New Upstream Snapshot - bioperl
Ready changes
Summary
Merged new upstream version: 1.7.8+git20220912.1.4c9acbe (was: 1.7.8).
Resulting package
Built on 2023-01-20T16:53 (took 12m9s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots bioperlapt install -t fresh-snapshots libbio-perl-perl
Lintian Result
Diff
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
new file mode 100644
index 0000000..eac211b
--- /dev/null
+++ b/CODE_OF_CONDUCT.md
@@ -0,0 +1,3 @@
+# BioPerl Code of Conduct
+
+As an affiliated member project of the Open Bioinformatics Foundation, BioPerl has adopted the Open Bioinformatics Foundation [Code of Conduct](https://github.com/OBF/obf-docs/tree/master/code-of-conduct).
diff --git a/Changes b/Changes
index 5eeff3b..f3b4d83 100644
--- a/Changes
+++ b/Changes
@@ -1,6 +1,8 @@
Summary of important user-visible changes for BioPerl
-----------------------------------------------------
+1.7.8 2023-01-20 16:47:23+00:00 UTC
+
1.7.8 2021-02-02 23:02:18-06:00 America/Chicago
* Bio::SeqIO::interpro has been moved to a separate repository to
deal with issues with XML::DOM::XPath bitrot [#347]
diff --git a/LICENSE b/LICENSE
index 49b72f6..1077d98 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,4 @@
-This software is copyright (c) 2021 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) 2021 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) 2021 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 e965e0b..6eb101e 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -1,5 +1,6 @@
-# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.017.
+# This file was automatically generated by Dist::Zilla::Plugin::Manifest v6.030.
AUTHORS
+CODE_OF_CONDUCT.md
Changes
HACKING.md
LICENSE
diff --git a/META.json b/META.json
index 9025395..617cdc9 100644
--- a/META.json
+++ b/META.json
@@ -4,7 +4,7 @@
"See individual modules"
],
"dynamic_config" : 1,
- "generated_by" : "Dist::Zilla version 6.017, CPAN::Meta::Converter version 2.150010",
+ "generated_by" : "Dist::Zilla version 6.030, CPAN::Meta::Converter version 2.150010",
"license" : [
"perl_5"
],
@@ -137,7 +137,7 @@
"version" : "1.7.8",
"x_Dist_Zilla" : {
"perl" : {
- "version" : "5.033001"
+ "version" : "5.036000"
},
"plugins" : [
{
@@ -154,42 +154,42 @@
}
},
"name" : "@BioPerl/@Filter/GatherDir",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::PruneCruft",
"name" : "@BioPerl/@Filter/PruneCruft",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::ManifestSkip",
"name" : "@BioPerl/@Filter/ManifestSkip",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::MetaYAML",
"name" : "@BioPerl/@Filter/MetaYAML",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::License",
"name" : "@BioPerl/@Filter/License",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::ExtraTests",
"name" : "@BioPerl/@Filter/ExtraTests",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::ExecDir",
"name" : "@BioPerl/@Filter/ExecDir",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::ShareDir",
"name" : "@BioPerl/@Filter/ShareDir",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::MakeMaker",
@@ -199,47 +199,47 @@
}
},
"name" : "@BioPerl/@Filter/MakeMaker",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::Manifest",
"name" : "@BioPerl/@Filter/Manifest",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::TestRelease",
"name" : "@BioPerl/@Filter/TestRelease",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::ConfirmRelease",
"name" : "@BioPerl/@Filter/ConfirmRelease",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::UploadToCPAN",
"name" : "@BioPerl/@Filter/UploadToCPAN",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::MetaConfig",
"name" : "@BioPerl/MetaConfig",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::MetaJSON",
"name" : "@BioPerl/MetaJSON",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::PkgVersion",
"name" : "@BioPerl/PkgVersion",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::PodSyntaxTests",
"name" : "@BioPerl/PodSyntaxTests",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::Test::Compile",
@@ -272,22 +272,22 @@
{
"class" : "Dist::Zilla::Plugin::AutoPrereqs",
"name" : "@BioPerl/AutoPrereqs",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::MetaResources",
"name" : "@BioPerl/MetaResources",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::Encoding",
"name" : "@BioPerl/Encoding",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::NextRelease",
"name" : "@BioPerl/NextRelease",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::Git::Check",
@@ -304,12 +304,12 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.28.0",
+ "git_version" : "2.39.0",
"repo_root" : "."
}
},
"name" : "@BioPerl/Git::Check",
- "version" : "2.047"
+ "version" : "2.048"
},
{
"class" : "Dist::Zilla::Plugin::Git::Commit",
@@ -328,7 +328,7 @@
"changelog" : "Changes"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.28.0",
+ "git_version" : "2.39.0",
"repo_root" : "."
},
"Dist::Zilla::Role::Git::StringFormatter" : {
@@ -336,7 +336,7 @@
}
},
"name" : "@BioPerl/Git::Commit",
- "version" : "2.047"
+ "version" : "2.048"
},
{
"class" : "Dist::Zilla::Plugin::Git::Tag",
@@ -350,7 +350,7 @@
"tag_message" : "%N-v%v"
},
"Dist::Zilla::Role::Git::Repo" : {
- "git_version" : "2.28.0",
+ "git_version" : "2.39.0",
"repo_root" : "."
},
"Dist::Zilla::Role::Git::StringFormatter" : {
@@ -358,7 +358,7 @@
}
},
"name" : "@BioPerl/Git::Tag",
- "version" : "2.047"
+ "version" : "2.048"
},
{
"class" : "Dist::Zilla::Plugin::OSPrereqs",
@@ -379,12 +379,12 @@
}
},
"name" : "bin_bp_fetch_RuntimeSuggests",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : "PodWeaver-Ready",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::PodWeaver",
@@ -400,92 +400,92 @@
{
"class" : "Pod::Weaver::Plugin::EnsurePod5",
"name" : "@CorePrep/EnsurePod5",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Plugin::H1Nester",
"name" : "@CorePrep/H1Nester",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Name",
"name" : "@BioPerl/Name",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Version",
"name" : "@BioPerl/Version",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Region",
"name" : "@BioPerl/prelude",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Generic",
"name" : "SYNOPSIS",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Generic",
"name" : "DESCRIPTION",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Generic",
"name" : "OVERVIEW",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Collect",
"name" : "ATTRIBUTES",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Collect",
"name" : "METHODS",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Collect",
"name" : "FUNCTIONS",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Collect",
"name" : "INTERNAL METHODS",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Leftovers",
"name" : "@BioPerl/Leftovers",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Region",
"name" : "@BioPerl/postlude",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::GenerateSection",
"name" : "FEEDBACK",
- "version" : "1.06"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::GenerateSection",
"name" : "Mailing lists",
- "version" : "1.06"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::GenerateSection",
"name" : "Support",
- "version" : "1.06"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::GenerateSection",
"name" : "Reporting bugs",
- "version" : "1.06"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Section::Legal::Complicated",
@@ -500,12 +500,12 @@
{
"class" : "Pod::Weaver::Plugin::SingleEncoding",
"name" : "SingleEncoding",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Plugin::Transformer",
"name" : "@BioPerl/List",
- "version" : "4.015"
+ "version" : "4.019"
},
{
"class" : "Pod::Weaver::Plugin::EnsureUniqueSections",
@@ -516,67 +516,67 @@
}
},
"name" : "PodWeaver",
- "version" : "4.008"
+ "version" : "4.010"
},
{
"class" : "Dist::Zilla::Plugin::MetaResources",
"name" : "MetaResources",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : "PruneFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : ":InstallModules",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : ":IncModules",
- "version" : "6.017"
+ "version" : "6.030"
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{
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"name" : ":TestFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : ":ExtraTestFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::FinderCode",
"name" : ":ExecFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::FinderCode",
"name" : ":PerlExecFiles",
- "version" : "6.017"
+ "version" : "6.030"
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{
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"name" : ":ShareFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
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"name" : ":MainModule",
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+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::FinderCode",
"name" : ":AllFiles",
- "version" : "6.017"
+ "version" : "6.030"
},
{
"class" : "Dist::Zilla::Plugin::FinderCode",
"name" : ":NoFiles",
- "version" : "6.017"
+ "version" : "6.030"
}
],
"zilla" : {
@@ -584,11 +584,11 @@
"config" : {
"is_trial" : 0
},
- "version" : "6.017"
+ "version" : "6.030"
}
},
- "x_generated_by_perl" : "v5.33.1",
- "x_serialization_backend" : "Cpanel::JSON::XS version 4.25",
+ "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 a53ff54..3e18a37 100644
--- a/META.yml
+++ b/META.yml
@@ -15,7 +15,7 @@ build_requires:
configure_requires:
ExtUtils::MakeMaker: '0'
dynamic_config: 1
-generated_by: 'Dist::Zilla version 6.017, CPAN::Meta::Converter version 2.150010'
+generated_by: 'Dist::Zilla version 6.030, CPAN::Meta::Converter version 2.150010'
license: perl
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -100,7 +100,7 @@ resources:
version: 1.7.8
x_Dist_Zilla:
perl:
- version: '5.033001'
+ version: '5.036000'
plugins:
-
class: Dist::Zilla::Plugin::GatherDir
@@ -114,79 +114,79 @@ x_Dist_Zilla:
prune_directory: []
root: .
name: '@BioPerl/@Filter/GatherDir'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::PruneCruft
name: '@BioPerl/@Filter/PruneCruft'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::ManifestSkip
name: '@BioPerl/@Filter/ManifestSkip'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::MetaYAML
name: '@BioPerl/@Filter/MetaYAML'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::License
name: '@BioPerl/@Filter/License'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::ExtraTests
name: '@BioPerl/@Filter/ExtraTests'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::ExecDir
name: '@BioPerl/@Filter/ExecDir'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::ShareDir
name: '@BioPerl/@Filter/ShareDir'
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+ version: '6.030'
-
class: Dist::Zilla::Plugin::MakeMaker
config:
Dist::Zilla::Role::TestRunner:
default_jobs: 1
name: '@BioPerl/@Filter/MakeMaker'
- version: '6.017'
+ version: '6.030'
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class: Dist::Zilla::Plugin::Manifest
name: '@BioPerl/@Filter/Manifest'
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+ version: '6.030'
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class: Dist::Zilla::Plugin::TestRelease
name: '@BioPerl/@Filter/TestRelease'
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class: Dist::Zilla::Plugin::ConfirmRelease
name: '@BioPerl/@Filter/ConfirmRelease'
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+ version: '6.030'
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class: Dist::Zilla::Plugin::UploadToCPAN
name: '@BioPerl/@Filter/UploadToCPAN'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::MetaConfig
name: '@BioPerl/MetaConfig'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::MetaJSON
name: '@BioPerl/MetaJSON'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::PkgVersion
name: '@BioPerl/PkgVersion'
- version: '6.017'
+ version: '6.030'
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class: Dist::Zilla::Plugin::PodSyntaxTests
name: '@BioPerl/PodSyntaxTests'
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+ version: '6.030'
-
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
@@ -207,19 +207,19 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::AutoPrereqs
name: '@BioPerl/AutoPrereqs'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::MetaResources
name: '@BioPerl/MetaResources'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::Encoding
name: '@BioPerl/Encoding'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::NextRelease
name: '@BioPerl/NextRelease'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::Git::Check
config:
@@ -232,17 +232,17 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: 2.39.0
repo_root: .
name: '@BioPerl/Git::Check'
- version: '2.047'
+ 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
- signoff: '0'
+ signoff: 0
Dist::Zilla::Role::Git::DirtyFiles:
allow_dirty:
- Changes
@@ -250,12 +250,12 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Commit'
- version: '2.047'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Git::Tag
config:
@@ -267,12 +267,12 @@ x_Dist_Zilla:
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: 2.39.0
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Tag'
- version: '2.047'
+ version: '2.048'
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class: Dist::Zilla::Plugin::OSPrereqs
config:
@@ -287,11 +287,11 @@ x_Dist_Zilla:
phase: runtime
type: suggests
name: bin_bp_fetch_RuntimeSuggests
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+ version: '6.030'
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name: PodWeaver-Ready
- version: '6.017'
+ version: '6.030'
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class: Dist::Zilla::Plugin::PodWeaver
config:
@@ -304,75 +304,75 @@ x_Dist_Zilla:
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class: Pod::Weaver::Plugin::EnsurePod5
name: '@CorePrep/EnsurePod5'
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class: Pod::Weaver::Section::Region
name: '@BioPerl/prelude'
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Generic
name: SYNOPSIS
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Generic
name: DESCRIPTION
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Generic
name: OVERVIEW
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Collect
name: ATTRIBUTES
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Collect
name: METHODS
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Collect
name: FUNCTIONS
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Collect
name: 'INTERNAL METHODS'
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Leftovers
name: '@BioPerl/Leftovers'
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::Region
name: '@BioPerl/postlude'
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Section::GenerateSection
name: FEEDBACK
- version: '1.06'
+ version: '4.019'
-
class: Pod::Weaver::Section::GenerateSection
name: 'Mailing lists'
- version: '1.06'
+ version: '4.019'
-
class: Pod::Weaver::Section::GenerateSection
name: Support
- version: '1.06'
+ version: '4.019'
-
class: Pod::Weaver::Section::GenerateSection
name: 'Reporting bugs'
- version: '1.06'
+ version: '4.019'
-
class: Pod::Weaver::Section::Legal::Complicated
name: '@BioPerl/Legal'
@@ -384,70 +384,70 @@ x_Dist_Zilla:
-
class: Pod::Weaver::Plugin::SingleEncoding
name: SingleEncoding
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Plugin::Transformer
name: '@BioPerl/List'
- version: '4.015'
+ version: '4.019'
-
class: Pod::Weaver::Plugin::EnsureUniqueSections
name: EnsureUniqueSections
version: '0.163250'
name: PodWeaver
- version: '4.008'
+ version: '4.010'
-
class: Dist::Zilla::Plugin::MetaResources
name: MetaResources
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::PruneFiles
name: PruneFiles
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':InstallModules'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':IncModules'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':TestFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExtraTestFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExecFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':PerlExecFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ShareFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':MainModule'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':AllFiles'
- version: '6.017'
+ version: '6.030'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':NoFiles'
- version: '6.017'
+ version: '6.030'
zilla:
class: Dist::Zilla::Dist::Builder
config:
- is_trial: '0'
- version: '6.017'
-x_generated_by_perl: v5.33.1
+ is_trial: 0
+ version: '6.030'
+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 5646bea..fa82529 100644
--- a/Makefile.PL
+++ b/Makefile.PL
@@ -1,4 +1,4 @@
-# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.017.
+# This file was automatically generated by Dist::Zilla::Plugin::MakeMaker v6.030.
use strict;
use warnings;
diff --git a/bin/bp_seqcut b/bin/bp_seqcut
index 86f7a12..c1e5c6b 100644
--- a/bin/bp_seqcut
+++ b/bin/bp_seqcut
@@ -17,13 +17,13 @@ bp_seqcut.pl - cut FASTA sequences with a given range
=head1 Description
-A script to cut FASTA sequences with a given range `fastacut -s 1 -e 10 *.fasta` or `fastacut 1-10 *.fasta`.
+A script to cut FASTA sequences with a given range `bp_seqcut.pl -s 1 -e 10 *.fasta` or `bp_seqcut.pl 1-10 *.fasta`.
This is just a convenience wrapper around the Bio::SeqIO module. Useful if you wish to trim out a section of an
alignment to build a profile of a specific region of sequence.
=head1 AUTHOR
-B<Matt Oates> - I<Matt.Oates@bristol.ac.uk>
+B<Matt Oates> - I<mattoates+support@gmail.com>
=head1 FEEDBACK
diff --git a/debian/changelog b/debian/changelog
index 4087b0a..565c94d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bioperl (1.7.8+git20220912.1.4c9acbe-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Fri, 20 Jan 2023 16:49:01 -0000
+
bioperl (1.7.8-1) unstable; urgency=medium
* Team Upload.
diff --git a/lib/Bio/SeqIO/fasta.pm b/lib/Bio/SeqIO/fasta.pm
index 8f3011d..b0ad878 100644
--- a/lib/Bio/SeqIO/fasta.pm
+++ b/lib/Bio/SeqIO/fasta.pm
@@ -311,10 +311,10 @@ sub write_seq {
# for large seqs, don't call seq(), it defeats the
# purpose of the largeseq functionality. instead get
# chunks of the seq, $width at a time
- my $buff_max = 2000;
+ my $buff_max = 200000;
my $buff_size = int($buff_max/$width)*$width; #< buffer is even multiple of widths
my $seq_length = $seq->length;
- my $num_chunks = int($seq_length/$buff_size+1);
+ my $num_chunks = int(($seq_length-1)/$buff_size+1);
for( my $c = 0; $c < $num_chunks; $c++ ) {
my $buff_end = $buff_size*($c+1);
$buff_end = $seq_length if $buff_end > $seq_length;
Debdiff
File lists identical (after any substitutions)
No differences were encountered between the control files of package bioperl
No differences were encountered between the control files of package libbio-perl-perl