Mon Apr 29 10:26:04 UTC 2024 I: starting to build python-cooler/trixie/arm64 on jenkins on '2024-04-29 10:25' Mon Apr 29 10:26:04 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_18/38512/console.log Mon Apr 29 10:26:04 UTC 2024 I: Downloading source for trixie/python-cooler=0.9.3-1 --2024-04-29 10:26:04-- 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% 341M=0s 2024-04-29 10:26:04 (341 MB/s) - ‘python-cooler_0.9.3-1.dsc’ saved [2825/2825] Mon Apr 29 10:26:04 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----- Mon Apr 29 10:26:04 UTC 2024 I: Checking whether the package is not for us Mon Apr 29 10:26:04 UTC 2024 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon Apr 29 10:26:04 UTC 2024 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon Apr 29 10:29:18 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 28 22:26:07 -12 2024 I: pbuilder-time-stamp: 1714386367 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/3682874/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='3234e170fa514ec8869951421e359dd5' 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='3682874' 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.dcn6zHJx/pbuilderrc_L4Gu --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.dcn6zHJx/b1 --logfile b1/build.log python-cooler_0.9.3-1.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 23 11:23 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3682874/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: arm64 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 ... 19941 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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 30 newly installed, 0 to remove and 0 not upgraded. Need to get 18.6 MB of archives. After unpacking 75.9 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-python but it is not installable Depends: pybuild-plugin-pyproject but it is not installable Depends: python3-all but it is not installable Depends: python3-hatchling but it is not installable Depends: python3-hatch-vcs but it is not installable Depends: python3-simplejson but it is not installable Depends: python3-pandas (>= 2.1) but it is not installable Depends: python3-scipy (>= 1.10~) but it is not installable Depends: python3-h5py but it is not installable Depends: python3-asciitree but it is not installable Depends: python3-multiprocess but it is not installable Depends: python3-click but it is not installable Depends: python3-cytoolz but it is not installable Depends: python3-pytest but it is not installable Depends: python3-biopython but it is not installable Depends: python3-pyfaidx but it is not installable Depends: python3-pysam but it is not installable Depends: python3-pairix but it is not installable Depends: python3-yaml but it is not installable Depends: python3-dask but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) dh-python [6.20240422 (testing)] 4) fontconfig-config [2.15.0-1.1 (testing)] 5) fonts-urw-base35 [20200910-8 (testing)] 6) ibverbs-providers [50.0-2+b1 (testing)] 7) libaec0 [1.1.3-1 (testing)] 8) libblis4-serial [0.9.0-1+b2 (testing)] 9) libbrotli1 [1.1.0-2+b3 (testing)] 10) libbsd0 [0.12.2-1 (testing)] 11) libcairo2 [1.18.0-1+b1 (testing)] 12) libcbor0.10 [0.10.2-1.1 (testing)] 13) libcurl3t64-gnutls [8.7.1-3 (testing)] 14) libcurl4t64 [8.7.1-3 (testing)] 15) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 16) libdeflate0 [1.20-1 (testing)] 17) libedit2 [3.1-20230828-1+b1 (testing)] 18) libevent-core-2.1-7t64 [2.1.12-stable-8.1+b3 (testing)] 19) libevent-pthreads-2.1-7t64 [2.1.12-stable-8.1+b3 (testing)] 20) libexpat1 [2.6.2-1 (testing)] 21) libfabric1 [1.17.0-3+b1 (testing)] 22) libfido2-1 [1.14.0-1+b2 (testing)] 23) libfontconfig1 [2.15.0-1.1 (testing)] 24) libfontenc1 [1:1.1.8-1 (testing)] 25) libfreetype6 [2.13.2+dfsg-1+b4 (testing)] 26) libfribidi0 [1.0.13-3+b1 (testing)] 27) libgfortran5 [14-20240330-1 (testing)] 28) libglib2.0-0t64 [2.78.4-7 (testing)] 29) libgraphite2-3 [1.3.14-2 (testing)] 30) libharfbuzz0b [8.3.0-2+b1 (testing)] 31) libhdf5-openmpi-103-1 [1.10.10+repack-3+b1 (testing)] 32) libhdf5-openmpi-hl-100 [1.10.10+repack-3+b1 (testing)] 33) libhts3 [1.19+ds-1 (testing)] 34) libhtscodecs2 [1.6.0-1+b1 (testing)] 35) libhwloc-plugins [2.10.0-1+b1 (testing)] 36) libhwloc15 [2.10.0-1+b1 (testing)] 37) libibverbs1 [50.0-2+b1 (testing)] 38) libimagequant0 [2.18.0-1+b1 (testing)] 39) libjbig0 [2.1-6.1+b1 (testing)] 40) libjpeg62-turbo [1:2.1.5-2+b2 (testing)] 41) liblapack3 [3.12.0-3 (testing)] 42) liblbfgsb0 [3.0+dfsg.4-1+b1 (testing)] 43) liblcms2-2 [2.14-2+b1 (testing)] 44) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 45) liblerc4 [4.0.0+ds-4+b1 (testing)] 46) liblzf1 [3.6-4+b1 (testing)] 47) libmunge2 [0.5.15-4 (testing)] 48) libnghttp2-14 [1.59.0-1 (testing)] 49) libnl-3-200 [3.7.0-0.3 (testing)] 50) libnl-route-3-200 [3.7.0-0.3 (testing)] 51) libopenjp2-7 [2.5.0-2+b3 (testing)] 52) libopenmpi3 [4.1.6-5 (testing)] 53) libpciaccess0 [0.17-3+b1 (testing)] 54) libpixman-1-0 [0.42.2-1+b1 (testing)] 55) libpmix2 [5.0.1-4+b1 (testing)] 56) libpng16-16t64 [1.6.43-5 (testing)] 57) libpsl5t64 [0.21.2-1.1 (testing)] 58) libpython3-stdlib [3.11.8-1 (testing)] 59) libpython3.11-minimal [3.11.9-1 (testing)] 60) libpython3.11-stdlib [3.11.9-1 (testing)] 61) libpython3.12-minimal [3.12.3-1 (testing)] 62) libpython3.12-stdlib [3.12.3-1 (testing)] 63) libraqm0 [0.10.1-1+b1 (testing)] 64) librdmacm1t64 [50.0-2+b1 (testing)] 65) libreadline8t64 [8.2-4 (testing)] 66) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 67) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 68) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 69) libsharpyuv0 [1.3.2-0.4+b1 (testing)] 70) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 71) libssl3t64 [3.2.1-3 (testing)] 72) libsz2 [1.1.3-1 (testing)] 73) libtiff6 [4.5.1+git230720-4 (testing)] 74) libucx0 [1.15.0-1 (testing)] 75) libwebp7 [1.3.2-0.4+b1 (testing)] 76) libwebpdemux2 [1.3.2-0.4+b1 (testing)] 77) libwebpmux3 [1.3.2-0.4+b1 (testing)] 78) libx11-6 [2:1.8.7-1+b1 (testing)] 79) libx11-data [2:1.8.7-1 (testing)] 80) libxau6 [1:1.0.9-1+b1 (testing)] 81) libxcb-render0 [1.15-1 (testing)] 82) libxcb-shm0 [1.15-1 (testing)] 83) libxcb1 [1.15-1 (testing)] 84) libxdmcp6 [1:1.1.2-3+b1 (testing)] 85) libxext6 [2:1.3.4-1+b1 (testing)] 86) libxnvctrl0 [535.171.04-1 (testing)] 87) libxrender1 [1:0.9.10-1.1+b1 (testing)] 88) libyaml-0-2 [0.2.5-1+b1 (testing)] 89) media-types [10.1.0 (testing)] 90) mpi-default-bin [1.15 (testing)] 91) netbase [6.4 (testing)] 92) ocl-icd-libopencl1 [2.3.2-1+b1 (testing)] 93) openmpi-bin [4.1.6-5 (testing)] 94) openmpi-common [4.1.6-5 (testing)] 95) openssh-client [1:9.6p1-4 (testing)] 96) pybuild-plugin-pyproject [6.20240422 (testing)] 97) python3 [3.11.8-1 (testing)] 98) python3-all [3.11.8-1 (testing)] 99) python3-asciitree [0.3.3-4 (testing)] 100) python3-biopython [1.81+dfsg-3 (testing)] 101) python3-build [1.1.1-1 (testing)] 102) python3-cairo [1.26.0-1 (testing)] 103) python3-chardet [5.2.0+dfsg-1 (testing)] 104) python3-click [8.1.7-1 (testing)] 105) python3-cloudpickle [3.0.0-2 (testing)] 106) python3-colorama [0.4.6-4 (testing)] 107) python3-cytoolz [0.12.2-2 (testing)] 108) python3-dask [2023.12.1+dfsg-2 (testing)] 109) python3-dateutil [2.9.0-2 (testing)] 110) python3-decorator [5.1.1-5 (testing)] 111) python3-dill [0.3.8-1 (testing)] 112) python3-distutils [3.12.3-1 (testing)] 113) python3-freetype [2.4.0-1 (testing)] 114) python3-fsspec [2024.3.1-1 (testing)] 115) python3-h5py [3.10.0-1 (testing)] 116) python3-h5py-mpi [3.10.0-1 (testing)] 117) python3-hatch-vcs [0.4.0-1 (testing)] 118) python3-hatchling [1.24.2-1 (testing)] 119) python3-importlib-metadata [4.12.0-1 (testing)] 120) python3-iniconfig [1.1.1-2 (testing)] 121) python3-installer [0.7.0+dfsg1-3 (testing)] 122) python3-lib2to3 [3.12.3-1 (testing)] 123) python3-locket [1.0.0-2 (testing)] 124) python3-minimal [3.11.8-1 (testing)] 125) python3-more-itertools [10.2.0-1 (testing)] 126) python3-mpi4py [3.1.5-5 (testing)] 127) python3-multiprocess [0.70.16-2 (testing)] 128) python3-numpy [1:1.24.2-2 (testing)] 129) python3-packaging [24.0-1 (testing)] 130) python3-pairix [0.3.7-7 (testing)] 131) python3-pandas [2.1.4+dfsg-5 (testing)] 132) python3-pandas-lib [2.1.4+dfsg-5 (testing)] 133) python3-partd [1.4.1-1 (testing)] 134) python3-pathspec [0.12.1-1 (testing)] 135) python3-pil [10.3.0-2 (testing)] 136) python3-pkg-resources [68.1.2-2 (testing)] 137) python3-pluggy [1.5.0-1 (testing)] 138) python3-pyfaidx [0.8.1.1-2 (testing)] 139) python3-pyproject-hooks [1.0.0-2 (testing)] 140) python3-pysam [0.22.0+ds-1+b1 (testing)] 141) python3-pytest [7.4.4-3 (testing)] 142) python3-reportlab [4.1.0-4 (testing)] 143) python3-rlpycairo [0.3.0-3 (testing)] 144) python3-scipy [1.11.4-6 (testing)] 145) python3-setuptools [68.1.2-2 (testing)] 146) python3-setuptools-scm [8.0.4-2 (testing)] 147) python3-simplejson [3.19.2-1+b1 (testing)] 148) python3-six [1.16.0-6 (testing)] 149) python3-toml [0.10.2-1 (testing)] 150) python3-toolz [0.12.1-1 (testing)] 151) python3-trove-classifiers [2024.1.31-1 (testing)] 152) python3-typing-extensions [4.10.0-1 (testing)] 153) python3-tz [2024.1-2 (testing)] 154) python3-wheel [0.43.0-1 (testing)] 155) python3-yaml [6.0.1-2 (testing)] 156) python3-zipp [1.0.0-6 (testing)] 157) python3.11 [3.11.9-1 (testing)] 158) python3.11-minimal [3.11.9-1 (testing)] 159) python3.12 [3.12.3-1 (testing)] 160) python3.12-minimal [3.12.3-1 (testing)] 161) readline-common [8.2-4 (testing)] 162) sgml-base [1.31 (testing)] 163) tzdata [2024a-3 (testing)] 164) w3c-sgml-lib [1.3-3 (testing)] 165) x11-common [1:7.7+23 (testing)] 166) xfonts-encodings [1:1.0.4-2.2 (testing)] 167) xfonts-utils [1:7.7+6 (testing)] 168) xml-core [0.19 (testing)] 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-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} ibverbs-providers{a} intltool-debian{a} libaec0{a} libarchive-zip-perl{a} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.10{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdb5.3t64{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libevent-core-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-openmpi-103-1{a} libhdf5-openmpi-hl-100{a} libhts3{a} libhtscodecs2{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzf1{a} libmagic-mgc{a} libmagic1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-route-3-200{a} libopenjp2-7{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpixman-1-0{a} libpmix2{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} librdmacm1t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libssh2-1t64{a} libssl3t64{a} libsub-override-perl{a} libsz2{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{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} libxnvctrl0{a} libxrender1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} netbase{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{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-mpi{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-mpi4py{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 will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-core fonts-dejavu-extra git 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 xauth xdg-user-dirs 0 packages upgraded, 196 newly installed, 2 to remove and 0 not upgraded. Need to get 112 MB of archives. After unpacking 508 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [625 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libedit2 arm64 3.1-20230828-1+b1 [89.1 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libcbor0.10 arm64 0.10.2-1.1 [27.0 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 libfido2-1 arm64 1.14.0-1+b2 [73.4 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 openssh-client arm64 1:9.6p1-4 [913 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 46 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 67 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libnl-3-200 arm64 3.7.0-0.3 [56.5 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libnl-route-3-200 arm64 3.7.0-0.3 [165 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libibverbs1 arm64 50.0-2+b1 [58.2 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 ibverbs-providers arm64 50.0-2+b1 [315 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libaec0 arm64 1.1.3-1 [22.1 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libblis4-serial arm64 0.9.0-1+b2 [791 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libevent-core-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [125 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-8.1+b3 [54.3 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 librdmacm1t64 arm64 50.0-2+b1 [66.6 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libfabric1 arm64 1.17.0-3+b1 [479 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libhwloc15 arm64 2.10.0-1+b1 [140 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libmunge2 arm64 0.5.15-4 [19.2 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libpciaccess0 arm64 0.17-3+b1 [51.1 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libxnvctrl0 arm64 535.171.04-1 [13.8 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 ocl-icd-libopencl1 arm64 2.3.2-1+b1 [39.3 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libhwloc-plugins arm64 2.10.0-1+b1 [18.0 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libpmix2 arm64 5.0.1-4+b1 [573 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libucx0 arm64 1.15.0-1 [806 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libopenmpi3 arm64 4.1.6-5 [2166 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libsz2 arm64 1.1.3-1 [7664 B] Get: 115 http://deb.debian.org/debian trixie/main arm64 libhdf5-openmpi-103-1 arm64 1.10.10+repack-3+b1 [1083 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libhdf5-openmpi-hl-100 arm64 1.10.10+repack-3+b1 [59.9 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 liblzf1 arm64 3.6-4+b1 [10.3 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 132 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.3.2-0.4+b1 [107 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.3.2-0.4+b1 [119 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 openmpi-common all 4.1.6-5 [168 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 openmpi-bin arm64 4.1.6-5 [224 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 mpi-default-bin arm64 1.15 [2408 B] Get: 139 http://deb.debian.org/debian trixie/main arm64 python3-typing-extensions all 4.10.0-1 [66.2 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 1.0.0-6 [6696 B] Get: 142 http://deb.debian.org/debian trixie/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-build all 1.1.1-1 [32.5 kB] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-asciitree all 0.3.3-4 [5612 B] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.3.0-2 [552 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.0-1 [139 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.1.0-4 [1113 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.81+dfsg-3 [1611 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-colorama all 0.4.6-4 [36.2 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-click all 8.1.7-1 [94.0 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-cloudpickle all 3.0.0-2 [25.4 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-toolz all 0.12.1-1 [43.9 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-cytoolz arm64 0.12.2-2 [396 kB] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-fsspec all 2024.3.1-1 [115 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 python3-locket all 1.0.0-2 [5820 B] Get: 170 http://deb.debian.org/debian trixie/main arm64 python3-partd all 1.4.1-1 [15.2 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-dask all 2023.12.1+dfsg-2 [921 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-dill all 0.3.8-1 [81.7 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-mpi4py arm64 3.1.5-5 [663 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-h5py-mpi arm64 3.10.0-1 [1253 kB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-h5py all 3.10.0-1 [14.4 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-pathspec all 0.12.1-1 [28.1 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-trove-classifiers all 2024.1.31-1 [9968 B] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-hatchling all 1.24.2-1 [53.2 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-setuptools-scm all 8.0.4-2 [39.5 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 python3-hatch-vcs all 0.4.0-1 [8336 B] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-multiprocess all 0.70.16-2 [105 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-pairix arm64 0.3.7-7 [42.4 kB] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.1.4+dfsg-5 [6620 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.0+ds-1+b1 [3765 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 7.4.4-3 [239 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-simplejson arm64 3.19.2-1+b1 [66.7 kB] Fetched 112 MB in 0s (262 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. libpam-modules:arm64 depends on libdb5.3. (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 ... 19941 files and directories currently installed.) Removing libdb5.3:arm64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:arm64. (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 ... 19934 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_arm64.deb ... Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19940 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (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 ... 19927 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19942 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (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 ... 20258 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.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-3_all.deb ... Unpacking tzdata (2024a-3) ... 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:arm64. Preparing to unpack .../5-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21250 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../009-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../012-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../014-libbsd0_0.12.2-1_arm64.deb ... Unpacking libbsd0:arm64 (0.12.2-1) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../015-libedit2_3.1-20230828-1+b1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20230828-1+b1) ... Selecting previously unselected package libcbor0.10:arm64. Preparing to unpack .../016-libcbor0.10_0.10.2-1.1_arm64.deb ... Unpacking libcbor0.10:arm64 (0.10.2-1.1) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../017-libfido2-1_1.14.0-1+b2_arm64.deb ... Unpacking libfido2-1:arm64 (1.14.0-1+b2) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a9.6p1-4_arm64.deb ... Unpacking openssh-client (1:9.6p1-4) ... Selecting previously unselected package m4. Preparing to unpack .../019-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../020-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../021-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../022-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../023-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../024-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../025-libtool_2.4.7-7_all.deb ... 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Setting up libbsd0:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up libsz2:arm64 (1.1.3-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up libevent-pthreads-2.1-7t64:arm64 (2.1.12-stable-8.1+b3) ... Setting up libwebpdemux2:arm64 (1.3.2-0.4+b1) ... Setting up libedit2:arm64 (3.1-20230828-1+b1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.3) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libibverbs1:arm64 (50.0-2+b1) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:arm64 (8.7.1-3) ... Setting up ibverbs-providers:arm64 (50.0-2+b1) ... Setting up openssh-client (1:9.6p1-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:arm64 (535.171.04-1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up librdmacm1t64:arm64 (50.0-2+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up libfabric1:arm64 (1.17.0-3+b1) ... Setting up python3.11 (3.11.9-1) ... Setting up libucx0:arm64 (1.15.0-1) ... Setting up libhts3:arm64 (1.19+ds-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up libhwloc-plugins:arm64 (2.10.0-1+b1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-cloudpickle (3.0.0-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-simplejson (3.19.2-1+b1) ... Setting up python3-pil:arm64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-dill (0.3.8-1) ... Setting up python3-typing-extensions (4.10.0-1) ... Setting up python3-asciitree (0.3.3-4) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-trove-classifiers (2024.1.31-1) ... Setting up python3-toolz (0.12.1-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-multiprocess (0.70.16-2) ... Setting up python3-build (1.1.1-1) ... Setting up python3-pathspec (0.12.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-locket (1.0.0-2) ... Setting up python3-cytoolz (0.12.2-2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-partd (1.4.1-1) ... Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pairix:arm64 (0.3.7-7) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libpmix2:arm64 (5.0.1-4+b1) ... Setting up python3-colorama (0.4.6-4) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up python3-pytest (7.4.4-3) ... Setting up libopenmpi3:arm64 (4.1.6-5) ... Setting up python3-fsspec (2024.3.1-1) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-click (8.1.7-1) ... Setting up python3-setuptools-scm (8.0.4-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-hatchling (1.24.2-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up openmpi-bin (4.1.6-5) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libhdf5-openmpi-103-1:arm64 (1.10.10+repack-3+b1) ... Setting up python3-hatch-vcs (0.4.0-1) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-5) ... Setting up mpi-default-bin (1.15) ... Setting up python3-dask (2023.12.1+dfsg-2) ... Setting up python3-mpi4py (3.1.5-5) ... Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up libhdf5-openmpi-hl-100:arm64 (1.10.10+repack-3+b1) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-h5py-mpi (3.10.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-reportlab (4.1.0-4) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: 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 arm64 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:192: 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_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, 249 warnings in 22.23s ============ 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/tmpgeus62d2/tmpvnmb972q.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/tmp80wl9rp1/tmpwrg1qfi9.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/tmpy1_tfnje/tmpkqf8qozp.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/tmp71mif3hz/tmp6gravf4h.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/tmp8fj3xjim/tmprn531qpc.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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:81: 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:858: in wrapper method.__doc__ = _derived_from( /usr/lib/python3/dist-packages/dask/utils.py:811: in _derived_from method_args = get_named_args(method) /usr/lib/python3/dist-packages/dask/utils.py:572: 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:192: 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/tmpltlicrrm/tmprzg6n67t.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/tmp0_jvth_8/tmpi4152h7m.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/tmplncz5oyc/tmphyvpphg3.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_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, 252 warnings in 27.94s ============ 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/3682874 and its subdirectories Mon Apr 29 10:29:20 UTC 2024 W: No second build log, what happened?