[med-svn] [Git][med-team/snp-sites][master] 9 commits: remove obsolete autotools deps
Sascha Steinbiss
gitlab at salsa.debian.org
Thu Jun 14 23:19:02 BST 2018
Sascha Steinbiss pushed to branch master at Debian Med / snp-sites
Commits:
3c28879a by Sascha Steinbiss at 2018-06-15T00:15:42+02:00
remove obsolete autotools deps
- - - - -
457ee199 by Sascha Steinbiss at 2018-06-15T00:16:09+02:00
bump Standards-Version
- - - - -
01442663 by Sascha Steinbiss at 2018-06-15T00:16:34+02:00
dh 11
- - - - -
6b0dcdc3 by Sascha Steinbiss at 2018-06-15T00:16:56+02:00
use secure copyright format URL
- - - - -
9e1eb11b by Sascha Steinbiss at 2018-06-15T00:17:07+02:00
dch -r
- - - - -
5d552ef5 by Sascha Steinbiss at 2018-06-15T00:17:24+02:00
remove obsolete Testsuite entry
- - - - -
9f0e8daf by Sascha Steinbiss at 2018-06-15T00:17:36+02:00
use Salsa VCS-*
- - - - -
9e1a5fac by Sascha Steinbiss at 2018-06-15T00:17:51+02:00
remove obsolete patches
- - - - -
ed8450d2 by Sascha Steinbiss at 2018-06-15T00:18:42+02:00
fix file modes
- - - - -
17 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/docs
- debian/libsnp-sites1-dev.README.Debian
- − debian/patches/add_lib_subunit.patch
- − debian/patches/fix_manpage.patch
- − debian/patches/reproducible-build.patch
- − debian/patches/series
- debian/snp-sites.README.Debian
- debian/snp-sites.install
- debian/snp-sites.manpages
- debian/tests/alignment_file_one_line_per_sequence.aln.gz
- debian/tests/build-lib
- debian/tests/control
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
-snp-sites (2.4.0-1) UNRELEASED; urgency=medium
+snp-sites (2.4.0-1) unstable; urgency=medium
* New upstream version.
* Adjust watchfile to allow 'v' in version tags.
* Update upstream metadata (thanks Steffen Moeller).
+ * Remove obsolete autotools Build-Depends.
+ * Use debhelper 11.
+ * Bump Standards-Version.
+ * Use secure copyright format URL.
-- Sascha Steinbiss <satta at debian.org> Thu, 14 Jun 2018 17:29:53 +0200
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,18 +5,15 @@ Uploaders: Jorge Soares <j.s.soares at gmail.com>,
Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9.0.0),
- autotools-dev,
+Build-Depends: debhelper (>= 11),
zlib1g-dev,
check,
pkg-config,
- dh-autoreconf,
d-shlibs,
asciidoctor
-Standards-Version: 3.9.8
-Testsuite: autopkgtest
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snp-sites.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/snp-sites.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/snp-sites
+Vcs-Git: https://salsa.debian.org/med-team/snp-sites.git
Homepage: https://github.com/sanger-pathogens/snp-sites
Package: snp-sites
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snp-sites
Source: https://github.com/sanger-pathogens/snp-sites
=====================================
debian/docs
=====================================
=====================================
debian/libsnp-sites1-dev.README.Debian
=====================================
=====================================
debian/patches/add_lib_subunit.patch deleted
=====================================
--- a/debian/patches/add_lib_subunit.patch
+++ /dev/null
@@ -1,5 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 16 Sep 2015 15:08:04 +0200
-Bug-Debian: http://bugs.debian.org/799164
-Description: Add missing lib subunit
-
=====================================
debian/patches/fix_manpage.patch deleted
=====================================
--- a/debian/patches/fix_manpage.patch
+++ /dev/null
@@ -1,86 +0,0 @@
-Description: Fix manpage
-Author: Sascha Steinbiss <sascha at steinbiss.name>
-Forwarded: https://github.com/sanger-pathogens/snp-sites/pull/47
-Applied-Upstream: v2.2.1
---- a/snp-sites.txt
-+++ b/snp-sites.txt
-@@ -1,5 +1,5 @@
--SNP-SITESDOC(1)
--==============
-+SNP-SITES(1)
-+============
- :doctype: manpage
-
-
-@@ -15,10 +15,15 @@
- -----------
- This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in either of the following formats:
-
--a multi fasta alignment, VCF, relaxed phylip format.
-+ - multi fasta alignment
-+ - VCF
-+ - relaxed phylip format
-
- OPTIONS
- -------
-+*-r*::
-+ Output internal pseudo reference sequence
-+
- *-m*::
- Output a multi fasta alignment file (default)
-
-@@ -32,16 +37,18 @@
- Specify an output filename
-
- *-h*::
-- This document
-+ Show help message
-
- *-V*::
- Show version and exit
-
-+
- EXAMPLES
- --------
--snp-sites my-alignment.aln
-
--snp-sites my-gzipped-alignment.aln.gz
-+ snp-sites my-alignment.aln
-+
-+ snp-sites my-gzipped-alignment.aln.gz
-
-
- FORMAT OF THE INPUT FILE
-@@ -49,12 +56,12 @@
-
- Input files should look like this:
-
-->reference_sequence
--aaccggtt
-->comparison_sequence
--AACCGGTT
-->another_comparison_sequence
--AACCGCTT
-+ >reference_sequence
-+ aaccggtt
-+ >comparison_sequence
-+ AACCGGTT
-+ >another_comparison_sequence
-+ AACCGCTT
-
- For more examples, visit:
- https://github.com/sanger-pathogens/snp-sites/tree/master/tests/data
-@@ -63,6 +70,13 @@
- ------
- snp-sites was originally written by Andrew Page (ap13 at sanger.ac.uk)
-
-+CITATION
-+--------
-+If you use this program, please cite:
-+"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments",
-+Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris (2016),
-+bioRxiv doi: http://dx.doi.org/10.1101/038190
-+
- COPYING
- -------
- Wellcome Trust Sanger Institute Copyright (C) 2013 Wellcome Trust Sanger Institute
=====================================
debian/patches/reproducible-build.patch deleted
=====================================
--- a/debian/patches/reproducible-build.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Manually set the timestamp in the manpage to the last modification time
-
---- a/snp-sites.txt
-+++ b/snp-sites.txt
-@@ -1,6 +1,7 @@
- SNP-SITES(1)
- ============
- :doctype: manpage
-+:revdate: 2015-09-03
-
-
- NAME
=====================================
debian/patches/series deleted
=====================================
--- a/debian/patches/series
+++ /dev/null
=====================================
debian/snp-sites.README.Debian
=====================================
=====================================
debian/snp-sites.install
=====================================
--- a/debian/snp-sites.install
+++ b/debian/snp-sites.install
@@ -1 +1 @@
-usr/bin/snp-sites
\ No newline at end of file
+usr/bin/snp-sites
=====================================
debian/snp-sites.manpages
=====================================
=====================================
debian/tests/alignment_file_one_line_per_sequence.aln.gz
=====================================
Binary files a/debian/tests/alignment_file_one_line_per_sequence.aln.gz and b/debian/tests/alignment_file_one_line_per_sequence.aln.gz differ
=====================================
debian/tests/build-lib
=====================================
=====================================
debian/tests/control
=====================================
=====================================
debian/watch
=====================================
View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ab456e4206b714976b368b75469c6d6d3d1026ef...ed8450d20becfd99a99af382674140ff962f5816
--
View it on GitLab: https://salsa.debian.org/med-team/snp-sites/compare/ab456e4206b714976b368b75469c6d6d3d1026ef...ed8450d20becfd99a99af382674140ff962f5816
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