[med-svn] [Git][med-team/kleborate][master] 7 commits: Added myself to uploaders.

[Étienne Mollier]

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 <tille at debian.org>  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 <etienne.mollier at mailoo.org>  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 <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,
@@ -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 <etienne.mollier at mailoo.org>
+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
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