Please use our scripts to save time and enhance quality [Was: [Git][med-team/igdiscover][master] 2 commits: Adjusting build dependencies]
Hi,
since I have realised the upload of igdiscover to new and no according
commit message in our commit mailing list I added the commit hooks
manually. There would be no need for manual intervention if everybody
who creates a new repository would use
https://salsa.debian.org/med-team/community/helper-scripts/blob/master/inject-into-salsa-git
This script should be called from a new local git repository and will
create the remote one on salsa.d.o and sets all the hooks we want. I
would be happy if everybody would prefer this over manual creation of
repositories since usually this will not include all settings we want
to have.
Hope this helps
Andreas.
----- Forwarded message from Andreas Tille <gitlab@salsa.debian.org> -----
Date: Fri, 02 Aug 2019 03:28:05 +0000
From: Andreas Tille <gitlab@salsa.debian.org>
To: debian-med-commit@lists.alioth.debian.org
Subject: [Git][med-team/igdiscover][master] 2 commits: Adjusting build dependencies
Andreas Tille pushed to branch master at Debian Med / igdiscover
Commits:
1cc07041 by Steffen Möller at 2019-02-12T09:25:15Z
Adjusting build dependencies
- - - - -
df76dec7 by Steffen Möller at 2019-08-01T23:06:59Z
Fixed FTBFS with new cutadapt (>= 2.3)
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/minoverlap.patch
- + debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,11 @@
-igdiscover (0.11-1) UNRELEASED; urgency=medium
+igdiscover (0.11-2) unstable; urgency=medium
+
+ * Introduced patch for compatibility with later versions
+ of cutadapt - upstream has it already in their master branch.
+
+ -- Steffen Moeller <moeller@debian.org> Fri, 02 Aug 2019 00:55:02 +0200
+
+igdiscover (0.11-1) unstable; urgency=medium
* Initial release (Closes: #919718)
=====================================
debian/control
=====================================
@@ -38,9 +38,8 @@ Depends: ${python3:Depends},
python3-cutadapt,
python3-scipy (>=0.16.1),
python3-xopen (>=0.3.2),
+ python3-seaborn (>=0.9),
python3-ruamel.yaml
-Recommends: python3-seaborn (>=0.8.1),
- python3-matplotlib
Suggests: snakemake,
igdiscover-doc
Description: analyzes antibody repertoires to find new V genes
=====================================
debian/patches/minoverlap.patch
=====================================
@@ -0,0 +1,14 @@
+Index: igdiscover/igdiscover/utils.py
+===================================================================
+--- igdiscover.orig/igdiscover/utils.py
++++ igdiscover/igdiscover/utils.py
+@@ -330,8 +330,7 @@ def find_overlap(s, t, min_overlap=1):
+ >>> find_overlap('ABC', 'X') is None
+ True
+ """
+- aligner = Aligner(s, max_error_rate=0)
+- aligner.min_overlap = min_overlap
++ aligner = Aligner(s, max_error_rate=0, min_overlap=min_overlap)
+ result = aligner.locate(t)
+ if result is None:
+ return None
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+minoverlap.patch
View it on GitLab: https://salsa.debian.org/med-team/igdiscover/compare/dc8ee7231d33b6e526845fcb32a407ead20cb1a1...df76dec71814551cc3d7914005f4a2e15635b7be
--
View it on GitLab: https://salsa.debian.org/med-team/igdiscover/compare/dc8ee7231d33b6e526845fcb32a407ead20cb1a1...df76dec71814551cc3d7914005f4a2e15635b7be
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