Étienne Mollier pushed to branch master at Debian Med / srst2
Commits: ddfe1ba9 by Étienne Mollier at 2020-11-10T15:36:22+01:00 add myself to Uploaders - - - - - 885df8b5 by Étienne Mollier at 2020-11-10T15:38:17+01:00 add biopython-1.78.patch - - - - - 1f1df59a by Étienne Mollier at 2020-11-10T15:49:22+01:00 bump to watch file version 4 - - - - - 10442c46 by Étienne Mollier at 2020-11-10T15:50:24+01:00 routine-update: Standards-Version: 4.5.0 - - - - - f6ffed33 by Étienne Mollier at 2020-11-10T15:50:24+01:00 routine-update: debhelper-compat 13 - - - - - 4728ecea by Étienne Mollier at 2020-11-10T15:50:27+01:00 routine-update: Add salsa-ci file - - - - - e0b984bd by Étienne Mollier at 2020-11-10T15:50:28+01:00 routine-update: Rules-Requires-Root: no - - - - - 9f60831a by Étienne Mollier at 2020-11-10T15:50:29+01:00 Set upstream metadata fields: Bug-Database, Bug-Submit. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-missing-bug-tracking See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html - - - - - ddbddc74 by Étienne Mollier at 2020-11-10T15:51:18+01:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - debian/changelog - debian/control - + debian/patches/biopython-1.78.patch - debian/patches/series - + debian/salsa-ci.yml - debian/upstream/metadata - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +srst2 (0.2.0-9) unstable; urgency=medium + + * Add myself to Uploaders. + * Add patch biopython-1.78 for compatibility with Bio.Alphabet removal.. + * Bump watch file to version 4. + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Set upstream metadata fields: Bug-Database, Bug-Submit. + + -- Étienne Mollier <[email protected]> Tue, 10 Nov 2020 15:50:29 +0100 + srst2 (0.2.0-7) unstable; urgency=medium * Use 2to3 to port from Python2 to Python3 ===================================== debian/control ===================================== @@ -1,9 +1,10 @@ Source: srst2 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, @@ -13,10 +14,11 @@ Build-Depends: debhelper-compat (= 12), python3-scipy <!nocheck>, bowtie2 <!nocheck>, samtools <!nocheck> -Standards-Version: 4.4.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/srst2 Vcs-Git: https://salsa.debian.org/med-team/srst2.git Homepage: https://katholt.github.io/srst2/ +Rules-Requires-Root: no Package: srst2 Architecture: any ===================================== debian/patches/biopython-1.78.patch ===================================== @@ -0,0 +1,47 @@ +Description: remove imports of Bio.Alphabet + This is needed for compatibility with Biopython 1.78. +Author: Étienne Mollier <[email protected]> +Bug: https://github.com/katholt/srst2/pull/133 +Last-Update: 2020-11-10 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- srst2.orig/database_clustering/VFDBgenus.py ++++ srst2/database_clustering/VFDBgenus.py +@@ -10,7 +10,6 @@ + from Bio import SeqIO + from Bio.Seq import Seq + from Bio.SeqRecord import SeqRecord +-from Bio.Alphabet import IUPAC + + def parse_args(): + parser = ArgumentParser(description='Extract virulence genes by genus from the VFDB database available at http://www.mgc.ac.cn/VFs/Down/CP_VFs.ffn.gz') +--- srst2.orig/database_clustering/csv_to_gene_db.py ++++ srst2/database_clustering/csv_to_gene_db.py +@@ -16,7 +16,6 @@ + from Bio import SeqIO + from Bio.Seq import Seq + from Bio.SeqRecord import SeqRecord +-from Bio.Alphabet import IUPAC + + def main(): + +@@ -73,8 +72,7 @@ + + if seqid_col: + seq = fields.pop(seqid_col-1) +- record = SeqRecord(Seq(seq, +- IUPAC.unambiguous_dna), ++ record = SeqRecord(Seq(seq), + id=db_id, + description=db_id) + elif seqs_file_col: +--- srst2.orig/scripts/consensus_alignment.py ++++ srst2/scripts/consensus_alignment.py +@@ -11,7 +11,6 @@ + from Bio import SeqIO + from Bio.Seq import Seq + from Bio.SeqRecord import SeqRecord +-from Bio.Alphabet import IUPAC + + def parse_args(): + "Parse the input arguments, use '-h' for help." ===================================== debian/patches/series ===================================== @@ -3,3 +3,4 @@ add_usr_bin_python_to_scripts.patch fix_test.patch fix_grep_call.patch 2to3.patch +biopython-1.78.patch ===================================== 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 ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Bug-Database: https://github.com/katholt/srst2/issues +Bug-Submit: https://github.com/katholt/srst2/issues/new Reference: Author: > Michael Inouye and Harriet Dashnow and Lesley-Ann Raven and ===================================== debian/watch ===================================== @@ -1,3 +1,3 @@ -version=3 +version=4 https://github.com/katholt/srst2/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) View it on GitLab: https://salsa.debian.org/med-team/srst2/-/compare/bb677a4e51b328d985454f5cd29a0e724a41b8f2...ddbddc74f6cd3dec8a90c677087747af811bfee2 -- View it on GitLab: https://salsa.debian.org/med-team/srst2/-/compare/bb677a4e51b328d985454f5cd29a0e724a41b8f2...ddbddc74f6cd3dec8a90c677087747af811bfee2 You're receiving this email because of your account on salsa.debian.org.
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