cmd: autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-3blbq6mf/python-click-doc_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-click_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-pairtools-examples_1.1.2-1_amd64.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-pairtools_1.1.2-1_amd64.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/pairtools_1.1.2-1.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1140235/system.tar.xz
output (contains stdout and stderr):
autopkgtest [15:48:15]: starting date and time: 2025-01-17 15:48:15+0000
autopkgtest [15:48:15]: version 5.38~bpo12+1
autopkgtest [15:48:15]: host debusine-worker-amd64-hades-06; command line: /usr/bin/autopkgtest --apt-upgrade --output-dir=artifact-dir --summary=artifact-dir/summary --no-built-binaries --needs-internet=run --copy=/etc/resolv.conf:/etc/resolv.conf /tmp/debusine-fetch-exec-upload-3blbq6mf/python-click-doc_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-click_8.2.0-1_all.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-pairtools-examples_1.1.2-1_amd64.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/python3-pairtools_1.1.2-1_amd64.deb /tmp/debusine-fetch-exec-upload-3blbq6mf/pairtools_1.1.2-1.dsc -- unshare --arch amd64 --release sid --tarball /var/lib/debusine/worker/system-images/1140235/system.tar.xz
autopkgtest [15:48:20]: testbed dpkg architecture: amd64
autopkgtest [15:48:20]: testbed apt version: 2.9.20
autopkgtest [15:48:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7324 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 Components [5045 kB]
Fetched 22.6 MB in 2s (9725 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following package was automatically installed and is no longer required:
libldap-2.5-0
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
libldap-common libldap2 libtext-charwidth-perl libtext-wrapi18n-perl
The following packages will be upgraded:
apt base-passwd binutils binutils-common binutils-x86-64-linux-gnu
bsdextrautils bsdutils dash diffutils dpkg dpkg-dev e2fsprogs gcc-14-base
gettext gettext-base gpg gpgconf gzip init-system-helpers libapt-pkg6.0t64
libatomic1 libaudit1 libbinutils libblkid1 libc-bin libc6 libcgi-pm-perl
libcom-err2 libcpanel-json-xs-perl libcrypt1 libctf-nobfd0 libctf0
libcurl3t64-gnutls libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-s1
libglib2.0-0t64 libgomp1 libgprofng0 libgssapi-krb5-2 libhtml-parser-perl
libicu72 libk5crypto3 libkrb5-3 libkrb5support0 liblz1 liblz4-1 libmount1
libsasl2-2 libsasl2-modules-db libsframe1 libsmartcols1 libss2 libssl3t64
libstdc++6 libsystemd0 libtext-markdown-discount-perl libudev1 libuuid1
libxs-parse-keyword-perl libxxhash0 libzstd1 login logsave mount openssl
openssl-provider-legacy sysvinit-utils tzdata ucf util-linux
72 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.7 MB of archives.
After this operation, 1324 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.4-1 [106 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-11 [95.5 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-2 [384 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14.2.0-14 [9288 B]
Get:5 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-14 [137 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-14 [48.6 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-14 [72.7 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-14 [713 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.40-5 [2810 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-4 [60.1 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.4.0-2 [301 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.6+dfsg-2 [300 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.4.0-2 [2302 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257.2-2 [450 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257.2-2 [148 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.22 [1115 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.14 [1537 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.13-1 [138 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 bsdextrautils amd64 2.40.4-1 [92.2 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.4-1 [169 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.4-1 [200 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.4-1 [140 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.4-1 [155 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.4-1 [36.2 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.4-1 [1213 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.277 [10.4 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.6 [53.1 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.22 [1382 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.68 [38.7 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.40-5 [627 kB]
Get:32 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.13-1 [33.2 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.2-1 [23.9 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.2-1 [212 kB]
Get:35 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.2-1 [590 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2+b1 [55.2 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.4-1 [88.4 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 tzdata all 2024b-6 [257 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get:42 http://deb.debian.org/debian sid/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get:43 http://deb.debian.org/debian sid/main amd64 ucf all 3.0048 [42.0 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.43.50.20250108-1 [807 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 libctf0 amd64 2.43.50.20250108-1 [88.4 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.43.50.20250108-1 [155 kB]
Get:47 http://deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.43.50.20250108-1 [2277 kB]
Get:48 http://deb.debian.org/debian sid/main amd64 libbinutils amd64 2.43.50.20250108-1 [532 kB]
Get:49 http://deb.debian.org/debian sid/main amd64 binutils amd64 2.43.50.20250108-1 [68.5 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 binutils-common amd64 2.43.50.20250108-1 [2628 kB]
Get:51 http://deb.debian.org/debian sid/main amd64 libsframe1 amd64 2.43.50.20250108-1 [77.7 kB]
Get:52 http://deb.debian.org/debian sid/main amd64 dpkg-dev all 1.22.14 [1334 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 libdpkg-perl all 1.22.14 [646 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 gpg amd64 2.2.46-1+b1 [532 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 gpgconf amd64 2.2.46-1+b1 [121 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 libcgi-pm-perl all 4.67-1 [217 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get:60 http://deb.debian.org/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.39-1 [130 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get:67 http://deb.debian.org/debian sid/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get:68 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB]
Get:69 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB]
Get:70 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get:71 http://deb.debian.org/debian sid/main amd64 libldap-common all 2.6.9+dfsg-1 [34.5 kB]
Get:72 http://deb.debian.org/debian sid/main amd64 liblz1 amd64 1.15-1 [38.9 kB]
Get:73 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.2-1 [28.7 kB]
Get:74 http://deb.debian.org/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.17-1 [12.9 kB]
Get:75 http://deb.debian.org/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.48-1 [65.6 kB]
Get:76 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.4.0-2 [1422 kB]
Preconfiguring packages ...
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Setting up libxs-parse-keyword-perl (0.48-1) ...
Setting up libatomic1:amd64 (14.2.0-14) ...
Setting up libss2:amd64 (1.47.2-1) ...
Setting up ucf (3.0048) ...
Setting up libk5crypto3:amd64 (1.21.3-4) ...
Setting up libdpkg-perl (1.22.14) ...
Setting up logsave (1.47.2-1) ...
Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8+b1) ...
Setting up mount (2.40.4-1) ...
Setting up libhtml-parser-perl:amd64 (3.83-1+b2) ...
Setting up gpgconf (2.2.46-1+b1) ...
Setting up libkrb5-3:amd64 (1.21.3-4) ...
Setting up libbinutils:amd64 (2.43.50.20250108-1) ...
Setting up openssl (3.4.0-2) ...
Setting up libldap2:amd64 (2.6.9+dfsg-1) ...
Setting up gpg (2.2.46-1+b1) ...
Setting up login (1:4.16.0-2+really2.40.4-1) ...
Setting up libctf0:amd64 (2.43.50.20250108-1) ...
Setting up gettext (0.23.1-1) ...
Setting up libcgi-pm-perl (4.67-1) ...
Setting up e2fsprogs (1.47.2-1) ...
Setting up libglib2.0-0t64:amd64 (2.82.4-2) ...
No schema files found: doing nothing.
Setting up libgprofng0:amd64 (2.43.50.20250108-1) ...
Setting up libgssapi-krb5-2:amd64 (1.21.3-4) ...
Setting up binutils-x86-64-linux-gnu (2.43.50.20250108-1) ...
Setting up libcurl3t64-gnutls:amd64 (8.11.1-1+b1) ...
Setting up binutils (2.43.50.20250108-1) ...
Setting up dpkg-dev (1.22.14) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for debianutils (5.21) ...
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
libldap-2.5-0*
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 578 kB disk space will be freed.
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(Reading database ... 17092 files and directories currently installed.)
Removing libldap-2.5-0:amd64 (2.5.19+dfsg-1) ...
Processing triggers for libc-bin (2.40-5) ...
autopkgtest [15:48:38]: testbed running kernel: Linux 6.1.0-29-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.123-1 (2025-01-02)
autopkgtest [15:48:38]: @@@@@@@@@@@@@@@@@@@@ source /tmp/debusine-fetch-exec-upload-3blbq6mf/pairtools_1.1.2-1.dsc
gpg: Signature made Sat Dec 21 20:37:34 2024 UTC
gpg: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A
gpg: issuer "tchet@debian.org"
gpg: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for /tmp/autopkgtest.q7jLGV/pairtools_1.1.2-1.dsc: no acceptable signature found
dpkg-source: info: extracting pairtools in src
dpkg-source: info: unpacking pairtools_1.1.2.orig.tar.gz
dpkg-source: info: unpacking pairtools_1.1.2-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying makefile
dpkg-source: info: applying fix-spelling
dpkg-source: info: applying tests-to-python3
dpkg-source: info: applying fix-pysam-ftbfs.patch
dpkg-source: info: applying do-not-run-coverage.patch
dpkg-source: info: applying no_install_depends_cython.patch
dpkg-source: info: applying syntax_warning.patch
autopkgtest [15:48:39]: testing package pairtools version 1.1.2-1
autopkgtest [15:48:39]: build not needed
autopkgtest [15:48:39]: test upstream-tests: preparing testbed
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
apt-utils
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 329 kB of archives.
After this operation, 1100 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 apt-utils amd64 2.9.22 [329 kB]
Fetched 329 kB in 0s (8214 kB/s)
Selecting previously unselected package apt-utils.
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(Reading database ... 17082 files and directories currently installed.)
Preparing to unpack .../apt-utils_2.9.22_amd64.deb ...
Unpacking apt-utils (2.9.22) ...
Setting up apt-utils (2.9.22) ...
Processing triggers for man-db (2.13.0-1) ...
Ign:1 file:/tmp/autopkgtest.q7jLGV/binaries InRelease
Get:2 file:/tmp/autopkgtest.q7jLGV/binaries Release [816 B]
Get:2 file:/tmp/autopkgtest.q7jLGV/binaries Release [816 B]
Ign:3 file:/tmp/autopkgtest.q7jLGV/binaries Release.gpg
Get:4 file:/tmp/autopkgtest.q7jLGV/binaries Packages [5377 B]
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Starting pkgProblemResolver with broken count: 0
Starting 2 pkgProblemResolver with broken count: 0
Done
The following NEW packages will be installed:
blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libblas3
libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5
libgraphite2-3 libharfbuzz0b libhts3t64 libhtscodecs2 libimagequant0
libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0
liblcms2-2 liblerc4 libopenjp2-7 libpng16-16t64 libpython3-stdlib
libpython3.13-minimal libpython3.13-stdlib libqhull-r8.0 libraqm0
libsharpyuv0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3
libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1
libxslt1.1 libxss1 media-types python-is-python3 python-matplotlib-data
python3 python3-attr python3-bioframe python3-brotli python3-certifi
python3-chardet python3-charset-normalizer python3-click python3-contourpy
python3-cycler python3-dateutil python3-decorator python3-fonttools
python3-fs python3-idna python3-iniconfig python3-kiwisolver python3-lxml
python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-numpy
python3-packaging python3-pairtools python3-pandas python3-pandas-lib
python3-pil python3-pil.imagetk python3-platformdirs python3-pluggy
python3-pyparsing python3-pysam python3-pytest python3-requests
python3-scipy python3-standard-pipes python3-sympy python3-tk python3-tz
python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-yaml
python3.12-tk python3.13 python3.13-minimal python3.13-tk tk8.6-blt2.5
unicode-data x11-common
0 upgraded, 103 newly installed, 0 to remove and 0 not upgraded.
Need to get 88.8 MB/89.2 MB of archives.
After this operation, 468 MB of additional disk space will be used.
Get:1 file:/tmp/autopkgtest.q7jLGV/binaries python3-click 8.2.0-1 [98.6 kB]
Get:2 file:/tmp/autopkgtest.q7jLGV/binaries python3-pairtools 1.1.2-1 [262 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 python3.13 amd64 3.13.1-3 [740 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get:11 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.45-1 [281 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23.2 [216 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B]
Get:32 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.3-1 [190 kB]
Get:33 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB]
Get:34 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get:35 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get:36 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-14 [837 kB]
Get:37 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get:38 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get:39 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB]
Get:40 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB]
Get:41 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get:42 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get:43 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get:44 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:45 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:46 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB]
Get:47 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get:48 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get:49 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get:50 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB]
Get:51 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB]
Get:52 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get:53 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get:54 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get:55 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get:56 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get:57 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get:58 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get:59 http://deb.debian.org/debian sid/main amd64 python-is-python3 all 3.11.4-1 [3044 B]
Get:60 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get:61 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.3.0-1 [68.8 kB]
Get:62 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:63 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.4.0-1.1 [522 kB]
Get:64 http://deb.debian.org/debian sid/main amd64 python3.12-tk amd64 3.12.8-5 [113 kB]
Get:65 http://deb.debian.org/debian sid/main amd64 python3.13-tk amd64 3.13.1-3 [103 kB]
Get:66 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.13.1-1 [9464 B]
Get:67 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.4.0-1.1 [79.6 kB]
Get:68 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:69 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [4736 kB]
Get:70 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB]
Get:71 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B]
Get:72 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB]
Get:73 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.2-1 [31.0 kB]
Get:74 http://deb.debian.org/debian sid/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get:75 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-6 [95.1 kB]
Get:76 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB]
Get:77 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB]
Get:78 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:79 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB]
Get:80 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get:81 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.13.3-1 [4147 kB]
Get:82 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get:83 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB]
Get:84 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB]
Get:85 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.55.3-1 [1632 kB]
Get:86 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB]
Get:87 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get:88 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB]
Get:89 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB]
Get:90 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get:91 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get:92 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB]
Get:93 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.8-2 [41.6 kB]
Get:94 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 2.2.3-4 [112 kB]
Get:95 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get:96 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:97 http://deb.debian.org/debian sid/main amd64 python3-bioframe all 0.4.1-1 [71.6 kB]
Get:98 http://deb.debian.org/debian sid/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:99 http://deb.debian.org/debian sid/main amd64 python3-standard-pipes all 3.13.0-5 [7376 B]
Get:100 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB]
Get:101 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB]
Get:102 http://deb.debian.org/debian sid/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:103 http://deb.debian.org/debian sid/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Preconfiguring packages ...
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Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ...
Selecting previously unselected package libexpat1:amd64.
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Unpacking python3.13-minimal (3.13.1-3) ...
Setting up libpython3.13-minimal:amd64 (3.13.1-3) ...
Setting up libexpat1:amd64 (2.6.4-1) ...
Setting up python3.13-minimal (3.13.1-3) ...
Selecting previously unselected package python3-minimal.
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Selecting previously unselected package python3.13.
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Unpacking python3.13 (3.13.1-3) ...
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Preparing to unpack .../libpython3-stdlib_3.13.1-2_amd64.deb ...
Unpacking libpython3-stdlib:amd64 (3.13.1-2) ...
Setting up python3-minimal (3.13.1-2) ...
Selecting previously unselected package python3.
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Setting up python3-numpy (1:1.26.4+ds-13) ...
Setting up python3-urllib3 (2.2.3-4) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up python3-lxml:amd64 (5.3.0-1+b1) ...
Setting up libharfbuzz0b:amd64 (10.2.0-1) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up python3-contourpy (1.3.1-1) ...
Setting up libxss1:amd64 (1:1.2.3-1+b3) ...
Setting up libfontconfig1:amd64 (2.15.0-2) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up python-is-python3 (3.11.4-1) ...
Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.13.3-1) ...
Setting up python3-attr (24.3.0-1) ...
Setting up libxft2:amd64 (2.3.6-1+b3) ...
Setting up python3-pysam (0.22.1+ds-2+b2) ...
Setting up python3-scipy (1.14.1-3) ...
Setting up python3-standard-pipes (3.13.0-5) ...
Setting up python3-lz4 (4.4.0+dfsg-1) ...
Setting up python3-charset-normalizer (3.4.0-1+b1) ...
Setting up python3-pytest (8.3.4-1) ...
Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ...
Setting up libtk8.6:amd64 (8.6.16-1) ...
Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ...
Setting up python3.12-tk (3.12.8-5) ...
Setting up python3-yaml (6.0.2-1+b1) ...
Setting up python3.13-tk (3.13.1-3) ...
Setting up python3-pandas (2.2.3+dfsg-5) ...
Setting up libraqm0:amd64 (0.10.2-1) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
Setting up blt (2.5.3+dfsg-7) ...
Setting up python3-tk:amd64 (3.13.1-1) ...
Setting up python3-pil:amd64 (10.4.0-1.1) ...
Setting up python3-pil.imagetk:amd64 (10.4.0-1.1) ...
Setting up python3-fonttools (4.55.3-1) ...
Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-3+b1) ...
Setting up python3-bioframe (0.4.1-1) ...
Setting up python3-pairtools (1.1.2-1) ...
Processing triggers for libc-bin (2.40-5) ...
Processing triggers for man-db (2.13.0-1) ...
autopkgtest [15:49:14]: test upstream-tests: [-----------------------
rm -rf pairtools
pytest-3 --ignore=.pc
============================= test session starts ==============================
platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
rootdir: /tmp/autopkgtest.q7jLGV/build.yTm/src
configfile: pytest.ini
testpaths: tests
collected 34 items
tests/test_dedup.py E [ 2%]
tests/test_filterbycov.py E [ 5%]
tests/test_flip.py F [ 8%]
tests/test_header.py F [ 11%]
tests/test_headerops.py ....... [ 32%]
tests/test_markasdup.py F [ 35%]
tests/test_merge.py E [ 38%]
tests/test_parse.py .FF [ 47%]
tests/test_parse2.py FFFF [ 58%]
tests/test_restrict.py F [ 61%]
tests/test_scaling.py F [ 64%]
tests/test_select.py FFFFFFF [ 85%]
tests/test_sort.py F [ 88%]
tests/test_split.py E [ 91%]
tests/test_stats.py FF. [100%]
==================================== ERRORS ====================================
_____________________ ERROR at setup of test_mock_pairsam ______________________
@pytest.fixture
def setup_dedup():
try:
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"dedup",
mock_pairsam_path_dedup,
"--output",
dedup_path,
"--output-dups",
dups_path,
"--output-unmapped",
unmapped_path,
"--max-mismatch",
str(max_mismatch),
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"dedup",
mock_pairsam_path_dedup,
"--output",
dedup_path_cython,
"--output-dups",
dups_path_cython,
"--output-unmapped",
unmapped_path_cython,
"--max-mismatch",
str(max_mismatch),
"--backend",
"cython",
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"dedup",
mock_pairsam_path_dedup,
"--output",
dedup_max_path,
"--output-dups",
dups_max_path,
"--output-unmapped",
unmapped_max_path,
"--max-mismatch",
str(max_mismatch),
"--method",
"max",
],
)
subprocess.check_output(
[
"python",
"-m",
"pairtools",
"dedup",
mock_pairsam_path_dedup,
"--mark-dups",
"--output",
dedup_markdups_path,
"--output-dups",
dups_markdups_path,
"--output-unmapped",
unmapped_markdups_path,
"--max-mismatch",
str(max_mismatch),
],
)
subprocess.check_output(
[
"python",
"-m",
"pairtools",
"dedup",
mock_pairsam_path_dedup_diff_colnames,
"--mark-dups",
"--output",
dedup_path_diff_colnames,
"--output-dups",
dups_path_diff_colnames,
"--output-unmapped",
unmapped_path_diff_colnames,
"--max-mismatch",
str(max_mismatch),
"--c1",
"chr1",
"--c2",
"chr2",
"--p1",
"p1",
"--p2",
"p2",
"--s1",
"str1",
"--s2",
"str2",
],
)
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_dedup.py:157:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_dedup.py:51: in setup_dedup
subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'dedup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4dedup.pairsam', '--output', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'dedup', '/tmp/au...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'dedup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4dedup.pairsam', '--output', '/tmp/tmpywi3u_mm/dedup.pairsam', '--output-dups', '/tmp/tmpywi3u_mm/dups.pairsam', '--output-unmapped', '/tmp/tmpywi3u_mm/unmapped.pairsam', '--max-mismatch', '1']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
---------------------------- Captured stdout setup -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'dedup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4dedup.pairsam', '--output', '/tmp/tmpywi3u_mm/dedup.pairsam', '--output-dups', '/tmp/tmpywi3u_mm/dups.pairsam', '--output-unmapped', '/tmp/tmpywi3u_mm/unmapped.pairsam', '--max-mismatch', '1']), <traceback object at 0x7fb2191bf580>)
---------------------------- Captured stderr setup -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________ ERROR at setup of test_mock_pairs _______________________
@pytest.fixture
def setup_filterbycov():
try:
for p in params:
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"filterbycov",
mock_pairs_path_filterbycov,
"--output",
p["lowcov_path"],
"--output-highcov",
p["highcov_path"],
"--output-unmapped",
p["unmapped_path"],
"--max-dist",
str(p["max_dist"]),
"--max-cov",
str(p["max_cov"]),
]
)
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_filterbycov.py:63:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_filterbycov.py:41: in setup_filterbycov
subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'filterbycov', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4filterbycov.pairs', '--output', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'filterbycov', '/...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'filterbycov', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4filterbycov.pairs', '--output', '/tmp/tmplb2a_fwp/lowcov.0.3.pairs', '--output-highcov', '/tmp/tmplb2a_fwp/highcov.0.3.pairs', '--output-unmapped', '/tmp/tmplb2a_fwp/unmapped.0.3.pairs', '--max-dist', '0', '--max-cov', '3']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
---------------------------- Captured stdout setup -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'filterbycov', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4filterbycov.pairs', '--output', '/tmp/tmplb2a_fwp/lowcov.0.3.pairs', '--output-highcov', '/tmp/tmplb2a_fwp/highcov.0.3.pairs', '--output-unmapped', '/tmp/tmplb2a_fwp/unmapped.0.3.pairs', '--max-dist', '0', '--max-cov', '3']), <traceback object at 0x7fb2155ad100>)
---------------------------- Captured stderr setup -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_____________________ ERROR at setup of test_mock_pairsam ______________________
@pytest.fixture
def setup_sort_two():
try:
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"sort",
mock_pairsam_path_1,
"--output",
mock_sorted_pairsam_path_1,
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"sort",
mock_pairsam_path_2,
"--output",
mock_sorted_pairsam_path_2,
],
)
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_merge.py:51:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_merge.py:25: in setup_sort_two
subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'sort', '/tmp/aut...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output', '/tmp/tmp6tu1spxw/1.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
---------------------------- Captured stdout setup -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output', '/tmp/tmp6tu1spxw/1.pairsam']), <traceback object at 0x7fb215482200>)
---------------------------- Captured stderr setup -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_________________________ ERROR at setup of test_split _________________________
@pytest.fixture
def setup_split():
try:
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"split",
mock_pairsam_path,
"--output-pairs",
pairs_path,
"--output-sam",
sam_path,
],
)
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_split.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_split.py:23: in setup_split
subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'split', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output-pairs', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'split', '/tmp/au...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'split', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output-pairs', '/tmp/tmpbsg4zwyd/out.pairs', '--output-sam', '/tmp/tmpbsg4zwyd/out.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
---------------------------- Captured stdout setup -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'split', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam', '--output-pairs', '/tmp/tmpbsg4zwyd/out.pairs', '--output-sam', '/tmp/tmpbsg4zwyd/out.sam']), <traceback object at 0x7fb215430f80>)
---------------------------- Captured stderr setup -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
=================================== FAILURES ===================================
__________________________________ test_flip ___________________________________
def test_flip():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"flip",
mock_pairs_path,
"-c",
mock_chromsizes_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_flip.py:31:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_flip.py:17: in test_flip
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'flip', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4flip.pairs', '-c', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'flip', '/tmp/aut...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'flip', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4flip.pairs', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'flip', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4flip.pairs', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes']), <traceback object at 0x7fb2155d6480>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
________________________________ test_generate _________________________________
def test_generate():
"""Test generation of the header.
Example run:
pairtools header generate tests/data/mock.pairsam \
--chroms-path tests/data/mock.chrom.sizes --pairsam \
--sam-path tests/data/mock.sam
"""
mock_sam_path = os.path.join(testdir, "data", "mock.sam")
mock_pairs_path = os.path.join(testdir, "data", "mock.pairsam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"header",
"generate",
"--chroms-path",
mock_chroms_path,
"--sam-path",
mock_sam_path,
"--pairsam",
mock_pairs_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_header.py:44:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_header.py:26: in test_generate
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'header', 'generate', '--chroms-path', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'header', 'genera...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'header', 'generate', '--chroms-path', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--sam-path', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.sam', '--pairsam', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'header', 'generate', '--chroms-path', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--sam-path', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.sam', '--pairsam', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2155d1840>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________________ test_mock_pairsam _______________________________
def test_mock_pairsam():
mock_pairsam_path = os.path.join(testdir, "data", "mock.pairsam")
try:
result = subprocess.check_output(
[currpy, "-m", "pairtools", "markasdup", mock_pairsam_path],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_markasdup.py:22:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_markasdup.py:16: in test_mock_pairsam
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'markasdup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'markasdup', '/tm...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'markasdup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'markasdup', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb215575500>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_______________________________ test_mock_pysam ________________________________
def test_mock_pysam():
"""Parse non-chimeric alignments with walks-policy mask with pysam backend."""
mock_sam_path = os.path.join(testdir, "data", "mock.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"parse",
"--walks-policy",
"mask",
"-c",
mock_chroms_path,
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse.py:24: in test_mock_pysam
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'mask', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'parse', '--walks...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'mask', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'mask', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.sam']), <traceback object at 0x7fb215575b80>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
__________________________ test_mock_pysam_parse_all ___________________________
def test_mock_pysam_parse_all():
"""Parse all alignment in each read with walks-policy all and pysam backend."""
mock_sam_path = os.path.join(testdir, "data", "mock.parse-all.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"parse",
"--walks-policy",
"all",
"-c",
mock_chroms_path,
"--add-pair-index",
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse.py:85:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse.py:68: in test_mock_pysam_parse_all
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'all', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'parse', '--walks...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'all', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse-all.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'parse', '--walks-policy', 'all', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse-all.sam']), <traceback object at 0x7fb2155b97c0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_________________________ test_mock_pysam_parse2_read __________________________
def test_mock_pysam_parse2_read():
mock_sam_path = os.path.join(testdir, "data", "mock.parse2.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"parse2",
"-c",
mock_chroms_path,
"--add-pair-index",
"--flip",
"--report-position",
"junction",
"--report-orientation",
"pair",
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse2.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse2.py:19: in test_mock_pysam_parse2_read
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'parse2', '-c', '...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '--flip', '--report-position', 'junction', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '--flip', '--report-position', 'junction', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2.sam']), <traceback object at 0x7fb2153af840>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_________________________ test_mock_pysam_parse2_pair __________________________
def test_mock_pysam_parse2_pair():
mock_sam_path = os.path.join(testdir, "data", "mock.parse-all.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"parse2",
"-c",
mock_chroms_path,
"--add-pair-index",
"--flip",
"--report-position",
"outer",
"--report-orientation",
"pair",
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse2.py:99:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse2.py:79: in test_mock_pysam_parse2_pair
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'parse2', '-c', '...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '--flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse-all.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--add-pair-index', '--flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse-all.sam']), <traceback object at 0x7fb2155fbc40>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________ test_mock_pysam_parse2_single_end _______________________
def test_mock_pysam_parse2_single_end():
"""Testing single-end mode for parse2, no-flip mode.
--report-position is outer (parse2 default)
--report-orientation is pair (parse2 default)
"""
mock_sam_path = os.path.join(testdir, "data", "mock.parse2-single-end.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
"python",
"-m",
"pairtools",
"parse2",
"-c",
mock_chroms_path,
"--single-end",
"--add-pair-index",
"--no-flip",
"--report-position",
"outer",
"--report-orientation",
"pair",
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse2.py:165:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse2.py:144: in test_mock_pysam_parse2_single_end
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python', '-m', 'pairtools', 'parse2', '-c', '/...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--single-end', '--add-pair-index', '--no-flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2-single-end.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--single-end', '--add-pair-index', '--no-flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2-single-end.sam']), <traceback object at 0x7fb215603500>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
___________________ test_mock_pysam_parse2_single_end_expand ___________________
def test_mock_pysam_parse2_single_end_expand():
"""Testing single-end mode for parse2, no-flip mode, with --expand.
--report-position is outer (parse2 default)
--report-orientation is pair (parse2 default)
"""
mock_sam_path = os.path.join(testdir, "data", "mock.parse2-single-end.expand.sam")
mock_chroms_path = os.path.join(testdir, "data", "mock.chrom.sizes")
try:
result = subprocess.check_output(
[
"python",
"-m",
"pairtools",
"parse2",
"-c",
mock_chroms_path,
"--single-end",
"--expand",
"--add-pair-index",
"--no-flip",
"--report-position",
"outer",
"--report-orientation",
"pair",
mock_sam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_parse2.py:233:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_parse2.py:211: in test_mock_pysam_parse2_single_end_expand
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python', '-m', 'pairtools', 'parse2', '-c', '/...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--single-end', '--expand', '--add-pair-index', '--no-flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2-single-end.expand.sam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python', '-m', 'pairtools', 'parse2', '-c', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '--single-end', '--expand', '--add-pair-index', '--no-flip', '--report-position', 'outer', '--report-orientation', 'pair', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.parse2-single-end.expand.sam']), <traceback object at 0x7fb215458bc0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
________________________________ test_restrict _________________________________
def test_restrict():
"""Restrict pairs file"""
mock_pairs_path = os.path.join(testdir, "data", "mock.test-restr.pairs")
mock_rfrag_path = os.path.join(testdir, "data", "mock.rsites.bed")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"restrict",
"-f",
mock_rfrag_path,
mock_pairs_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_restrict.py:34:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_restrict.py:20: in test_restrict
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'restrict', '-f', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.rsites.bed', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'restrict', '-f',...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'restrict', '-f', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.rsites.bed', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.test-restr.pairs']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'restrict', '-f', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.rsites.bed', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.test-restr.pairs']), <traceback object at 0x7fb21559dac0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_________________________________ test_scaling _________________________________
def test_scaling():
mock_pairsam_path = os.path.join(testdir, "data", "mock.pairsam")
try:
result = subprocess.check_output(
[currpy, "-m", "pairtools", "scaling", mock_pairsam_path],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_scaling.py:24:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scaling.py:18: in test_scaling
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'scaling', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'scaling', '/tmp/...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'scaling', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'scaling', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb21540aac0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
________________________________ test_preserve _________________________________
def test_preserve():
try:
result = subprocess.check_output(
[currpy, "-m", "pairtools", "select", "True", mock_pairsam_path],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:24:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:18: in test_preserve
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'True', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'True',...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'True', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'True', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2153e9e80>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
__________________________________ test_equal __________________________________
def test_equal():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
'(pair_type == "RU") or (pair_type == "UR") or (pair_type == "UU")',
mock_pairsam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:52:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:39: in test_equal
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', '(pair_type == "RU") or (pair_type == "UR") or (pair_type == "UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', '(pair_...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', '(pair_type == "RU") or (pair_type == "UR") or (pair_type == "UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', '(pair_type == "RU") or (pair_type == "UR") or (pair_type == "UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb21555d800>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
___________________________________ test_csv ___________________________________
def test_csv():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
'csv_match(pair_type, "RU,UR,UU")',
mock_pairsam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:85:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:72: in test_csv
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'csv_match(pair_type, "RU,UR,UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'csv_ma...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'csv_match(pair_type, "RU,UR,UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'csv_match(pair_type, "RU,UR,UU")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2153b4880>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
________________________________ test_wildcard _________________________________
def test_wildcard():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
'wildcard_match(pair_type, "*U")',
mock_pairsam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:118:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:105: in test_wildcard
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'wildcard_match(pair_type, "*U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'wildca...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'wildcard_match(pair_type, "*U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'wildcard_match(pair_type, "*U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb21540fbc0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
__________________________________ test_regex __________________________________
def test_regex():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
'regex_match(pair_type, "[NM]U")',
mock_pairsam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:153:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:140: in test_regex
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'regex_match(pair_type, "[NM]U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'regex_...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'regex_match(pair_type, "[NM]U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'regex_match(pair_type, "[NM]U")', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb21558db40>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________________ test_chrom_subset _______________________________
def test_chrom_subset():
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
"True",
"--chrom-subset",
mock_chromsizes_path,
mock_pairsam_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:188:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:173: in test_chrom_subset
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'True', '--chrom-subset', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'True',...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'True', '--chrom-subset', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'True', '--chrom-subset', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.chrom.sizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2155f61c0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_____________________________ test_remove_columns ______________________________
def test_remove_columns():
"""Test removal of columns from the file
Example run:
pairtools select True --remove-columns sam1,sam2 tests/data/mock.pairsam
"""
mock_pairs_path = os.path.join(testdir, "data", "mock.pairsam")
try:
result = subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"select",
"True",
"--remove-columns",
"sam1,sam2",
mock_pairs_path,
],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_select.py:241:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_select.py:225: in test_remove_columns
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'select', 'True', '--remove-columns', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'select', 'True',...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'select', 'True', '--remove-columns', 'sam1,sam2', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'select', 'True', '--remove-columns', 'sam1,sam2', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2155973c0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________________ test_mock_pairsam _______________________________
def test_mock_pairsam():
mock_pairsam_path = os.path.join(testdir, "data", "mock.pairsam")
try:
result = subprocess.check_output(
[currpy, "-m", "pairtools", "sort", mock_pairsam_path],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_sort.py:22:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_sort.py:16: in test_mock_pairsam
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'sort', '/tmp/aut...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'sort', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.pairsam']), <traceback object at 0x7fb2151c1400>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
______________________________ test_mock_pairsam _______________________________
def test_mock_pairsam():
mock_pairsam_path = os.path.join(testdir, "data", "mock.4stats.pairs")
try:
result = subprocess.check_output(
[currpy, "-m", "pairtools", "stats", "--yaml", mock_pairsam_path],
).decode("ascii")
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_stats.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_stats.py:20: in test_mock_pairsam
result = subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'stats', '--yaml', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs'],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'stats', '--yaml'...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'stats', '--yaml', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'stats', '--yaml', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs']), <traceback object at 0x7fb2155d4a80>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
_______________________________ test_merge_stats _______________________________
def test_merge_stats():
mock_pairsam_path = os.path.join(testdir, "data", "mock.4stats.pairs")
try:
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"stats",
"--with-chromsizes",
mock_pairsam_path,
"--output",
"mock.stats",
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"stats",
"--no-chromsizes",
mock_pairsam_path,
"--output",
"mock.no_chromsizes.stats",
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"stats",
"mock.stats",
"mock.stats",
"--merge",
"--output",
"mock.merged_chromsizes.stats",
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"stats",
"mock.stats",
"mock.no_chromsizes.stats",
"--merge",
"--output",
"mock.merged_mixed.stats",
],
)
subprocess.check_output(
[
currpy,
"-m",
"pairtools",
"stats",
"mock.no_chromsizes.stats",
"mock.no_chromsizes.stats",
"--merge",
"--output",
"mock.merged_no_chromsizes.stats",
],
)
except subprocess.CalledProcessError as e:
print(e.output)
print(sys.exc_info())
> raise e
tests/test_stats.py:139:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_stats.py:72: in test_merge_stats
subprocess.check_output(
/usr/lib/python3.13/subprocess.py:472: in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
input = None, capture_output = False, timeout = None, check = True
popenargs = (['python3', '-m', 'pairtools', 'stats', '--with-chromsizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs', ...],)
kwargs = {'stdout': -1}
process = <Popen: returncode: 1 args: ['python3', '-m', 'pairtools', 'stats', '--with-...>
stdout = b'', stderr = None, retcode = 1
def run(*popenargs,
input=None, capture_output=False, timeout=None, check=False, **kwargs):
"""Run command with arguments and return a CompletedProcess instance.
The returned instance will have attributes args, returncode, stdout and
stderr. By default, stdout and stderr are not captured, and those attributes
will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
or pass capture_output=True to capture both.
If check is True and the exit code was non-zero, it raises a
CalledProcessError. The CalledProcessError object will have the return code
in the returncode attribute, and output & stderr attributes if those streams
were captured.
If timeout (seconds) is given and the process takes too long,
a TimeoutExpired exception will be raised.
There is an optional argument "input", allowing you to
pass bytes or a string to the subprocess's stdin. If you use this argument
you may not also use the Popen constructor's "stdin" argument, as
it will be used internally.
By default, all communication is in bytes, and therefore any "input" should
be bytes, and the stdout and stderr will be bytes. If in text mode, any
"input" should be a string, and stdout and stderr will be strings decoded
according to locale encoding, or by "encoding" if set. Text mode is
triggered by setting any of text, encoding, errors or universal_newlines.
The other arguments are the same as for the Popen constructor.
"""
if input is not None:
if kwargs.get('stdin') is not None:
raise ValueError('stdin and input arguments may not both be used.')
kwargs['stdin'] = PIPE
if capture_output:
if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
raise ValueError('stdout and stderr arguments may not be used '
'with capture_output.')
kwargs['stdout'] = PIPE
kwargs['stderr'] = PIPE
with Popen(*popenargs, **kwargs) as process:
try:
stdout, stderr = process.communicate(input, timeout=timeout)
except TimeoutExpired as exc:
process.kill()
if _mswindows:
# Windows accumulates the output in a single blocking
# read() call run on child threads, with the timeout
# being done in a join() on those threads. communicate()
# _after_ kill() is required to collect that and add it
# to the exception.
exc.stdout, exc.stderr = process.communicate()
else:
# POSIX _communicate already populated the output so
# far into the TimeoutExpired exception.
process.wait()
raise
except: # Including KeyboardInterrupt, communicate handled that.
process.kill()
# We don't call process.wait() as .__exit__ does that for us.
raise
retcode = process.poll()
if check and retcode:
> raise CalledProcessError(retcode, process.args,
output=stdout, stderr=stderr)
E subprocess.CalledProcessError: Command '['python3', '-m', 'pairtools', 'stats', '--with-chromsizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs', '--output', 'mock.stats']' returned non-zero exit status 1.
/usr/lib/python3.13/subprocess.py:577: CalledProcessError
----------------------------- Captured stdout call -----------------------------
b''
(<class 'subprocess.CalledProcessError'>, CalledProcessError(1, ['python3', '-m', 'pairtools', 'stats', '--with-chromsizes', '/tmp/autopkgtest.q7jLGV/build.yTm/src/tests/data/mock.4stats.pairs', '--output', 'mock.stats']), <traceback object at 0x7fb215602bc0>)
----------------------------- Captured stderr call -----------------------------
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/lib/python3/dist-packages/pairtools/__main__.py", line 1, in <module>
from .cli import cli
File "/usr/lib/python3/dist-packages/pairtools/cli/__init__.py", line 188, in <module>
from . import (
...<16 lines>...
)
File "/usr/lib/python3/dist-packages/pairtools/cli/scaling.py", line 11, in <module>
from ..lib.scaling import compute_scaling
File "/usr/lib/python3/dist-packages/pairtools/lib/scaling.py", line 6, in <module>
import bioframe
File "/usr/lib/python3/dist-packages/bioframe/__init__.py", line 3, in <module>
from .io import *
File "/usr/lib/python3/dist-packages/bioframe/io/__init__.py", line 6, in <module>
from . import resources
File "/usr/lib/python3/dist-packages/bioframe/io/resources.py", line 13, in <module>
import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'
=============================== warnings summary ===============================
../../../../usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2
/usr/lib/python3/dist-packages/pairtools/lib/fileio.py:2: DeprecationWarning: pipes was removed in Python 3.13. Please be aware that you are currently NOT using standard 'pipes', but instead a separately installed 'standard-pipes'.
import pipes
tests/test_stats.py::test_find_dist_freq_convergence_distance
/usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: divide by zero encountered in scalar divide
strands: n_cis_pairs / norm_factor
tests/test_stats.py::test_find_dist_freq_convergence_distance
/usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: divide by zero encountered in scalar divide
sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor )
tests/test_stats.py::test_find_dist_freq_convergence_distance
/usr/lib/python3/dist-packages/pairtools/lib/stats.py:410: RuntimeWarning: invalid value encountered in divide
np.abs(dist_freqs_by_strands[strands] - avg_freq_all_strands)
tests/test_stats.py::test_find_dist_freq_convergence_distance
/usr/lib/python3/dist-packages/pairtools/lib/stats.py:466: RuntimeWarning: invalid value encountered in scalar divide
strands: n_cis_pairs / norm_factor
tests/test_stats.py::test_find_dist_freq_convergence_distance
/usr/lib/python3/dist-packages/pairtools/lib/stats.py:474: RuntimeWarning: invalid value encountered in scalar divide
sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor )
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_flip.py::test_flip - subprocess.CalledProcessError: Command...
FAILED tests/test_header.py::test_generate - subprocess.CalledProcessError: C...
FAILED tests/test_markasdup.py::test_mock_pairsam - subprocess.CalledProcessE...
FAILED tests/test_parse.py::test_mock_pysam - subprocess.CalledProcessError: ...
FAILED tests/test_parse.py::test_mock_pysam_parse_all - subprocess.CalledProc...
FAILED tests/test_parse2.py::test_mock_pysam_parse2_read - subprocess.CalledP...
FAILED tests/test_parse2.py::test_mock_pysam_parse2_pair - subprocess.CalledP...
FAILED tests/test_parse2.py::test_mock_pysam_parse2_single_end - subprocess.C...
FAILED tests/test_parse2.py::test_mock_pysam_parse2_single_end_expand - subpr...
FAILED tests/test_restrict.py::test_restrict - subprocess.CalledProcessError:...
FAILED tests/test_scaling.py::test_scaling - subprocess.CalledProcessError: C...
FAILED tests/test_select.py::test_preserve - subprocess.CalledProcessError: C...
FAILED tests/test_select.py::test_equal - subprocess.CalledProcessError: Comm...
FAILED tests/test_select.py::test_csv - subprocess.CalledProcessError: Comman...
FAILED tests/test_select.py::test_wildcard - subprocess.CalledProcessError: C...
FAILED tests/test_select.py::test_regex - subprocess.CalledProcessError: Comm...
FAILED tests/test_select.py::test_chrom_subset - subprocess.CalledProcessErro...
FAILED tests/test_select.py::test_remove_columns - subprocess.CalledProcessEr...
FAILED tests/test_sort.py::test_mock_pairsam - subprocess.CalledProcessError:...
FAILED tests/test_stats.py::test_mock_pairsam - subprocess.CalledProcessError...
FAILED tests/test_stats.py::test_merge_stats - subprocess.CalledProcessError:...
ERROR tests/test_dedup.py::test_mock_pairsam - subprocess.CalledProcessError:...
ERROR tests/test_filterbycov.py::test_mock_pairs - subprocess.CalledProcessEr...
ERROR tests/test_merge.py::test_mock_pairsam - subprocess.CalledProcessError:...
ERROR tests/test_split.py::test_split - subprocess.CalledProcessError: Comman...
============= 21 failed, 9 passed, 6 warnings, 4 errors in 11.39s ==============
autopkgtest [15:49:26]: test upstream-tests: -----------------------]
autopkgtest [15:49:26]: test upstream-tests: - - - - - - - - - - results - - - - - - - - - -
upstream-tests FAIL non-zero exit status 1
autopkgtest [15:49:26]: @@@@@@@@@@@@@@@@@@@@ summary
upstream-tests FAIL non-zero exit status 1
aborted: False
returncode: 4
Files in working directory:
artifact-dir
artifact-dir/binaries
artifact-dir/binaries/python-click-doc.deb
artifact-dir/binaries/python3-click.deb
artifact-dir/binaries/python3-pairtools-examples.deb
artifact-dir/binaries/python3-pairtools.deb
artifact-dir/log
artifact-dir/summary
artifact-dir/testbed-packages
artifact-dir/testinfo.json
artifact-dir/testpkg-version
artifact-dir/upstream-tests-packages
artifact-dir/upstream-tests-stderr
artifact-dir/upstream-tests-stdout
--------------------