Étienne Mollier pushed to branch master at Debian Med / kleborate
Commits: 533bbc42 by Étienne Mollier at 2020-09-19T16:14:12+02:00 Added myself to uploaders. - - - - - b32aa167 by Étienne Mollier at 2020-09-19T17:51:57+02:00 improved build reproducibility - - - - - 7cf27a2a by Étienne Mollier at 2020-09-19T17:54:09+02:00 added fix-ftbfs-biopython-1.78.patch - - - - - 59eeca34 by Étienne Mollier at 2020-09-19T18:06:02+02:00 routine-update: debhelper-compat 13 - - - - - 66cdc707 by Étienne Mollier at 2020-09-19T18:06:05+02:00 routine-update: Add salsa-ci file - - - - - 0b8c329f by Étienne Mollier at 2020-09-19T18:06:05+02:00 routine-update: Rules-Requires-Root: no - - - - - 30da58f4 by Étienne Mollier at 2020-09-19T18:08:11+02:00 routine-update: Ready to upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - + debian/patches/fix-ftbfs-biopython-1.78.patch - debian/patches/series - debian/rules - + debian/salsa-ci.yml Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,17 @@ -kleborate (1.0.0-4) UNRELEASED; urgency=medium +kleborate (1.0.0-4) unstable; urgency=medium + [ Andreas Tille ] * Comment debugging code in postinst - -- Andreas Tille <[email protected]> Wed, 29 Jan 2020 13:56:28 +0100 + [ Étienne Mollier ] + * Added myself to uploaders. + * Improved build reproducibility. + * Fixed FTBFS with python-biopython 1.78. + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Étienne Mollier <[email protected]> Sat, 19 Sep 2020 18:06:07 +0200 kleborate (1.0.0-3) unstable; urgency=medium ===================================== debian/control ===================================== @@ -1,9 +1,10 @@ Source: kleborate Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Étienne Mollier <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, @@ -14,6 +15,7 @@ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/kleborate Vcs-Git: https://salsa.debian.org/med-team/kleborate.git Homepage: https://github.com/katholt/Kleborate +Rules-Requires-Root: no Package: kleborate Architecture: any ===================================== debian/patches/fix-ftbfs-biopython-1.78.patch ===================================== @@ -0,0 +1,28 @@ +Description: fix FTBFS with python-biopython 1.78 + The module Bio.Alphabet has been removed in version 1.78. + More details are available at: + https://biopython.org/wiki/Alphabet +Author: Étienne Mollier <[email protected]> +Forwarded: no +Last-Update: 2020-09-19 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- kleborate.orig/kleborate/truncation.py ++++ kleborate/kleborate/truncation.py +@@ -13,7 +13,6 @@ + """ + + from Bio.Seq import Seq +-from Bio.Alphabet import IUPAC + + from .misc import reverse_complement + +@@ -51,7 +50,7 @@ + # denominator for coverage. + ref_aa_length = (hit.ref_length - 3) // 3 + +- coding_dna = Seq(nucl_seq, IUPAC.unambiguous_dna) ++ coding_dna = Seq(nucl_seq) + translation = str(coding_dna.translate(table='Bacterial', to_stop=True)) + + coverage = 100.0 * len(translation) / ref_aa_length ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ python3.patch use_debian_installed_kaptive.patch +fix-ftbfs-biopython-1.78.patch ===================================== debian/rules ===================================== @@ -1,5 +1,7 @@ #!/usr/bin/make -f +export LC_ALL=C + %: dh $@ --with python3 --buildsystem=pybuild ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828 -- View it on GitLab: https://salsa.debian.org/med-team/kleborate/-/compare/15f181816c2f1bff70b161c033a5166901d748cc...30da58f476cf8b54301c7878615e2b64fa4e4828 You're receiving this email because of your account on salsa.debian.org.
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