debian/changelog

+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@debian.org>  Tue, 30 Oct 2018 12:02:06 +0100
+
 roary (3.12.0+dfsg-1) unstable; urgency=medium
 
   * New upstream release.

debian/compat

-10
+11

debian/control

 Source: roary
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <satta@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/patches/add_abstract.patch

-Description: add abstract line
-Author: Sascha Steinbiss <satta@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

-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@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

-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@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

-Description: spelling fixed
-Author: Sascha Steinbiss <satta@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