Étienne Mollier pushed to branch master at Debian Med / kaptive
Commits: bc5edcba by Étienne Mollier at 2021-09-22T17:21:39+02:00 add fix-which-error-output.patch; fix `which` parsing - - - - - 10868232 by Étienne Mollier at 2021-09-22T17:22:32+02:00 routine-update: Fix watchfile to detect new versions on github - - - - - 8664b4b0 by Étienne Mollier at 2021-09-22T17:23:45+02:00 routine-update: Standards-Version: 4.6.0 - - - - - 4f2432d7 by Étienne Mollier at 2021-09-22T17:23:57+02:00 Apply multi-arch hints. + kaptive-data, kaptive-example: Add Multi-Arch: foreign. Changes-By: apply-multiarch-hints - - - - - 2d9d650c by Étienne Mollier at 2021-09-22T17:37:19+02:00 d/t/run-unit-test: run kaptive.py multi threaded This restores the autopkgtest to its initial condition, since the bug #970344 is resolved. - - - - - 7d83b141 by Étienne Mollier at 2021-09-22T17:43:15+02:00 ready for team upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/fix-which-error-output.patch - debian/patches/series - debian/tests/run-unit-test - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,18 @@ +kaptive (0.7.3-4) unstable; urgency=medium + + * Team upload. + * Add fix-which-error-output.patch to fix the way kaptive.py parses `which` + output; this is necessary since `which` in Debian issues a deprecation + warning. + * Fix watchfile to detect new versions on github (routine-update) + * Standards-Version: 4.6.0 (routine-update) + * Apply multi-arch hints. + + kaptive-data, kaptive-example: Add Multi-Arch: foreign. + * d/t/run-unit-test: run kaptive.py in multiple threads again, since the bug + #970344, affecting tblastn, is now solved. + + -- Étienne Mollier <[email protected]> Wed, 22 Sep 2021 17:38:14 +0200 + kaptive (0.7.3-3) unstable; urgency=high * Team upload. ===================================== debian/control ===================================== @@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13), python3-all, python3-setuptools, python3-biopython <!nocheck> -Standards-Version: 4.5.0 +Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/kaptive Vcs-Git: https://salsa.debian.org/med-team/kaptive.git Homepage: https://github.com/katholt/Kaptive @@ -54,6 +54,7 @@ Package: kaptive-data Architecture: all Depends: ${misc:Depends} Enhances: kaptive +Multi-Arch: foreign Description: reference data for kaptive for Klebsiella genome assemblies Kaptive reports information about K and O types for Klebsiella genome assemblies. @@ -89,6 +90,7 @@ Package: kaptive-example Architecture: all Depends: ${misc:Depends} Enhances: kaptive +Multi-Arch: foreign Description: example data for kaptive for Klebsiella genome assemblies Kaptive reports information about K and O types for Klebsiella genome assemblies. ===================================== debian/patches/fix-which-error-output.patch ===================================== @@ -0,0 +1,30 @@ +Description: address handling of `which` command + kaptive.py is unable to run any meaningful computation, due to the way it + handles the output of the command `which makeblastdb` in a context of `which` + outputing deprecation messages in the standard error. The patch is a way to + approximate the behavior of the regular shell use of the command `which` which + consists in checking the error code of the command, and discarding the + standard output. Standard error is left around in case the command `which` + were to have interesting diagnostic messages to the user. +Author: Étienne Mollier <[email protected]> +Forwarded: no +Last-Update: 2021-09-22 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- kaptive.orig/kaptive.py ++++ kaptive/kaptive.py +@@ -171,9 +171,11 @@ + + def find_program(name): + """Checks to see if a program exists.""" +- process = subprocess.Popen(['which', name], stdout=subprocess.PIPE, stderr=subprocess.PIPE) +- out, err = process.communicate() +- return bool(out) and not bool(err) ++ try: ++ subprocess.check_call(['which', name], stdout=subprocess.DEVNULL) ++ except subprocess.CalledProcessError: ++ return False ++ return True + + + def fix_paths(args): ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ blastdb_4 extend_bad_versions +fix-which-error-output.patch ===================================== debian/tests/run-unit-test ===================================== @@ -14,6 +14,4 @@ cd "${AUTOPKGTEST_TMP}" gunzip -r * -echo "FIXME: Due to bug #970344 we are using single threaded mode (-t 1) here." -kaptive.py -t 1 -a exact_match.fasta -k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test -echo "FIXME: Make sure to remove '-t 1' from the kaptive call once bug #970344 is fixed." +kaptive.py -a exact_match.fasta -k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test ===================================== debian/watch ===================================== @@ -1,3 +1,3 @@ version=4 -https://github.com/katholt/Kaptive/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@ +https://github.com/katholt/Kaptive/releases .*/v?@ANY_VERSION@@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0 -- View it on GitLab: https://salsa.debian.org/med-team/kaptive/-/compare/61bc03e075a93af23653f5d3aabec210444f91a7...7d83b1410ebc16f1b69cc77f09faf41f3e3de5f0 You're receiving this email because of your account on salsa.debian.org.
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