[med-svn] [Git][med-team/sambamba][master] 3 commits: Refresh patch
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 17 20:09:17 GMT 2019
Andreas Tille pushed to branch master at Debian Med / sambamba
Commits:
9145a95f by Andreas Tille at 2019-12-17T20:08:42Z
Refresh patch
- - - - -
b879f5e8 by Andreas Tille at 2019-12-17T20:08:42Z
Use 2to3 to port from Python2 to Python3
- - - - -
21245277 by Andreas Tille at 2019-12-17T20:08:42Z
Set upstream metadata fields: Repository, Repository-Browse.
- - - - -
5 changed files:
- debian/changelog
- debian/patches/02_disable-assert.patch
- + debian/patches/2to3.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+sambamba (0.7.1-2) UNRELEASED; urgency=medium
+
+ * Use 2to3 to port from Python2 to Python3
+ Closes: #938431
+ * Set upstream metadata fields: Repository, Repository-Browse.
+
+ -- Andreas Tille <tille at debian.org> Tue, 17 Dec 2019 21:03:13 +0100
+
sambamba (0.7.1-1) unstable; urgency=medium
[ Andreas Tille ]
=====================================
debian/patches/02_disable-assert.patch
=====================================
@@ -4,9 +4,9 @@ Author: Gianfranco Costamagna <locutusofborg at debian.org>
Bug-Debian: https://bugs.debian.org/893664
Last-Update: 2018-03-21
---- sambamba-0.6.7.orig/sambamba/markdup.d
-+++ sambamba-0.6.7/sambamba/markdup.d
-@@ -606,7 +606,7 @@ struct PairedEndsInfo {
+--- a/sambamba/markdup.d
++++ b/sambamba/markdup.d
+@@ -610,7 +610,7 @@ struct PairedEndsInfo {
}
}
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,117 @@
+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/938431
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 17 Dec 2019 21:03:13 +0100
+
+--- a/INSTALL.md
++++ b/INSTALL.md
+@@ -15,12 +15,12 @@
+ After checking out the source from github with git submodules is is
+ possibleto install the build tools with GNU Guix
+
+- guix package -i gcc-toolchain gdb bash ld-wrapper ldc which python2 git
++ guix package -i gcc-toolchain gdb bash ld-wrapper ldc which python3 git
+
+ Even better, with Guix, you can create a light-weight container in the source tree
+ and run our development setup (gold was added lately by ldc)
+
+- guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
++ guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python3 git binutils-gold vim
+ make clean
+ make -j 4
+ make check
+--- a/RELEASE-NOTES.md
++++ b/RELEASE-NOTES.md
+@@ -69,7 +69,7 @@ Generation 3 Sep 25 2018 09:39:08
+ branch: origin/master
+ commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
+
+-guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
++guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python3 git
+ make clean && make -j 16 && make check
+
+ for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
+--- a/gen_ldc_version_info.py
++++ b/gen_ldc_version_info.py
+@@ -1,6 +1,6 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
++
+
+-from __future__ import print_function
+ import re, sys, subprocess
+
+ if len(sys.argv) < 2:
+@@ -16,7 +16,7 @@ if not match:
+ sys.exit("ERROR: failed to generated LDC version information")
+
+ print("module utils.ldc_version_info_;")
+-for component, version in match.groupdict().items():
++for component, version in list(match.groupdict().items()):
+ if version is None:
+ version = "version not available"
+ print("immutable {0}_VERSION_STRING = \"{1}\";".format(component, version))
+--- a/scripts/bioconda_push.sh
++++ b/scripts/bioconda_push.sh
+@@ -2,7 +2,7 @@ RECIPES=~/github/bioconda-recipes # loca
+ REMOTE=bioconda # bioconda/bioconda-recipes remote
+
+ UPDATED_RECIPE=/tmp/sambamba.yaml
+-python bioconda_yaml_gen.py > $UPDATED_RECIPE
++python3 bioconda_yaml_gen.py > $UPDATED_RECIPE
+ VERSION=`grep version $UPDATED_RECIPE | cut -d\' -f2`
+
+ cd $RECIPES
+--- a/scripts/bioconda_yaml_gen.py
++++ b/scripts/bioconda_yaml_gen.py
+@@ -28,7 +28,7 @@ about:
+ summary: Tools for working with SAM/BAM data"""
+
+ import json
+-from urllib2 import urlopen
++from urllib.request import urlopen
+ from hashlib import md5
+
+ latest_release = json.loads(urlopen("https://api.github.com/repos/biod/sambamba/releases").read())[0]
+@@ -48,7 +48,7 @@ def md5sum(download):
+ linux_md5 = md5sum(downloads['linux'])
+ osx_md5 = md5sum(downloads['osx'])
+
+-print template.format(version=sambamba_version,
++print(template.format(version=sambamba_version,
+ linux_url=downloads['linux'],
+ osx_url=downloads['osx'],
+- linux_md5=linux_md5, osx_md5=osx_md5)
++ linux_md5=linux_md5, osx_md5=osx_md5))
+--- a/test/test_depth.py
++++ b/test/test_depth.py
+@@ -14,7 +14,7 @@ def referenceSequences(bam_fn):
+ return {item['SN']: item['LN'] for item in msgpack.unpackb(header)[2]}
+
+ def randomIntervals(ref_seqs, n, max_length=1000):
+- keys = ref_seqs.keys()
++ keys = list(ref_seqs.keys())
+ result = []
+ for i in range(n):
+ overlap = i > 0 and random.randint(1, 100) <= 20
+@@ -95,14 +95,14 @@ def compareResults(report, expected, pre
+ fn_expected = prefix + "expected_report.txt"
+ saveRegionReport(report, fn_failed)
+ saveRegionReport(expected, fn_expected)
+- print 'TEST FAILURE'
+- print "results saved to " + fn_expected + " and " + fn_failed
+- print "different results:"
+- print "expected: ", expected_entry
+- print "got: ", entry
++ print('TEST FAILURE')
++ print("results saved to " + fn_expected + " and " + fn_failed)
++ print("different results:")
++ print("expected: ", expected_entry)
++ print("got: ", entry)
+ n_wrong += 1
+ if n_wrong >= 10:
+- print "10 or more errors detected, exiting"
++ print("10 or more errors detected, exiting")
+ break
+ else:
+ n_correct += 1
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
01_add-meson-build.patch
02_disable-assert.patch
+2to3.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,25 @@
Reference:
- Author: >
- Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac
- J. Nijman and Pjotr Prins
- Title: "Sambamba: fast processing of NGS alignment formats"
- Journal: Bioinformatics
- Year: 2015
- Volume: 31
- Number: 12
- Pages: 2032-2034
- DOI: 10.1093/bioinformatics/btv098
- PMID: 25697820
- URL: "https://academic.oup.com/bioinformatics/article-lookup/doi/\
- 10.1093/bioinformatics/btv098"
- eprint: "https://academic.oup.com/bioinformatics/article-pdf/\
- 31/12/2032/568750/btv098.pdf"
+ Author: >
+ Artem Tarasov and Albert J. Vilella and Edwin Cuppen and Isaac
+ J. Nijman and Pjotr Prins
+ Title: 'Sambamba: fast processing of NGS alignment formats'
+ Journal: Bioinformatics
+ Year: 2015
+ Volume: 31
+ Number: 12
+ Pages: 2032-2034
+ DOI: 10.1093/bioinformatics/btv098
+ PMID: 25697820
+ URL: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv098
+ eprint: https://academic.oup.com/bioinformatics/article-pdf/31/12/2032/568750/btv098.pdf
Registry:
- - Name: bio.tools
- Entry: Sambamba
- - Name: OMICtools
- Entry: OMICS_07586
- - Name: SciCrunch
- Entry: NA
- - Name: conda:bioconda
- Entry: sambamba
+- Name: bio.tools
+ Entry: Sambamba
+- Name: OMICtools
+ Entry: OMICS_07586
+- Name: SciCrunch
+ Entry: NA
+- Name: conda:bioconda
+ Entry: sambamba
+Repository: https://github.com/lomereiter/sambamba.git
+Repository-Browse: https://github.com/lomereiter/sambamba
View it on GitLab: https://salsa.debian.org/med-team/sambamba/compare/8dd7a7b958308ffc996d30862c5d6ba604400f9d...212452776ff320a98e3f7d6a8e45e49814a54fd6
--
View it on GitLab: https://salsa.debian.org/med-team/sambamba/compare/8dd7a7b958308ffc996d30862c5d6ba604400f9d...212452776ff320a98e3f7d6a8e45e49814a54fd6
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