[med-svn] [Git][med-team/roary][master] 9 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Tue Oct 30 11:47:52 GMT 2018
Andreas Tille pushed to branch master at Debian Med / roary
Commits:
2856e951 by Andreas Tille at 2018-10-30T10:36:22Z
debhelper 11
- - - - -
0036a274 by Andreas Tille at 2018-10-30T10:40:44Z
Point Vcs fields to salsa.debian.org
- - - - -
e1db1b37 by Andreas Tille at 2018-10-30T10:40:44Z
Standards-Version: 4.2.1
- - - - -
871e3115 by Andreas Tille at 2018-10-30T10:43:43Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
- - - - -
5ebe2ac5 by Andreas Tille at 2018-10-30T10:43:43Z
Remove trailing whitespace in debian/changelog
- - - - -
bbddf18d by Andreas Tille at 2018-10-30T10:43:43Z
Remove trailing whitespace in debian/copyright
- - - - -
75d7a593 by Andreas Tille at 2018-10-30T10:57:47Z
Remove unused patches
- - - - -
583e58bf by Andreas Tille at 2018-10-30T11:00:40Z
Hmmm, seems the test is not automatically run anyway by the build system
- - - - -
bf0d8809 by Andreas Tille at 2018-10-30T11:06:10Z
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- − debian/patches/add_abstract.patch
- − debian/patches/fix_log_message.patch
- − debian/patches/prank_seed.patch
- − debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+roary (3.12.0+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.2.1
+ * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+ * Remove trailing whitespace in debian/changelog
+ * Remove trailing whitespace in debian/copyright
+ * Remove unused patches
+
+ -- Andreas Tille <tille at debian.org> Tue, 30 Oct 2018 12:02:06 +0100
+
roary (3.12.0+dfsg-1) unstable; urgency=medium
* New upstream release.
@@ -162,7 +175,7 @@ roary (3.6.0+dfsg-1) unstable; urgency=medium
roary (3.5.9+dfsg-2) unstable; urgency=medium
* Change priority to extra due to parallel and fasttree being extra.
- * Bump Standards-Version.
+ * Bump Standards-Version.
* Add Lintian overrides.
-- Sascha Steinbiss <sascha at steinbiss.name> Thu, 25 Feb 2016 21:40:11 +0000
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -1,9 +1,9 @@
Source: roary
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Sascha Steinbiss <satta at debian.org>
-Build-Depends: debhelper (>= 10),
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 11~),
dh-dist-zilla,
libdist-zilla-plugin-podweaver-perl,
bioperl,
@@ -35,9 +35,9 @@ Build-Depends: debhelper (>= 10),
mafft,
fasttree
Build-Depends-Indep: perl
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/roary.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/roary.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/roary
+Vcs-Git: https://salsa.debian.org/med-team/roary.git
Homepage: http://sanger-pathogens.github.io/Roary/
Package: roary
=====================================
debian/copyright
=====================================
@@ -14,7 +14,7 @@ License: GPL-3
License: GPL-3
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
- the Free Software Foundation; version 3.
+ the Free Software Foundation; version 3.
.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
=====================================
debian/patches/add_abstract.patch deleted
=====================================
@@ -1,14 +0,0 @@
-Description: add abstract line
-Author: Sascha Steinbiss <satta at debian.org>
-Bug: https://github.com/sanger-pathogens/Roary/pull/220
-Applied-Upstream: https://github.com/sanger-pathogens/Roary/pull/220
---- a/lib/Bio/Roary/SplitGroups.pm
-+++ b/lib/Bio/Roary/SplitGroups.pm
-@@ -1,6 +1,6 @@
- package Bio::Roary::SplitGroups;
-
--# ABSTRACT:
-+# ABSTRACT: split groups
-
- =head1 SYNOPSIS
-
=====================================
debian/patches/fix_log_message.patch deleted
=====================================
@@ -1,23 +0,0 @@
-Description: use correct parameter for easy_init
- The original code triggered a warning message in newer log4perl
- versions, breaking the autopkgtest.
-Author: Sascha Steinbiss <satta at debian.org>
-Forwarded: https://github.com/sanger-pathogens/Roary/pull/246
---- a/lib/Bio/Roary/CommandLine/Common.pm
-+++ b/lib/Bio/Roary/CommandLine/Common.pm
-@@ -19,7 +19,7 @@
- sub _build_logger
- {
- my ($self) = @_;
-- Log::Log4perl->easy_init(level => $ERROR);
-+ Log::Log4perl->easy_init($ERROR);
- my $logger = get_logger();
- return $logger;
- }
-@@ -54,4 +54,4 @@
- };
-
- no Moose;
--1;
-\ No newline at end of file
-+1;
=====================================
debian/patches/prank_seed.patch deleted
=====================================
@@ -1,63 +0,0 @@
-Description: make PRANK honour SOURCE_DATE_EPOCH
- For reproducibility, the -seed parameter in PRANK is set to a fixed
- time instead of the default system time. This is expected to fix
- some failing tests.
-Author: Sascha Steinbiss <satta at debian.org>
---- a/lib/Bio/Roary/External/Prank.pm
-+++ b/lib/Bio/Roary/External/Prank.pm
-@@ -22,6 +22,7 @@
- has 'input_filename' => ( is => 'ro', isa => 'Str', required => 1 );
- has 'output_filename' => ( is => 'ro', isa => 'Str', default => 'output' );
- has 'exec' => ( is => 'ro', isa => 'Str', default => 'prank' );
-+has 'seed' => ( is => 'rw', isa => 'Int', default => 0 );
-
- # Overload Role
- has 'memory_in_mb' => ( is => 'ro', isa => 'Int', lazy => 1, builder => '_build_memory_in_mb' );
-@@ -34,18 +35,26 @@
-
- sub _command_to_run {
- my ($self) = @_;
--
-+ my ($repstr) = "";
-+ if ($ENV{"SOURCE_DATE_EPOCH"})
-+ {
-+ $self->seed($ENV{"SOURCE_DATE_EPOCH"} + 0);
-+ }
- if(! -e $self->input_filename)
- {
- $self->logger->error( "Input file to PRANK missing: " . $self->input_filename );
- }
--
-+ if($self->seed > 0)
-+ {
-+ $repstr = "-reproducible -seed=" . $self->seed;
-+ }
- return join(
- ' ',
- (
- $self->exec,
- "-d=" . $self->input_filename,
- "-o=" . $self->output_filename,
-+ $repstr,
- '-codon', '-F', '-quiet', '-once', '> /dev/null 2>&1',
- '&&', 'mv', $self->output_filename . '*.fas',
- $self->output_filename
---- a/t/Bio/Roary/External/Prank.t
-+++ b/t/Bio/Roary/External/Prank.t
-@@ -22,11 +22,11 @@
- 'initialise prank obj'
- );
-
--is(
-- $obj->_command_to_run,
--'prank -d=t/data/prank_input.fa -o=t/data/prank_input.fa.aln -codon -F -quiet -once > /dev/null 2>&1 && mv t/data/prank_input.fa.aln*.fas t/data/prank_input.fa.aln',
-- 'Command constructed as expected'
--);
-+#is(
-+# $obj->_command_to_run,
-+#'prank -d=t/data/prank_input.fa -o=t/data/prank_input.fa.aln -codon -F -quiet -once > /dev/null 2>&1 && mv t/data/prank_input.fa.aln*.fas t/data/prank_input.fa.aln',
-+# 'Command constructed as expected'
-+#);
-
- ok( $obj->run(), 'run prank' );
-
=====================================
debian/patches/spelling.patch deleted
=====================================
@@ -1,52 +0,0 @@
-Description: spelling fixed
-Author: Sascha Steinbiss <satta at debian.org>
-Bug: https://github.com/sanger-pathogens/Roary/pull/220
-Applied-Upstream: https://github.com/sanger-pathogens/Roary/pull/220
---- a/bin/pan_genome_assembly_statistics
-+++ b/bin/pan_genome_assembly_statistics
-@@ -2,12 +2,12 @@
-
- package Bio::Roary::Main::AssemblyStatistics;
-
--# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
-+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
- # PODNAME: pan_genome_assembly_statistics
-
- =head1 SYNOPSIS
-
--Given a spreadsheet of gene presence and absense calculate some statistics
-+Given a spreadsheet of gene presence and absence calculate some statistics
-
- =cut
-
---- a/lib/Bio/Roary/AssemblyStatistics.pm
-+++ b/lib/Bio/Roary/AssemblyStatistics.pm
-@@ -1,10 +1,10 @@
- package Bio::Roary::AssemblyStatistics;
-
--# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
-+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
-
- =head1 SYNOPSIS
-
--Given a spreadsheet of gene presence and absense calculate some statistics
-+Given a spreadsheet of gene presence and absence calculate some statistics
-
- =cut
-
---- a/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
-+++ b/lib/Bio/Roary/CommandLine/AssemblyStatistics.pm
-@@ -1,11 +1,11 @@
- undef $VERSION;
- package Bio::Roary::CommandLine::AssemblyStatistics;
-
--# ABSTRACT: Given a spreadsheet of gene presence and absense calculate some statistics
-+# ABSTRACT: Given a spreadsheet of gene presence and absence calculate some statistics
-
- =head1 SYNOPSIS
-
--Given a spreadsheet of gene presence and absense calculate some statistics
-+Given a spreadsheet of gene presence and absence calculate some statistics
-
- =cut
-
=====================================
debian/rules
=====================================
@@ -8,4 +8,7 @@ override_dh_dzil_build:
dh_dzil_build --
override_dh_auto_test:
- # pass
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+ # Hmmm, seems the test is not automatically run anyway by the build system
+ dh_auto_test || true
+endif
View it on GitLab: https://salsa.debian.org/med-team/roary/compare/5ca5fce35ef4c764b384aa92cf5f2a32e3d4fa46...bf0d88099466e32f610df6d0cdb18d963afbeb7d
--
View it on GitLab: https://salsa.debian.org/med-team/roary/compare/5ca5fce35ef4c764b384aa92cf5f2a32e3d4fa46...bf0d88099466e32f610df6d0cdb18d963afbeb7d
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