[med-svn] [Git][med-team/bioperl-run][master] 8 commits: d/control: add myself to uploaders
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Jul 14 12:30:15 BST 2021
Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits:
febb2871 by Étienne Mollier at 2021-07-14T09:55:36+02:00
d/control: add myself to uploaders
- - - - -
6e437263 by Étienne Mollier at 2021-07-14T10:11:26+02:00
d/watch: fix broken link to github & fix mangling
URL scanning and version mangling needed adjustment, compared to
regular github packages, mostly because of the unusual tagging
convention:
release-$MAJOR-$MINOR-$PATCHLEVEL
instead of more common:
v$MAJOR.$MINOR.$PATCHLEVEL
- - - - -
fa50a1aa by Étienne Mollier at 2021-07-14T11:14:33+02:00
add fix-whatis-entries.patch
This patch addresses a couple of bad-whatis-entry lintian warnings.
- - - - -
2167fc73 by Étienne Mollier at 2021-07-14T11:22:58+02:00
adjust lintian override for former script
The script in question is bp_bioperl_application_installer.pl, but it
does not seem to be provided upstream anymore, so the override is now
unjustified.
- - - - -
f733d45d by Étienne Mollier at 2021-07-14T11:38:21+02:00
add unscramble-erpin.patch
This fixes a national-encoding lintian warning, and maybe a couple of
typos in the Perl module documentation.
- - - - -
5a149c51 by Étienne Mollier at 2021-07-14T11:55:25+02:00
fix-whatis-entries.patch: dep3 header
- - - - -
8c841541 by Étienne Mollier at 2021-07-14T12:16:06+02:00
add fix-pod-conversion.patch
This patch addresses the lintian warning pod-conversion-message
affecting the module Bio::DB::SoapEUtilities::Result.
- - - - -
d68f33e8 by Étienne Mollier at 2021-07-14T12:18:08+02:00
update changelog
- - - - -
8 changed files:
- debian/bioperl-run.lintian-overrides
- debian/changelog
- debian/control
- + debian/patches/fix-pod-conversion.patch
- + debian/patches/fix-whatis-entries.patch
- debian/patches/series
- + debian/patches/unscramble-erpin.patch
- debian/watch
Changes:
=====================================
debian/bioperl-run.lintian-overrides
=====================================
@@ -1,5 +1,4 @@
# see https://lists.debian.org/debian-med/2018/06/msg00043.html
-bioperl-run: script-with-language-extension usr/bin/bp_bioperl_application_installer.pl
bioperl-run: script-with-language-extension usr/bin/bp_multi_hmmsearch.pl
bioperl-run: script-with-language-extension usr/bin/bp_panalysis.pl
bioperl-run: script-with-language-extension usr/bin/bp_papplmaker.pl
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+bioperl-run (1.7.3-7) UNRELEASED; urgency=medium
+
+ * d/watch: fix broken link to github and adjust version mangling to fit
+ upstream's tagging convention (tag "release-x-y-z" for version "x.y.z")
+ * adjust lintian override on bp_bioperl_application_installer.pl file
+ extension, which is not provided anymore
+ * add fix-whatis-entries.patch; fixes lintian warnings on bad-whatis-entry
+ by providing a convenient description in the NAME field where needed
+ * add unscramble-erpin.patch; fixes a kind of typo in ERPIN.pm documentation,
+ flagged by lintian warning national-encoding
+ * add fix-pod-conversion.patch; address the lintian warning
+ pod-conversion-message affecting Bio::DB::SoapEUtilities::Result.
+ * d/control: add myself to uploaders
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 14 Jul 2021 11:40:03 +0200
+
bioperl-run (1.7.3-6) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
Source: bioperl-run
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Testsuite: autopkgtest-pkg-perl
Priority: optional
=====================================
debian/patches/fix-pod-conversion.patch
=====================================
@@ -0,0 +1,21 @@
+Description: fix lintian warning about pod-conversion-message
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2021-07-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl-run.orig/lib/Bio/DB/SoapEUtilities/Result.pm
++++ bioperl-run/lib/Bio/DB/SoapEUtilities/Result.pm
+@@ -134,10 +134,10 @@
+
+ =back
+
+-=over
+-
+ Other methods
+
++=over
++
+ =item accessors()
+
+ An array of available data accessor names. This
=====================================
debian/patches/fix-whatis-entries.patch
=====================================
@@ -0,0 +1,131 @@
+Description: fix whatis entries in multiple Bio Perl modules
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2021-07-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Blat.pm
++++ bioperl-run/lib/Bio/Tools/Run/Alignment/Blat.pm
+@@ -6,7 +6,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Alignment::Blat
++Bio::Tools::Run::Alignment::Blat - wrapper modules for the Blat program
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Exonerate.pm
++++ bioperl-run/lib/Bio/Tools/Run/Alignment/Exonerate.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Alignment::Exonerate
++Bio::Tools::Run::Alignment::Exonerate - wrapper for the exonerate alignment program
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/FastTree.pm
++++ bioperl-run/lib/Bio/Tools/Run/Phylo/FastTree.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Phylo::FastTree
++Bio::Tools::Run::Phylo::FastTree - Bio::Tree getter from DNA alignment
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
++++ bioperl-run/lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
+@@ -10,7 +10,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Phylo::Phylip::PhylipConf
++Bio::Tools::Run::Phylo::Phylip::PhylipConf - manage Phylip menu configuration
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Phylo/Raxml.pm
++++ bioperl-run/lib/Bio/Tools/Run/Phylo/Raxml.pm
+@@ -11,7 +11,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Phylo::Raxml
++Bio::Tools::Run::Phylo::Raxml - Bio::Tree getter from DNA alignment through raxml
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Primate.pm
++++ bioperl-run/lib/Bio/Tools/Run/Primate.pm
+@@ -11,8 +11,8 @@
+
+ =head1 NAME
+
+-Wrapper for Primate, Guy Slater's near exact match finder for short sequence
+-tags.
++Bio::Tools::Run::Primate - wrapper for Primate, Guy Slater's near exact match
++finder for short sequence tags.
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Prints.pm
++++ bioperl-run/lib/Bio/Tools/Run/Prints.pm
+@@ -5,7 +5,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Prints
++Bio::Tools::Run::Prints - PRINTS fingerprint identification algorithm
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Profile.pm
++++ bioperl-run/lib/Bio/Tools/Run/Profile.pm
+@@ -6,7 +6,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Profile
++Bio::Tools::Run::Profile - wrapper for the pfscan program
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Signalp.pm
++++ bioperl-run/lib/Bio/Tools/Run/Signalp.pm
+@@ -9,7 +9,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Signalp
++Bio::Tools::Run::Signalp - wrapper for the Signalp program
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/TribeMCL.pm
++++ bioperl-run/lib/Bio/Tools/Run/TribeMCL.pm
+@@ -12,7 +12,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::TribeMCL
++Bio::Tools::Run::TribeMCL - Markov method for CLustering proteins
+
+ =head1 SYNOPSIS
+
+--- bioperl-run.orig/lib/Bio/Tools/Run/Vista.pm
++++ bioperl-run/lib/Bio/Tools/Run/Vista.pm
+@@ -10,9 +10,7 @@
+
+ =head1 NAME
+
+-Bio::Tools::Run::Vista
+-
+-Wrapper for Vista
++Bio::Tools::Run::Vista - Wrapper for Vista
+
+ =head1 SYNOPSIS
+
=====================================
debian/patches/series
=====================================
@@ -15,3 +15,6 @@ skip_tests_for_soap.patch
get-overlap.patch
alternate-data.patch
skip-test-for-kalign.patch
+fix-whatis-entries.patch
+unscramble-erpin.patch
+fix-pod-conversion.patch
=====================================
debian/patches/unscramble-erpin.patch
=====================================
@@ -0,0 +1,21 @@
+Description: replace exotic character by seemingly correct plain old dash '-'
+ A couple of ISO-8859 characters trigger the lintian warning national-encoding.
+ Looking into details, it seems that a plain old dash '-' got replaced by a
+ more exotic character 'Ð'. This patch brings the '-' in the description of
+ the affected Perl module ERPIN.pm.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2021-07-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl-run.orig/lib/Bio/Tools/Run/ERPIN.pm
++++ bioperl-run/lib/Bio/Tools/Run/ERPIN.pm
+@@ -31,7 +31,7 @@
+ 'cutoff' => [0, 10, 15, 20]
+ ]
+ # or use a simple string...
+- #strategy => 'umask 4 add 5 -nomask -cutoff 0 10 15',
++ #strategy => '-umask 4 -add 5 -nomask -cutoff 0 10 15',
+ pcw => 100
+ );
+
=====================================
debian/watch
=====================================
@@ -1,5 +1,6 @@
version=4
-opts="uversionmangle=s/[-_]/./g" \
-https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$
+opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g" \
+ https://github.com/bioperl/bioperl-run/tags \
+ (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz debian uupdate
# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c
--
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7d03cd80fba51cd78e9f99768072788ed2b4d08c...d68f33e89b89c7486fc86a5c8fcbb84398bb521c
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