Andreas Tille pushed to branch master at Debian Med / samtools
Commits: 0b80afbb by Andreas Tille at 2019-12-03T10:45:22Z Port Python2 script to Python3 using 2to3 - - - - - 30c29179 by Andreas Tille at 2019-12-03T10:45:41Z Standards-Version: 4.4.1 - - - - - 909aa9ba by Andreas Tille at 2019-12-03T10:45:44Z Set fields Upstream-Name in debian/copyright. - - - - - 8bf7ff1d by Andreas Tille at 2019-12-03T10:45:44Z Set upstream metadata fields: Repository-Browse. - - - - - 82f11d9c by Andreas Tille at 2019-12-03T10:45:45Z Remove obsolete fields Name from debian/upstream/metadata. - - - - - 0a09a539 by Andreas Tille at 2019-12-03T10:50:48Z Use python3 dependency once the script was converted - - - - - 49f62d75 by Andreas Tille at 2019-12-03T10:55:41Z Upload to unstable - - - - - 6 changed files: - debian/changelog - debian/control - debian/copyright - + debian/patches/2to3.patch - debian/patches/series - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +samtools (1.9-6) unstable; urgency=medium + + * Port Python2 script to Python3 using 2to3 + Closes: #945735 + * Standards-Version: 4.4.1 + * Set fields Upstream-Name in debian/copyright. + * Set upstream metadata fields: Repository-Browse. + * Remove obsolete fields Name from debian/upstream/metadata. + + -- Andreas Tille <[email protected]> Tue, 03 Dec 2019 11:51:08 +0100 + samtools (1.9-5) unstable; urgency=medium [ Andreas Tille ] ===================================== debian/control ===================================== @@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 12), pkg-config, tabix (>= 1.0) # tabix is needed for the regression tests. -Standards-Version: 4.4.0 +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/samtools Vcs-Git: https://salsa.debian.org/med-team/samtools.git Homepage: http://www.htslib.org/ @@ -24,7 +24,7 @@ Package: samtools Architecture: any-amd64 arm64 armel armhf mips mips64el mipsel ppc64el s390x alpha hppa ia64 m68k powerpc powerpcspe ppc64 riscv64 sh4 sparc64 x32 Depends: ${shlibs:Depends}, ${misc:Depends} -Recommends: python, +Recommends: python3, cwltool Description: processing sequence alignments in SAM, BAM and CRAM formats Samtools is a set of utilities that manipulate nucleotide sequence alignments ===================================== debian/copyright ===================================== @@ -1,5 +1,6 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz +Upstream-Name: SAM tools Files: * Copyright: © 2008–2016, Genome Research Ltd. (GRL) ===================================== debian/patches/2to3.patch ===================================== @@ -0,0 +1,31 @@ +Description: Port Python2 script to Python3 using 2to3 +Bug-Debian: https://bugs.debian.org/945735 +Author: Andreas Tille <[email protected]> +Last-Update: Tue, 03 Dec 2019 11:42:57 +0100 + +--- a/misc/varfilter.py ++++ b/misc/varfilter.py +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python3 + # + # Copyright (C) 2009, 2010 Genome Research Ltd. + # +@@ -54,7 +54,7 @@ import sys + import getopt + + def usage(): +- print '''usage: varfilter.py [options] [cns-pileup] ++ print('''usage: varfilter.py [options] [cns-pileup] + + Options: -Q INT minimum RMS mapping quality for SNPs + -q INT minimum RMS mapping quality for gaps +@@ -72,7 +72,7 @@ Options: -Q INT minimum RMS mapping qual + + -l INT window size for filtering adjacent gaps + +- -p print filtered variants''' ++ -p print filtered variants''') + + def varFilter_aux(first, is_print): + try: ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ spelling.patch sort-tests-memory-limit.patch +2to3.patch ===================================== debian/upstream/metadata ===================================== @@ -1,5 +1,4 @@ Changelog: https://raw.github.com/samtools/samtools/HEAD/NEWS -Name: SAM tools Reference: author: > Heng Li and Bob Handsaker and Alec Wysoker and Tim Fennell and Jue @@ -17,11 +16,12 @@ Reference: eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/btp352v1.pdf Repository: https://github.com/samtools/samtools Registry: - - Name: bio.tools - Entry: samtools - - Name: SciCrunch - Entry: SCR_002105 - - Name: OMICtools - Entry: OMICS_00090 - - Name: conda:bioconda - Entry: samtools +- Name: bio.tools + Entry: samtools +- Name: SciCrunch + Entry: SCR_002105 +- Name: OMICtools + Entry: OMICS_00090 +- Name: conda:bioconda + Entry: samtools +Repository-Browse: https://github.com/samtools/samtools View it on GitLab: https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6 -- View it on GitLab: https://salsa.debian.org/med-team/samtools/compare/5b1c474ae5873ebf1a375fe0d0699dc37d3fe8b8...49f62d75292e384dc9f7a85d72a27c9ffba030d6 You're receiving this email because of your account on salsa.debian.org.
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