New Upstream Snapshot - libbio-tools-run-alignment-clustalw-perl
Ready changes
Summary
Merged new upstream version: 1.7.4+git20181219.1.f740c96 (was: 1.7.4).
Resulting package
Built on 2023-01-11T14:26 (took 11m57s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots libbio-tools-run-alignment-clustalw-perl
Lintian Result
- libbio-tools-run-alignment-clustalw-perl_1.7.4+git20181219.1.f740c96-1~jan+nus2.dsc
- libbio-tools-run-alignment-clustalw-perl_1.7.4+git20181219.1.f740c96-1~jan+nus2_all.deb
- libbio-tools-run-alignment-clustalw-perl_1.7.4+git20181219.1.f740c96-1~jan+nus2_amd64.buildinfo
- libbio-tools-run-alignment-clustalw-perl_1.7.4+git20181219.1.f740c96-1~jan+nus2_amd64.changes
Diff
diff --git a/Changes b/Changes
index cdba2bc..c08a908 100644
--- a/Changes
+++ b/Changes
@@ -1,6 +1,8 @@
Summary of important user-visible changes for Bio-Tools-Run-Alignment-Clustawl
------------------------------------------------------------------------------
+1.7.4 2023-01-11 14:21:50+00:00 UTC
+
1.7.4 2018-07-11 15:56:41+01:00 Europe/London
* Bio::Installer::Clustalw has been removed. It was installing a
very old version of clustalw, many years out of date and UNIX
diff --git a/LICENSE b/LICENSE
index 39f58ff..62d74b0 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-This software is copyright (c) 2018 by Peter Schattner <schattner@alum.mit.edu>.
+This software is copyright (c) 2023 by Peter Schattner <schattner@alum.mit.edu>.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
@@ -12,7 +12,7 @@ b) the "Artistic License"
--- The GNU General Public License, Version 1, February 1989 ---
-This software is Copyright (c) 2018 by Peter Schattner <schattner@alum.mit.edu>.
+This software is Copyright (c) 2023 by Peter Schattner <schattner@alum.mit.edu>.
This is free software, licensed under:
@@ -272,7 +272,7 @@ That's all there is to it!
--- The Artistic License 1.0 ---
-This software is Copyright (c) 2018 by Peter Schattner <schattner@alum.mit.edu>.
+This software is Copyright (c) 2023 by Peter Schattner <schattner@alum.mit.edu>.
This is free software, licensed under:
@@ -292,21 +292,21 @@ Definitions:
- "Package" refers to the collection of files distributed by the Copyright
Holder, and derivatives of that collection of files created through
- textual modification.
+ textual modification.
- "Standard Version" refers to such a Package if it has not been modified,
or has been modified in accordance with the wishes of the Copyright
- Holder.
+ Holder.
- "Copyright Holder" is whoever is named in the copyright or copyrights for
- the package.
+ the package.
- "You" is you, if you're thinking about copying or distributing this Package.
- "Reasonable copying fee" is whatever you can justify on the basis of media
cost, duplication charges, time of people involved, and so on. (You will
not be required to justify it to the Copyright Holder, but only to the
- computing community at large as a market that must bear the fee.)
+ computing community at large as a market that must bear the fee.)
- "Freely Available" means that no fee is charged for the item itself, though
there may be fees involved in handling the item. It also means that
recipients of the item may redistribute it under the same conditions they
- received it.
+ received it.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that you
@@ -373,7 +373,7 @@ products derived from this software without specific prior written permission.
9. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
-MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
The End
diff --git a/MANIFEST b/MANIFEST
index c499d4c..5b5707b 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,4 +1,4 @@
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+# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.029.
Changes
LICENSE
MANIFEST
diff --git a/META.json b/META.json
index 51d35d9..f9d7e67 100644
--- a/META.json
+++ b/META.json
@@ -4,7 +4,7 @@
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],
@@ -74,7 +74,7 @@
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@@ -91,42 +91,42 @@
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@@ -136,47 +136,47 @@
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"name" : "@BioPerl/@Filter/TestRelease",
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@@ -415,19 +415,20 @@
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@@ -438,7 +439,7 @@
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@@ -446,7 +447,7 @@
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diff --git a/META.yml b/META.yml
index db1ce6f..7d17293 100644
--- a/META.yml
+++ b/META.yml
@@ -13,7 +13,7 @@ configure_requires:
Devel::CheckBin: '0'
ExtUtils::MakeMaker: '0'
dynamic_config: 0
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license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -39,7 +39,7 @@ resources:
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@@ -53,74 +53,74 @@ x_Dist_Zilla:
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+ version: '4.018'
-
class: Pod::Weaver::Section::Collect
name: FUNCTIONS
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Section::Collect
name: 'INTERNAL METHODS'
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Section::Leftovers
name: '@BioPerl/Leftovers'
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Section::Region
name: '@BioPerl/postlude'
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Section::GenerateSection
name: FEEDBACK
- version: '1.06'
+ version: '4.018'
-
class: Pod::Weaver::Section::GenerateSection
name: 'Mailing lists'
- version: '1.06'
+ version: '4.018'
-
class: Pod::Weaver::Section::GenerateSection
name: Support
- version: '1.06'
+ version: '4.018'
-
class: Pod::Weaver::Section::GenerateSection
name: 'Reporting bugs'
- version: '1.06'
+ version: '4.018'
-
class: Pod::Weaver::Section::Legal::Complicated
name: '@BioPerl/Legal'
- version: '1.22'
+ version: '1.23'
-
class: Pod::Weaver::Section::Contributors
name: '@BioPerl/Contributors'
@@ -279,21 +279,21 @@ x_Dist_Zilla:
-
class: Pod::Weaver::Plugin::SingleEncoding
name: SingleEncoding
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Plugin::Transformer
name: '@BioPerl/List'
- version: '4.015'
+ version: '4.018'
-
class: Pod::Weaver::Plugin::EnsureUniqueSections
name: EnsureUniqueSections
version: '0.163250'
name: '@BioPerl/PodWeaver'
- version: '4.008'
+ version: '4.009'
-
class: Dist::Zilla::Plugin::NextRelease
name: '@BioPerl/NextRelease'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::Git::Check
config:
@@ -306,16 +306,17 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.18.0
+ git_version: 2.39.0
repo_root: .
name: '@BioPerl/Git::Check'
- version: '2.043'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Git::Commit
config:
Dist::Zilla::Plugin::Git::Commit:
add_files_in: []
- commit_msg: v%v%n%n%c
+ commit_msg: v%V%n%n%c
+ signoff: 0
Dist::Zilla::Role::Git::DirtyFiles:
allow_dirty:
- Changes
@@ -323,12 +324,12 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.18.0
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Commit'
- version: '2.043'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Git::Tag
config:
@@ -340,12 +341,12 @@ x_Dist_Zilla:
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
- git_version: 2.18.0
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Tag'
- version: '2.043'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::CheckBin
config:
@@ -357,47 +358,48 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::FinderCode
name: ':InstallModules'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':IncModules'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':TestFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExtraTestFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExecFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':PerlExecFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ShareFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':MainModule'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':AllFiles'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':NoFiles'
- version: '6.012'
+ version: '6.029'
zilla:
class: Dist::Zilla::Dist::Builder
config:
- is_trial: '0'
- version: '6.012'
-x_generated_by_perl: v5.26.2
+ is_trial: 0
+ version: '6.029'
+x_generated_by_perl: v5.36.0
x_serialization_backend: 'YAML::Tiny version 1.73'
+x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'
diff --git a/Makefile.PL b/Makefile.PL
index c2e1724..18b2dca 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -1,4 +1,4 @@
-# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.012.
+# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.029.
use strict;
use warnings;
diff --git a/debian/changelog b/debian/changelog
index abdbed8..d055f7b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,11 @@
-libbio-tools-run-alignment-clustalw-perl (1.7.4-4) UNRELEASED; urgency=medium
+libbio-tools-run-alignment-clustalw-perl (1.7.4+git20181219.1.f740c96-1) UNRELEASED; urgency=medium
* Set upstream metadata fields: Bug-Database.
* Update standards version to 4.6.2, no changes needed.
+ * New upstream snapshot.
+ * Drop patch doc-typos.patch, present upstream.
- -- Debian Janitor <janitor@jelmer.uk> Wed, 11 Jan 2023 12:14:38 -0000
+ -- Debian Janitor <janitor@jelmer.uk> Wed, 11 Jan 2023 14:22:08 -0000
libbio-tools-run-alignment-clustalw-perl (1.7.4-3) unstable; urgency=medium
diff --git a/debian/patches/doc-typos.patch b/debian/patches/doc-typos.patch
deleted file mode 100644
index a17f0f0..0000000
--- a/debian/patches/doc-typos.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Description: fix typos on POD documentation
-Author: David Miguel Susano Pinto <carandraug+dev@gmail.com>
-Forwarded: yes
-Applied-Upstream: commit:b1d81ea6847a940e3fde2eab79bb010a8a94757a
---- a/lib/Bio/Tools/Run/Alignment/Clustalw.pm
-+++ b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
-@@ -1001,7 +1001,7 @@
-
- Title : TYPE
- Description : (optional) sequence type: protein or DNA. This allows
-- you to explicitly overide the programs attempt at
-+ you to explicitly override the programs attempt at
- guessing the type of the sequence. It is only useful
- if you are using sequences with a VERY strange
- composition.
diff --git a/debian/patches/series b/debian/patches/series
index 46ed326..e69de29 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +0,0 @@
-doc-typos.patch
diff --git a/lib/Bio/Tools/Run/Alignment/Clustalw.pm b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
index 8020f4e..d79a93e 100644
--- a/lib/Bio/Tools/Run/Alignment/Clustalw.pm
+++ b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
@@ -1001,7 +1001,7 @@ the factory and read in the unaligned sequences.
Title : TYPE
Description : (optional) sequence type: protein or DNA. This allows
- you to explicitly overide the programs attempt at
+ you to explicitly override the programs attempt at
guessing the type of the sequence. It is only useful
if you are using sequences with a VERY strange
composition.
@@ -1151,14 +1151,13 @@ User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
- bioperl-l@bioperl.org - General discussion
- http://bioperl.org/Support.html - About the mailing lists
+ bioperl-l@bioperl.org - General discussion
+ https://bioperl.org/Support.html - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
-
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
diff --git a/t/author-pod-coverage.t b/t/author-pod-coverage.t
index 243340f..09473df 100644
--- a/t/author-pod-coverage.t
+++ b/t/author-pod-coverage.t
@@ -8,7 +8,8 @@ BEGIN {
}
# This file was automatically generated by Dist::Zilla::Plugin::PodCoverageTests.
-
+use strict;
+use warnings;
use Test::Pod::Coverage 1.08;
use Pod::Coverage::TrustPod;
Debdiff
File lists identical (after any substitutions)
No differences were encountered in the control files