chromsizes, bintable, mock_pairs): # not sorted by chrm1 # with h5py.File(testcool_path, 'w') as h5: bad_reads = { "chrms1": mock_pairs["chrms2"], "cuts1": mock_pairs["cuts2"], "chrms2": mock_pairs["chrms1"], "cuts2": mock_pairs["cuts1"], } with pytest.raises(ValueError): cooler.create.HDF5Aggregator(bad_reads, chromsizes, bintable, chunksize=66) # not triu bad_reads = { "chrms1": mock_pairs["chrms1"].copy(), "cuts1": mock_pairs["cuts1"].copy(), "chrms2": mock_pairs["chrms2"].copy(), "cuts2": mock_pairs["cuts2"].copy(), } bad_reads["chrms1"][0] = 0 bad_reads["chrms2"][0] = 0 bad_reads["cuts1"][0] = 10 bad_reads["cuts2"][0] = 9 binner = cooler.create.HDF5Aggregator( bad_reads, chromsizes, bintable, chunksize=66 ) with pytest.raises(ValueError): cooler.create.create(testcool_path, bintable, binner) def should_work_with_int32_cols(chromsizes, bintable, mock_pairs): # int64 binner = cooler.create.HDF5Aggregator( mock_pairs, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc1 = h5["indexes"]["chrom_offset"][:] ob1 = h5["indexes"]["bin1_offset"][:] p1 = cooler.api.pixels(h5, join=False) # int32 mock_pairs32 = { "chrms1": mock_pairs["chrms1"].astype(np.int32), "cuts1": mock_pairs["cuts1"].astype(np.int32), "chrms2": mock_pairs["chrms2"].astype(np.int32), "cuts2": mock_pairs["cuts2"].astype(np.int32), } binner = cooler.create.HDF5Aggregator( mock_pairs32, chromsizes, bintable, chunksize=66 ) cooler.create.create(testcool_path, bintable, binner) with h5py.File(testcool_path, "r") as h5: oc2 = h5["indexes"]["chrom_offset"][:] ob2 = h5["indexes"]["bin1_offset"][:] p2 = cooler.api.pixels(h5, join=False) assert np.all(oc1 == oc2) assert np.all(ob1 == ob2) assert np.all(p1.values == p2.values) def _mock_hdf5_pairs(): np.random.seed(1) chrms = np.random.randint(0, n_chroms, n_records * 2) cuts = np.random.randint(0, clen, n_records * 2) abs_cuts = np.array([clen * chrm + cut for chrm, cut in zip(chrms, cuts)]) abs_cuts1, abs_cuts2 = abs_cuts[:n_records], abs_cuts[n_records:] mock_pairs = { "chrms1": chrms[:n_records], "cuts1": cuts[:n_records], "chrms2": chrms[n_records:], "cuts2": cuts[n_records:], } # Triu-sort mask = abs_cuts1 > abs_cuts2 mock_pairs["chrms1"][mask], mock_pairs["chrms2"][mask] = ( mock_pairs["chrms2"][mask], mock_pairs["chrms1"][mask], ) mock_pairs["cuts1"][mask], mock_pairs["cuts2"][mask] = ( mock_pairs["cuts2"][mask], mock_pairs["cuts1"][mask], ) abs_cuts1[mask], abs_cuts2[mask] = abs_cuts2[mask], abs_cuts1[mask] idx = np.lexsort([abs_cuts2, abs_cuts1]) for key in mock_pairs: mock_pairs[key] = mock_pairs[key][idx] return mock_pairs n_chroms = 2 clen = 2000 n_records = 3000 chromsizes = pd.Series(index=["chr1", "chr2"], data=[clen, clen]) mock_pairs = _mock_hdf5_pairs() # uniform bins bintable = cooler.binnify(chromsizes, 100) > should_not_depend_on_chunksize(chromsizes, bintable, mock_pairs) tests/test_create_ingest.py:167: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/test_create_ingest.py:52: in should_not_depend_on_chunksize cooler.create.create(testcool_path, bintable, binner) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_tabix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.filterwarnings("ignore") @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"), ) ], ) def test_cload_tabix(bins_path, pairs_path, ref_path): > cload_tabix.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="hg19", nproc=8, zero_based=False, max_split=2, ) tests/test_create_ingest.py:190: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:240: in tabix create_cooler( cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_pairix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.cool"), ) ], ) def test_cload_pairix(bins_path, pairs_path, ref_path): > cload_pairix.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="hg19", nproc=8, zero_based=False, max_split=2, ) tests/test_create_ingest.py:221: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:308: in pairix create_cooler( cooler/create/_create.py:1024: in create_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz' ref_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool' @pytest.mark.skipif( _pandas_major_version < 1, reason="hash fix only works with pandas >= 1.0" ) @pytest.mark.parametrize( "bins_path,pairs_path,ref_path", [ ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ), ( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy_hash.pairs.gz"), op.join(testdir, "data", "toy.symm.upper.var.cool"), ) ], ) def test_cload_pairs(bins_path, pairs_path, ref_path): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback(bins_path, pairs_path, testcool_path, **kwargs) tests/test_create_ingest.py:286: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_field[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs' @pytest.mark.parametrize( "bins_path,pairs_path", [ ( op.join(testdir, "data", "toy.chrom.sizes") + ":2", op.join(testdir, "data", "toy.pairs"), ) ], ) def test_cload_field(bins_path, pairs_path): kwargs = dict( metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) > cload_pairs.callback( bins_path, pairs_path, testcool_path, field=("score=8:dtype=float",), **kwargs ) tests/test_create_ingest.py:326: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_cload_custom_tempdir[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] _ bins_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2' pairs_path = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs' @pytest.mark.parametrize( "bins_path,pairs_path", [ ( op.join(testdir, "data", "toy.chrom.sizes") + ":2", op.join(testdir, "data", "toy.pairs"), ) ], ) def test_cload_custom_tempdir(bins_path, pairs_path): for temp_dir in [op.join(testdir, "data"), "-"]: > cload_pairs.callback( bins_path, pairs_path, testcool_path, metadata=None, assembly="toy", chunksize=10, zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=temp_dir, no_delete_temp=False, storage_options=None, no_count=True, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=False, ) tests/test_create_ingest.py:345: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _____________________________ test_load_bg2_vs_coo _____________________________ def test_load_bg2_vs_coo(): kwargs = dict( metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) out_path1 = op.join(tmp, "test1.cool") out_path2 = op.join(tmp, "test2.cool") > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.bg2.gz"), out_path1, format="bg2", **kwargs ) tests/test_create_ingest.py:394: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _________________________ test_load_zero_one_based_bg2 _________________________ def test_load_zero_one_based_bg2(): kwargs = dict( format="bg2", metadata=None, assembly="toy", chunksize=10, field=(), count_as_float=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) # 1-based-start BG2 input ref = "toy.symm.upper.1.ob.bg2" bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1" pixels_path = op.join(testdir, "data", ref) > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs) tests/test_create_ingest.py:441: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _________________________ test_load_zero_one_based_coo _________________________ def test_load_zero_one_based_coo(): kwargs = dict( format="coo", metadata=None, assembly="toy", chunksize=10, field=(), count_as_float=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=False, ) # 1-based-start COO input ref = "toy.symm.upper.1.ob.coo" bins_path = op.join(testdir, "data", "toy.chrom.sizes") + ":1" pixels_path = op.join(testdir, "data", ref) > load.callback(bins_path, pixels_path, testcool_path, one_based=True, **kwargs) tests/test_create_ingest.py:490: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ____________________________ test_cload_append_mode ____________________________ def test_cload_append_mode(): for append in (True, False): out_path = op.join(tmp, "test.cool") with h5py.File(out_path, "w") as f: f.attrs["xxxx"] = True kwargs = dict( metadata=None, assembly="hg19", chunksize=int(15e6), zero_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, field=(), temp_dir=None, no_delete_temp=False, storage_options=None, no_count=False, max_merge=200, chrom1=2, pos1=3, chrom2=4, pos2=5, append=append, ) > cload_pairs.callback( op.join(testdir, "data", "toy.bins.var.bed"), op.join(testdir, "data", "toy.pairs"), out_path, **kwargs ) tests/test_create_ingest.py:551: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/cload.py:584: in pairs create_cooler( cooler/create/_create.py:1042: in create_cooler create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ____________________________ test_load_append_mode _____________________________ def test_load_append_mode(): for append in (True, False): out_path = op.join(tmp, "test.cool") with h5py.File(out_path, "w") as f: f.attrs["xxxx"] = True kwargs = dict( metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=None, no_delete_temp=False, storage_options=None, append=append, ) > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"), out_path, format="coo", **kwargs ) tests/test_create_ingest.py:588: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ___________________________ test_load_custom_tempdir ___________________________ def test_load_custom_tempdir(): for temp_dir in [op.join(testdir, "data"), "-"]: > load.callback( op.join(testdir, "data", "hg19.bins.2000kb.bed.gz"), op.join(testdir, "data", "hg19.GM12878-MboI.matrix.2000kb.coo.txt"), testcool_path, format="coo", metadata=None, assembly="hg19", chunksize=int(20e6), field=(), count_as_float=False, one_based=False, comment_char="#", input_copy_status="unique", no_symmetric_upper=False, temp_dir=temp_dir, no_delete_temp=False, storage_options=None, append=False, ) tests/test_create_ingest.py:608: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/cli/load.py:339: in load create_from_unordered( cooler/create/_create.py:723: in create_from_unordered create(uri, bins, chunk, columns=columns, dtypes=dtypes, mode="a", **kwargs) cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] _ path1 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' path2 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool' @pytest.mark.parametrize( "path1,path2", [ ( op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), op.join(datadir, "toy.asymm.2.cool") ) ], ) def test_merge(path1, path2): with isolated_filesystem(): > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6)) tests/test_reduce.py:30: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool] _ path1 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool' path2 = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool' @pytest.mark.parametrize( "path1,path2", [ ( op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), op.join(datadir, "toy.asymm.2.cool") ) ], ) def test_merge(path1, path2): with isolated_filesystem(): > merge_coolers("test.cool", [path1, path2], mergebuf=int(15e6)) tests/test_reduce.py:30: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _________________________________ test_merge2 __________________________________ def test_merge2(): with isolated_filesystem(): path1 = op.join(datadir, "toy.symm.upper.2.cool") path2 = op.join(datadir, "toy.symm.upper.2.cool") > merge_coolers( "test.cool", [path1, path2], mergebuf=3, agg={'count': 'mean'} ) tests/test_reduce.py:42: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _ test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool] _ input_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool' factor = 2 ref_uri = '/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool' @pytest.mark.parametrize( "input_uri,factor,ref_uri", [ ( op.join(datadir, "toy.symm.upper.2.cool"), 2, op.join(datadir, "toy.symm.upper.4.cool"), ), ( op.join(datadir, "toy.asymm.2.cool"), 2, op.join(datadir, "toy.asymm.4.cool") ), ( op.join(datadir, "toy.symm.upper.var.cool"), 2, op.join(datadir, "toy.symm.upper.var2x.cool"), ), ], ) def test_coarsen(input_uri, factor, ref_uri): with isolated_filesystem(): kwargs = dict( chunksize=10, nproc=1, columns=None, dtypes=None, agg=None ) > coarsen_cooler(input_uri, "test.cool", factor, **kwargs) tests/test_reduce.py:109: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError ______________________ test_coarsen_partitions_correctly _______________________ def test_coarsen_partitions_correctly(): kwargs = dict(nproc=1, columns=None, dtypes=None, agg=None) with isolated_filesystem(): f_ref = op.join(datadir, "odd.4.cool") f_in = op.join(datadir, "odd.1.cool") > coarsen_cooler(f_in, "odd.1.coarsen_4.cool", factor=4, chunksize=2, **kwargs) tests/test_reduce.py:145: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _________________________________ test_zoomify _________________________________ def test_zoomify(): kwargs = dict(chunksize=10, nproc=1, columns=None, dtypes=None, agg=None) with isolated_filesystem(): > zoomify_cooler( op.join(datadir, "toy.asymm.2.cool"), "test.2.mcool", resolutions=[4, 8, 16, 32], **kwargs ) tests/test_reduce.py:156: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:832: in zoomify_cooler coarsen_cooler( cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _____________________________ test_legacy_zoomify ______________________________ def test_legacy_zoomify(): infile = op.join(datadir, "hg19.GM12878-MboI.matrix.2000kb.cool") chunksize = int(10e6) # n_zooms = 2 n_cpus = 1 with isolated_filesystem(): > legacy_zoomify(infile, "test.multires.cool", n_cpus, chunksize) tests/test_reduce.py:197: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:900: in legacy_zoomify coarsen_cooler( cooler/reduce.py:712: in coarsen_cooler create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError _______________________________ test_append_mode _______________________________ def test_append_mode(): # merge path1 = path2 = op.join(datadir, "toy.asymm.2.cool") out_path = "test.cool" for append in (True, False): with isolated_filesystem(): with h5py.File("test.cool", "w") as f: f.attrs["xxxx"] = True > merge_coolers( out_path, [path1, path2], mergebuf=int(15e6), mode="a" if append else "w" ) tests/test_reduce.py:208: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ cooler/reduce.py:253: in merge_coolers create( cooler/create/_create.py:514: in create from dask.dataframe import DataFrame as dask_df /usr/lib/python3/dist-packages/dask/dataframe/__init__.py:98: in from dask.dataframe import backends, dispatch, rolling /usr/lib/python3/dist-packages/dask/dataframe/backends.py:15: in from dask.dataframe.core import DataFrame, Index, Scalar, Series, _Frame /usr/lib/python3/dist-packages/dask/dataframe/core.py:36: in from dask.dataframe import methods /usr/lib/python3/dist-packages/dask/dataframe/methods.py:34: in from dask.dataframe.utils import is_dataframe_like, is_index_like, is_series_like /usr/lib/python3/dist-packages/dask/dataframe/utils.py:20: in from dask.dataframe import ( # noqa: F401 register pandas extension types /usr/lib/python3/dist-packages/dask/dataframe/_dtypes.py:9: in from dask.dataframe.extensions import make_array_nonempty, make_scalar /usr/lib/python3/dist-packages/dask/dataframe/extensions.py:8: in from dask.dataframe.accessor import ( /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:126: in class DatetimeAccessor(Accessor): /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:81: in __init_subclass__ _bind_property(cls, pd_cls, attr, min_version) /usr/lib/python3/dist-packages/dask/dataframe/accessor.py:35: in _bind_property setattr(cls, attr, property(derived_from(pd_cls, version=min_version)(func))) /usr/lib/python3/dist-packages/dask/utils.py:983: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:936: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:697: in get_named_args s = inspect.signature(func) /usr/lib/python3.11/inspect.py:3263: in signature return Signature.from_callable(obj, follow_wrapped=follow_wrapped, /usr/lib/python3.11/inspect.py:3011: in from_callable return _signature_from_callable(obj, sigcls=cls, /usr/lib/python3.11/inspect.py:2599: in _signature_from_callable call = _descriptor_get(call, obj) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ descriptor = obj = def _descriptor_get(descriptor, obj): if isclass(descriptor): return descriptor get = getattr(type(descriptor), '__get__', _sentinel) if get is _sentinel: return descriptor > return get(descriptor, obj, type(obj)) E TypeError: descriptor '__call__' for 'type' objects doesn't apply to a 'property' object /usr/lib/python3.11/inspect.py:2432: TypeError =============================== warnings summary =============================== tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:44: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:47: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"].dtype) tests/test_api.py::test_bintable_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_api.py:51: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(chroms.dtype) tests/test_balance.py::test_balancing_other_options[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-0.01] tests/test_cli_ops.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/balance.py:112: RuntimeWarning: Mean of empty slice. scale = nzmarg.mean() tests/test_balance.py::test_balancing_other_options[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-0.01] tests/test_cli_ops.py::test_zoomify /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide ret = ret.dtype.type(ret / rcount) tests/test_cli.py::test_makebins /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/cli/makebins.py:55: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. bins["id"] = bins.groupby("chrom").cumcount() tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 2 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:730: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead is_cat = pd.api.types.is_categorical_dtype(bins["chrom"]) tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 1 warning /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:771: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. self._bins_grouped = bins.groupby("chrom", sort=False) tests/test_cli_ingest.py: 11 warnings tests/test_cli_ops.py: 2 warnings tests/test_create_ingest.py: 13 warnings tests/test_create_sanitize.py: 18 warnings tests/test_reduce.py: 6 warnings tests/test_util.py: 2 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/util.py:395: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. for _chrom, group in bins.groupby("chrom"): tests/test_cli_ingest.py: 11 warnings tests/test_create_ingest.py: 8 warnings tests/test_create_sanitize.py: 9 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/create/_ingest.py:133: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` chromsizes1 = gs.chromsizes[chrom1_ids].values tests/test_cli_ingest.py: 11 warnings tests/test_create_ingest.py: 8 warnings tests/test_create_sanitize.py: 9 warnings /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/create/_ingest.py:134: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` chromsizes2 = gs.chromsizes[chrom2_ids].values tests/test_cli_ingest.py::test_cload_field /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpzdnh0wes/tmpuq1i1fk_.multi.cool' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) tests/test_cli_ingest.py::test_load_field /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp5mehzdjr/tmpbr6id2ym.multi.cool' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) tests/test_cli_ops.py::test_coarsen tests/test_cli_ops.py::test_zoomify tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool] tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool] tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool] tests/test_reduce.py::test_coarsen_partitions_correctly tests/test_reduce.py::test_zoomify tests/test_reduce.py::test_legacy_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:548: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. return old_bins.groupby("chrom").apply(_each).reset_index(drop=True) tests/test_cli_ops.py::test_coarsen /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning: Exception ignored in: Traceback (most recent call last): File "/usr/lib/python3.11/tempfile.py", line 606, in __del__ self.close() File "/usr/lib/python3.11/tempfile.py", line 602, in close unlink(self.name) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpbnoagko2/tmphuetqlxm.multi.cool' warnings.warn(pytest.PytestUnraisableExceptionWarning(msg)) tests/test_cli_ops.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/cli/zoomify.py:198: UserWarning: Map is already < 256 x 256. Provide resolutions explicitly if you want to coarsen more. warnings.warn( tests/test_cli_ops.py::test_zoomify tests/test_cli_ops.py::test_zoomify tests/test_reduce.py::test_zoomify /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:792: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. n_bins_longest_chrom[base_binsize] = clr.bins()[:].groupby("chrom").size().max() tests/test_cli_ops.py::test_balance tests/test_cli_ops.py::test_balance tests/test_cli_ops.py::test_balance /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/balance.py:108: ConvergenceWarning: Iteration limit reached without convergence. warnings.warn( tests/test_cli_ops.py::test_balance /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/cli/balance.py:183: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. bins_grouped = clr.bins()[:].groupby('chrom') tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_core.py::test_put tests/test_create.py::test_write tests/test_create.py::test_write /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/core/_tableops.py:120: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead elif is_categorical_dtype(data): tests/test_core.py::test_put /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_core.py:94: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(out['chrom_enum'].dtype) tests/test_core.py::test_put /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_core.py:104: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert not pd.api.types.is_categorical_dtype(out['chrom_string'].dtype) tests/test_create.py::test_rename_chroms tests/test_create.py::test_many_contigs /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/create/_create.py:349: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead if is_categorical_dtype(bins["chrom"]): tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool] tests/test_reduce.py::test_merge2 tests/test_reduce.py::test_append_mode /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/cooler/reduce.py:247: DeprecationWarning: np.find_common_type is deprecated. Please use `np.result_type` or `np.promote_types`. See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information. (Deprecated NumPy 1.25) dtypes[col] = np.find_common_type(dtype_map[col], []) tests/test_util.py::test_bedslice /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_util.py:234: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning. grouped = bins.groupby('chrom') tests/test_util.py::test_check_bins /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/test_util.py:312: DeprecationWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, pd.CategoricalDtype) instead assert pd.api.types.is_categorical_dtype(bins["chrom"]) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_cli_export.py::test_dump - TypeError: descriptor '__call__'... FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[symm.upper-extra_args1] FAILED tests/test_cli_ingest.py::test_cload_symm_asymm[asymm-extra_args2] - a... FAILED tests/test_cli_ingest.py::test_cload_mergepass[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_cload_field - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_cload_other_options - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args0] FAILED tests/test_cli_ingest.py::test_load_symm_asymm[symm.upper-extra_args1] FAILED tests/test_cli_ingest.py::test_load_symm_asymm[asymm-extra_args2] - as... FAILED tests/test_cli_ingest.py::test_load_field - assert 1 == 0 FAILED tests/test_cli_ingest.py::test_load_field2 - assert 1 == 0 FAILED tests/test_cli_ops.py::test_merge - assert 1 == 0 FAILED tests/test_cli_ops.py::test_coarsen - assert 1 == 0 FAILED tests/test_cli_ops.py::test_zoomify - assert 1 == 0 FAILED tests/test_create.py::test_create_append[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create.py::test_create_custom_cols - TypeError: descriptor ... FAILED tests/test_create.py::test_create_cooler - TypeError: descriptor '__ca... FAILED tests/test_create.py::test_create_cooler_from_dask - TypeError: descri... FAILED tests/test_create.py::test_create_scool[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_from_hdf5_pairs - TypeError: descrip... FAILED tests/test_create_ingest.py::test_cload_tabix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.sorted.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_cload_pairix[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.bins.2000kb.bed.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_pairs[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.bins.var.bed-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy_hash.pairs.gz-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool] FAILED tests/test_create_ingest.py::test_cload_field[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] FAILED tests/test_create_ingest.py::test_cload_custom_tempdir[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.chrom.sizes:2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.pairs] FAILED tests/test_create_ingest.py::test_load_bg2_vs_coo - TypeError: descrip... FAILED tests/test_create_ingest.py::test_load_zero_one_based_bg2 - TypeError:... FAILED tests/test_create_ingest.py::test_load_zero_one_based_coo - TypeError:... FAILED tests/test_create_ingest.py::test_cload_append_mode - TypeError: descr... FAILED tests/test_create_ingest.py::test_load_append_mode - TypeError: descri... FAILED tests/test_create_ingest.py::test_load_custom_tempdir - TypeError: des... FAILED tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/hg19.GM12878-MboI.matrix.2000kb.cool] FAILED tests/test_reduce.py::test_merge[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool] FAILED tests/test_reduce.py::test_merge2 - TypeError: descriptor '__call__' f... FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.4.cool] FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.2.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.asymm.4.cool] FAILED tests/test_reduce.py::test_coarsen[/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var.cool-2-/build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build/tests/data/toy.symm.upper.var2x.cool] FAILED tests/test_reduce.py::test_coarsen_partitions_correctly - TypeError: d... FAILED tests/test_reduce.py::test_zoomify - TypeError: descriptor '__call__' ... FAILED tests/test_reduce.py::test_legacy_zoomify - TypeError: descriptor '__c... FAILED tests/test_reduce.py::test_append_mode - TypeError: descriptor '__call... ====== 44 failed, 86 passed, 6 skipped, 256 warnings in 94.49s (0:01:34) ======= E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=1: cd /build/reproducible-path/python-cooler-0.9.3/.pybuild/cpython3_3.11_cooler/build; python3.11 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13 make: *** [debian/rules:9: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/3598938 and its subdirectories Fri May 17 21:47:07 UTC 2024 W: No second build log, what happened?