[med-svn] [Git][med-team/bioperl-run][master] 5 commits: initialize changelog
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Feb 10 20:16:19 GMT 2022
Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits:
0c1e07eb by Étienne Mollier at 2022-02-10T20:03:27+01:00
initialize changelog
- - - - -
d09a2a1f by Étienne Mollier at 2022-02-10T20:40:09+01:00
Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch
Integration of newer muscle version in debian changed the code path in
the way the test may be skipped, breaking autopkgtest of bioperl-run.
- - - - -
ff03d92a by Étienne Mollier at 2022-02-10T20:44:07+01:00
update changelog
- - - - -
c15b6b71 by Étienne Mollier at 2022-02-10T20:44:23+01:00
Move libmodule-build-perl from Build-Depends-Indep to Build-Depends.
Changes-By: lintian-brush
Fixes: lintian: libmodule-build-perl-needs-to-be-in-build-depends
See-also: https://lintian.debian.org/tags/libmodule-build-perl-needs-to-be-in-build-depends.html
- - - - -
ee00d336 by Étienne Mollier at 2022-02-10T20:55:25+01:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/adjust-muscle-test.patch
- debian/patches/series
- − debian/patches/skip_tests_for_muscle.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+bioperl-run (1.7.3-8) unstable; urgency=medium
+
+ * Replace skip_tests_for_muscle.patch by adjust-muscle-test.patch.
+ Integration of newer muscle version in debian changed the code path in
+ the way the test may be skipped, breaking autopkgtest of bioperl-run..
+ * Move libmodule-build-perl from Build-Depends-Indep to Build-Depends.
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 10 Feb 2022 20:44:28 +0100
+
bioperl-run (1.7.3-7) unstable; urgency=medium
* d/watch: fix broken link to github and adjust version mangling to fit
=====================================
debian/control
=====================================
@@ -6,9 +6,8 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
-Build-Depends: debhelper-compat (= 13)
+Build-Depends: debhelper-compat (= 13), libmodule-build-perl
Build-Depends-Indep: perl,
- libmodule-build-perl,
bioperl (>= 1.7.4),
# Recommended in Build.PL:
libalgorithm-diff-perl,
=====================================
debian/patches/adjust-muscle-test.patch
=====================================
@@ -0,0 +1,25 @@
+Description: adjust skip count for Muscle test
+ The initial count looks like upstream might have forgotten to update it..
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2022-02-10
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl-run.orig/t/Muscle.t
++++ bioperl-run/t/Muscle.t
+@@ -33,7 +33,7 @@
+ unless ( $version >= 3.6 ) {
+ skip(
+ "Only muscle version 3.6 or higher is supported by these tests. Skipping tests",
+- 7
++ 10
+ );
+ exit(0);
+ }
+@@ -88,4 +88,4 @@
+
+ is( $s1_perid == 41 || $s1_perid == 42,
+ 1, 'diff versions of MUSCLE have different vals' );
+-}
+\ No newline at end of file
++}
=====================================
debian/patches/series
=====================================
@@ -7,7 +7,6 @@ skip_tests_for_wise.patch
skip_tests_for_phylip.patch
skip_tests_for_phyml.patch
skip_tests_for_infernal.patch
-skip_tests_for_muscle.patch
skip_tests_for_ncbi-blast+.patch
hyphy.patch
remove_tests_for_ensembl.patch
@@ -18,3 +17,4 @@ skip-test-for-kalign.patch
fix-whatis-entries.patch
unscramble-erpin.patch
fix-pod-conversion.patch
+adjust-muscle-test.patch
=====================================
debian/patches/skip_tests_for_muscle.patch deleted
=====================================
@@ -1,75 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
-Description: Exclude some failed test when using muscle. Seems Debian's muscle is newer
-
---- a/t/Muscle.t
-+++ b/t/Muscle.t
-@@ -5,7 +5,7 @@ use strict;
-
- BEGIN {
- use Bio::Root::Test;
-- test_begin( -tests => 16 );
-+ test_begin( -tests => 8 );
- use_ok('Bio::Tools::Run::Alignment::Muscle');
- use_ok('Bio::AlignIO');
- use_ok('Bio::SeqIO');
-@@ -39,10 +39,6 @@ SKIP: {
- }
- cmp_ok( $version, '>=', 3.6, "Code tested only on muscle versions > 3.6" );
-
-- $aln = $factory->align($inputfilename);
-- ok($aln);
-- is( $aln->num_sequences, 7 );
--
- my $str = Bio::SeqIO->new(
- -file => test_input_file("cysprot.fa"),
- -format => 'Fasta'
-@@ -53,11 +49,11 @@ SKIP: {
- }
- my $seq_array_ref = \@seq_array;
-
-- $aln = $factory->align($seq_array_ref);
-- is $aln->num_sequences, 7;
-- my $s1_perid = POSIX::ceil( $aln->average_percentage_identity );
-- is( $s1_perid == 43 || $s1_perid == 44,
-- 1, 'diff versions of MUSCLE have different vals' );
-+ #$aln = $factory->align($seq_array_ref);
-+ #is $aln->num_sequences, 7;
-+ #my $s1_perid = POSIX::ceil( $aln->average_percentage_identity );
-+ #is( $s1_perid == 43 || $s1_perid == 44,
-+ # 1, 'diff versions of MUSCLE have different vals' );
-
- my $logfile = test_output_file();
- my $outfile = test_output_file();
-@@ -75,17 +71,18 @@ SKIP: {
- );
- $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
- is( $factory->log, $logfile, 'log file' );
-- $aln = $factory->align($seq_array_ref);
-- is $aln->num_sequences, 7;
-- $s1_perid = POSIX::ceil( $aln->average_percentage_identity );
-- is( $s1_perid == 43 || $s1_perid == 44,
-- 1, 'diff versions of MUSCLE have different vals' );
-+ #$aln = $factory->align($seq_array_ref);
-+ #is $aln->num_sequences, 7;
-+ #$s1_perid = POSIX::ceil( $aln->average_percentage_identity );
-+ #is( $s1_perid == 43 || $s1_perid == 44,
-+ # 1, 'diff versions of MUSCLE have different vals' );
-+ my $s1_perid;
-
- $inputfilename = test_input_file("cysprot1a.fa");
-- $aln = $factory->align($inputfilename);
-- is $aln->num_sequences, 3;
-- $s1_perid = POSIX::ceil( $aln->average_percentage_identity );
--
-- is( $s1_perid == 41 || $s1_perid == 42,
-- 1, 'diff versions of MUSCLE have different vals' );
--}
-\ No newline at end of file
-+ #$aln = $factory->align($inputfilename);
-+ #is $aln->num_sequences, 3;
-+ #$s1_perid = POSIX::ceil( $aln->average_percentage_identity );
-+
-+ #is( $s1_perid == 41 || $s1_perid == 42,
-+ # 1, 'diff versions of MUSCLE have different vals' );
-+}
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7432ae75eecb558a717e3eebbe8de1c0bbf28b7d...ee00d3360a3607a279338e9b0c92f352eb47cec9
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