[med-svn] [Git][med-team/python-pysam][master] 5 commits: make the build reproducible

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-pysam


Commits:
6b346cfe by Andreas Tille at 2020-01-06T17:44:00+01:00
make the build reproducible

- - - - -
f63e5029 by Andreas Tille at 2020-01-06T17:44:20+01:00
routine-update: Standards-Version: 4.4.1

- - - - -
7483b5c2 by Andreas Tille at 2020-01-06T17:44:22+01:00
debian/copyright: use spaces rather than tabs to start continuation lines.

Fixes lintian: tab-in-licence-text
See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.

- - - - -
a6a8463f by Andreas Tille at 2020-01-06T17:44:22+01:00
Set upstream metadata fields: Bug-Database, Repository, Repository-Browse.
- - - - -
9f8aea85 by Andreas Tille at 2020-01-06T17:55:52+01:00
routine-update: Ready to upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/copyright
- debian/rules
- debian/upstream/metadata


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+python-pysam (0.15.3+ds-5) unstable; urgency=medium
+
+  [ Chris Lamb ]
+  * make the build reproducible
+    Closes: #948280
+
+  [ Andreas Tille ]
+  * Standards-Version: 4.4.1
+  * debian/copyright: use spaces rather than tabs to start continuation
+    lines.
+  * Set upstream metadata fields: Bug-Database, Repository, Repository-
+    Browse.
+
+ -- Andreas Tille <tille at debian.org>  Mon, 06 Jan 2020 17:44:23 +0100
+
 python-pysam (0.15.3+ds-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -21,7 +21,7 @@ Build-Depends: debhelper-compat (= 12),
                bcftools (>= 1.9) <!nocheck>,
                python-pytest <!nocheck>,
                python3-pytest <!nocheck>
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
 Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
 Homepage: https://pysam.readthedocs.org/en/latest


=====================================
debian/copyright
=====================================
@@ -6,26 +6,26 @@ Files-Excluded: htslib/*
 
 Files: *
 Copyright: 2009-2018 Andreas Heger,
-	             Tildon Grant Belgrad,
-		     Martin Goodson,
-		     Kevin Jacobs <jacobs at bionformed.com>
-	   2008-2010 Genome Research Ltd.
+ 	             Tildon Grant Belgrad,
+ 		     Martin Goodson,
+ 		     Kevin Jacobs <jacobs at bionformed.com>
+ 	   2008-2010 Genome Research Ltd.
 License: MIT
 
 Files: bcftools/*
 Copyright:
-	2013-2018 Genome Research Ltd.
-	2010-2011 Broad Institute
+ 	2013-2018 Genome Research Ltd.
+ 	2010-2011 Broad Institute
 License: MIT
 
 Files: samtools/*
 Copyright: 2009-2012 Broad Institute
-	   2008-2014 Genome Research Ltd.
+           2008-2014 Genome Research Ltd.
 License: MIT
 
 Files: samtools/bam_cat.*
 Copyright: 2008-2009, 2011-2013 Genome Research Ltd.
-	   2010 Illumina, Inc.
+           2010 Illumina, Inc.
 License: MIT
 
 Files: samtools/bam_color.*
@@ -35,8 +35,8 @@ License: MIT
 Files: samtools/bam_index.*
        samtools/bam_mate.*
 Copyright: 2008-2014 Genome Research Ltd.
-	   2010-2011 Broad Institute
-	   2012-2013 Peter Cock, The James Hutton Institute
+           2010-2011 Broad Institute
+           2012-2013 Peter Cock, The James Hutton Institute
 License: MIT
 
 Files: samtools/misc/ace2sam.*
@@ -45,8 +45,8 @@ License: MIT
 
 Files: samtools/padding.*
 Copyright: 2011-2012 Broad Institute
-	   2014 Genome Research Ltd.
-	   2012-2013 Peter Cock, The James Hutton Institute
+           2014 Genome Research Ltd.
+           2012-2013 Peter Cock, The James Hutton Institute
 License: MIT
 
 Files: win32/stdint.h
@@ -59,10 +59,10 @@ License: LGPL-2.1+
 
 Files: debian/*
 Copyright:
-	2015-2016 Afif Elghraoui <afif at debian.org>
-	2015 Jorge Soares <j.s.soares at gmail.com>
-	2014-2015 Charles Plessy <plessy at debian.org>
-	2014-2018 Andreas Tille <tille at debian.org>
+ 	2015-2016 Afif Elghraoui <afif at debian.org>
+ 	2015 Jorge Soares <j.s.soares at gmail.com>
+ 	2014-2015 Charles Plessy <plessy at debian.org>
+ 	2014-2018 Andreas Tille <tille at debian.org>
 License: MIT
 
 License: BSD-3-clause


=====================================
debian/rules
=====================================
@@ -54,10 +54,10 @@ pysam_data.%:
 clean-tests: pysam_data.clean cbcf_data.clean
 	find . -name "*.pyc" -delete
 	find . -name "*.pyxbldc" -delete
-	#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
+	find . -name "tmp_*.bam" -delete
 	find . -name "*.bai*" -delete
 	find . -name "*.cram*" -delete
-	#find . -name "*.bam" -delete # which deletes files tested
+	find . -name "pysam_uncompressed.bam" -delete
 	rm -rf	tests/pysam_test_work \
 		tests/example_htslib.gtf.gz.tbi \
 		tests/log.txt \


=====================================
debian/upstream/metadata
=====================================
@@ -1,10 +1,12 @@
 Registry:
- - Name: OMICtools
-   Entry: OMICS_19073
- - Name: SciCrunch
-   Entry: NA
- - Name: bio.tools
-   Entry: pysam
- - Name: conda:bioconda
-   Entry: pysam
-Repository: https://github.com/pysam-developers/pysam
+- Name: OMICtools
+  Entry: OMICS_19073
+- Name: SciCrunch
+  Entry: NA
+- Name: bio.tools
+  Entry: pysam
+- Name: conda:bioconda
+  Entry: pysam
+Repository: https://github.com/pysam-developers/pysam.git
+Bug-Database: https://github.com/pysam-developers/pysam/issues
+Repository-Browse: https://github.com/pysam-developers/pysam



View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/compare/5b7040fc8921a49f8f6c47d4f3235b8b2359e301...9f8aea852ea0382c141675f28300d87256c562ff
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