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 <ti...@debian.org>  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 <ti...@debian.org>
+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
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