[med-svn] [Git][med-team/srst2][master] 9 commits: add myself to Uploaders
Étienne Mollier
gitlab at salsa.debian.org
Tue Nov 10 15:03:38 GMT 2020
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 <etienne.mollier at mailoo.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Étienne Mollier <etienne.mollier at mailoo.org>
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 <etienne.mollier at mailoo.org>
+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
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