New Upstream Snapshot - libbio-variation-perl
Ready changes
Summary
Merged new upstream version: 1.7.5+git20200108.1.fde2830 (was: 1.7.5).
Resulting package
Built on 2023-01-19T11:38 (took 11m48s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots libbio-variation-perl
Lintian Result
Diff
diff --git a/Changes b/Changes
index 10aea9f..21bb6bc 100644
--- a/Changes
+++ b/Changes
@@ -1,6 +1,8 @@
Summary of important user-visible changes for Bio-Variation
-----------------------------------------------------------
+1.7.5 2023-01-19 11:34:06+00:00 UTC
+
1.7.5 2020-01-06 13:58:44-06:00 America/Chicago
* Remove Bio::DB::EMBL and Bio::DB::NCBIHelper dependencies, which cause a circular dependency (see issue #3)
diff --git a/LICENSE b/LICENSE
index 4033b68..1077d98 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-This software is copyright (c) 2020 by See individual modules.
+This software is copyright (c) 2023 by See individual modules.
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) 2020 by See individual modules.
+This software is Copyright (c) 2023 by See individual modules.
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) 2020 by See individual modules.
+This software is Copyright (c) 2023 by See individual modules.
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 dac47b3..e664922 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,4 +1,4 @@
-# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.012.
+# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.029.
Changes
LICENSE
MANIFEST
diff --git a/META.json b/META.json
index 98c5ab0..b8b2fed 100644
--- a/META.json
+++ b/META.json
@@ -5,7 +5,7 @@
"Heikki Lehvaslaiho <heikki@bioperl.org>"
],
"dynamic_config" : 0,
- "generated_by" : "Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010",
+ "generated_by" : "Dist::Zilla version 6.029, CPAN::Meta::Converter version 2.150010",
"license" : [
"perl_5"
],
@@ -78,7 +78,7 @@
"version" : "1.7.5",
"x_Dist_Zilla" : {
"perl" : {
- "version" : "5.028001"
+ "version" : "5.036000"
},
"plugins" : [
{
@@ -95,42 +95,42 @@
}
},
"name" : "@BioPerl/@Filter/GatherDir",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::PruneCruft",
"name" : "@BioPerl/@Filter/PruneCruft",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::ManifestSkip",
"name" : "@BioPerl/@Filter/ManifestSkip",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::MetaYAML",
"name" : "@BioPerl/@Filter/MetaYAML",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::License",
"name" : "@BioPerl/@Filter/License",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::ExtraTests",
"name" : "@BioPerl/@Filter/ExtraTests",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::ExecDir",
"name" : "@BioPerl/@Filter/ExecDir",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::ShareDir",
"name" : "@BioPerl/@Filter/ShareDir",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::MakeMaker",
@@ -140,47 +140,47 @@
}
},
"name" : "@BioPerl/@Filter/MakeMaker",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::Manifest",
"name" : "@BioPerl/@Filter/Manifest",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::TestRelease",
"name" : "@BioPerl/@Filter/TestRelease",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::ConfirmRelease",
"name" : "@BioPerl/@Filter/ConfirmRelease",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::UploadToCPAN",
"name" : "@BioPerl/@Filter/UploadToCPAN",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::MetaConfig",
"name" : "@BioPerl/MetaConfig",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::MetaJSON",
"name" : "@BioPerl/MetaJSON",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::PkgVersion",
"name" : "@BioPerl/PkgVersion",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::PodSyntaxTests",
"name" : "@BioPerl/PodSyntaxTests",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::Test::Compile",
@@ -208,7 +208,7 @@
{
"class" : "Dist::Zilla::Plugin::PodCoverageTests",
"name" : "@BioPerl/PodCoverageTests",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::MojibakeTests",
@@ -218,7 +218,7 @@
{
"class" : "Dist::Zilla::Plugin::AutoPrereqs",
"name" : "@BioPerl/AutoPrereqs",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::AutoMetaResources",
@@ -228,17 +228,17 @@
{
"class" : "Dist::Zilla::Plugin::MetaResources",
"name" : "@BioPerl/MetaResources",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::Encoding",
"name" : "@BioPerl/Encoding",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::NextRelease",
"name" : "@BioPerl/NextRelease",
- "version" : "6.012"
+ "version" : "6.029"
},
{
"class" : "Dist::Zilla::Plugin::Git::Check",
@@ -255,19 +255,20 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.20.1",
+ "git_version" : "2.39.0",
"repo_root" : "."
}
},
"name" : "@BioPerl/Git::Check",
- "version" : "2.045"
+ "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" : [
@@ -278,7 +279,7 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.20.1",
+ "git_version" : "2.39.0",
"repo_root" : "."
},
"Dist::Zilla::Role::Git::StringFormatter" : {
@@ -286,7 +287,7 @@
}
},
"name" : "@BioPerl/Git::Commit",
- "version" : "2.045"
+ "version" : "2.048"
},
{
"class" : "Dist::Zilla::Plugin::Git::Tag",
@@ -300,7 +301,7 @@
"tag_message" : "%N-v%v"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.20.1",
+ "git_version" : "2.39.0",
"repo_root" : "."
},
"Dist::Zilla::Role::Git::StringFormatter" : {
@@ -308,57 +309,57 @@
}
},
"name" : "@BioPerl/Git::Tag",
- "version" : "2.045"
+ "version" : "2.048"
},
{
"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" : {
@@ -366,10 +367,11 @@
"config" : {
"is_trial" : 0
},
- "version" : "6.012"
+ "version" : "6.029"
}
},
- "x_generated_by_perl" : "v5.28.1",
- "x_serialization_backend" : "Cpanel::JSON::XS version 4.09"
+ "x_generated_by_perl" : "v5.36.0",
+ "x_serialization_backend" : "Cpanel::JSON::XS version 4.32",
+ "x_spdx_expression" : "Artistic-1.0-Perl OR GPL-1.0-or-later"
}
diff --git a/META.yml b/META.yml
index 54a7230..9cb18fb 100644
--- a/META.yml
+++ b/META.yml
@@ -14,7 +14,7 @@ build_requires:
configure_requires:
ExtUtils::MakeMaker: '0'
dynamic_config: 0
-generated_by: 'Dist::Zilla version 6.012, CPAN::Meta::Converter version 2.150010'
+generated_by: 'Dist::Zilla version 6.029, CPAN::Meta::Converter version 2.150010'
license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -46,7 +46,7 @@ resources:
version: 1.7.5
x_Dist_Zilla:
perl:
- version: '5.028001'
+ version: '5.036000'
plugins:
-
class: Dist::Zilla::Plugin::GatherDir
@@ -60,79 +60,79 @@ x_Dist_Zilla:
prune_directory: []
root: .
name: '@BioPerl/@Filter/GatherDir'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::PruneCruft
name: '@BioPerl/@Filter/PruneCruft'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::ManifestSkip
name: '@BioPerl/@Filter/ManifestSkip'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::MetaYAML
name: '@BioPerl/@Filter/MetaYAML'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::License
name: '@BioPerl/@Filter/License'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::ExtraTests
name: '@BioPerl/@Filter/ExtraTests'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::ExecDir
name: '@BioPerl/@Filter/ExecDir'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::ShareDir
name: '@BioPerl/@Filter/ShareDir'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::MakeMaker
config:
Dist::Zilla::Role::TestRunner:
default_jobs: 1
name: '@BioPerl/@Filter/MakeMaker'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::Manifest
name: '@BioPerl/@Filter/Manifest'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::TestRelease
name: '@BioPerl/@Filter/TestRelease'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::ConfirmRelease
name: '@BioPerl/@Filter/ConfirmRelease'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::UploadToCPAN
name: '@BioPerl/@Filter/UploadToCPAN'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::MetaConfig
name: '@BioPerl/MetaConfig'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::MetaJSON
name: '@BioPerl/MetaJSON'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::PkgVersion
name: '@BioPerl/PkgVersion'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::PodSyntaxTests
name: '@BioPerl/PodSyntaxTests'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::Test::Compile
config:
Dist::Zilla::Plugin::Test::Compile:
- bail_out_on_fail: '0'
+ bail_out_on_fail: 0
fail_on_warning: author
fake_home: 0
filename: t/00-compile.t
@@ -149,7 +149,7 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::PodCoverageTests
name: '@BioPerl/PodCoverageTests'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::MojibakeTests
name: '@BioPerl/MojibakeTests'
@@ -157,7 +157,7 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::AutoPrereqs
name: '@BioPerl/AutoPrereqs'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::AutoMetaResources
name: '@BioPerl/AutoMetaResources'
@@ -165,15 +165,15 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::MetaResources
name: '@BioPerl/MetaResources'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::Encoding
name: '@BioPerl/Encoding'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::NextRelease
name: '@BioPerl/NextRelease'
- version: '6.012'
+ version: '6.029'
-
class: Dist::Zilla::Plugin::Git::Check
config:
@@ -186,16 +186,17 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.20.1
+ git_version: 2.39.0
repo_root: .
name: '@BioPerl/Git::Check'
- version: '2.045'
+ 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
@@ -203,12 +204,12 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.20.1
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Commit'
- version: '2.045'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Git::Tag
config:
@@ -220,56 +221,57 @@ x_Dist_Zilla:
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
- git_version: 2.20.1
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Tag'
- version: '2.045'
+ version: '2.048'
-
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: v5.28.1
+ 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 fb518a0..ec6164e 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/bin/bp_flanks b/bin/bp_flanks
index f3c5f3d..51c364a 100644
--- a/bin/bp_flanks
+++ b/bin/bp_flanks
@@ -23,9 +23,8 @@ use constant VERSION => '3.0';
my $help = '';
my $flank = 100; # flank length on both sides of the region
my $in_format = 'EMBL'; # format of the file to read in
-# my $db_class = 'Bio::DB::EMBL'; # class of
my @pos; # position(s) in the sequence
-
+my $db_class = 'Bio::DB::EMBL';
GetOptions ("help" => \$help, "flanklength=i" => \$flank,
@@ -59,24 +58,22 @@ sub get_seq {
'-format' => $IN_FORMAT);
$seq = $in->next_seq();
}
- elsif ($file =~ /\./) { # sequence version from GenBank
+ else {
+ if ($file =~ /\./) { # sequence version from GenBank
+ $db_class = "Bio::DB::GenBank";
+ }
+ eval "require $db_class";
+ if ($@) {
+ die "Encountered an error loading the module $db_class: $@";
+ }
eval {
- Bio::SeqIO->_load_module("Bio::DB::GenBank");
- my $gb = Bio::DB::GenBank->new();
+ my $gb = $db_class->new();
$seq = $gb->get_Seq_by_version($file);
};
if ($@) {
- die "Encountered an error: $@";
- }
- } else { # plain accession mumber from more reliable EMBL
- eval {
- Bio::SeqIO->_load_module("Bio::DB::EMBL");
- my $gb = Bio::DB::EMBL->new();
- $seq = $gb->get_Seq_by_acc($file);
- };
- if ($@) {
- die "Encountered an error: $@";
+ die "Encountered an error when retrieving sequence accession $file: $@";
}
+
}
print STDERR "Could not find sequence [$file]" && return unless $seq;
return $seq;
diff --git a/debian/changelog b/debian/changelog
index 43300e8..49d7fe9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+libbio-variation-perl (1.7.5+git20200108.1.fde2830-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Thu, 19 Jan 2023 11:34:23 -0000
+
libbio-variation-perl (1.7.5-3) unstable; urgency=medium
* Team upload.
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