[med-svn] [Git][med-team/libbio-db-ncbihelper-perl][upstream] New upstream version 1.7.8
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Dec 17 16:00:45 GMT 2023
Étienne Mollier pushed to branch upstream at Debian Med / libbio-db-ncbihelper-perl
Commits:
89ce83c5 by Étienne Mollier at 2023-12-17T16:51:15+01:00
New upstream version 1.7.8
- - - - -
14 changed files:
- Changes
- LICENSE
- MANIFEST
- META.json
- META.yml
- Makefile.PL
- dist.ini
- lib/Bio/DB/EntrezGene.pm
- lib/Bio/DB/GenBank.pm
- lib/Bio/DB/GenPept.pm
- lib/Bio/DB/NCBIHelper.pm
- lib/Bio/DB/Query/GenBank.pm
- lib/Bio/DB/Taxonomy/entrez.pm
- t/Taxonomy.t
Changes:
=====================================
Changes
=====================================
@@ -1,6 +1,10 @@
Summary of important user-visible changes for Bio-DB-NCBIHelper
---------------------------------------------------------------
+1.7.8 2023-12-14 22:22:13-06:00 America/Chicago
+ * Fix a series of failing tests caused by changes to the data on the
+ NCBI databases.
+
1.7.7 2021-06-30 08:52:57-05:00 America/Chicago
* Merge pull request to address taxonomic name change, which led to failing network tests (thx @MrCurtis!).
=====================================
LICENSE
=====================================
@@ -1,4 +1,4 @@
-This software is copyright (c) 2021 by Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
+This software is copyright (c) 2023 by Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
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 Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
+This software is Copyright (c) 2023 by Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
This is free software, licensed under:
@@ -270,110 +270,143 @@ necessary. Here a sample; alter the names:
That's all there is to it!
---- The Artistic License 1.0 ---
+--- The Perl Artistic License 1.0 ---
-This software is Copyright (c) 2021 by Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
+This software is Copyright (c) 2023 by Aaron Mackey <amackey at virginia.edu>, Brian Osborne <bosborne at alum.mit.edu>, Jason Stajich <jason at bioperl.org>, Lincoln Stein <lstein at cshl.org>.
This is free software, licensed under:
- The Artistic License 1.0
+ The Perl Artistic License 1.0
-The Artistic License
-Preamble
-The intent of this document is to state the conditions under which a Package
-may be copied, such that the Copyright Holder maintains some semblance of
-artistic control over the development of the package, while giving the users of
-the package the right to use and distribute the Package in a more-or-less
-customary fashion, plus the right to make reasonable modifications.
+
+
+ The "Artistic License"
+
+ Preamble
+
+The intent of this document is to state the conditions under which a
+Package may be copied, such that the Copyright Holder maintains some
+semblance of artistic control over the development of the package,
+while giving the users of the package the right to use and distribute
+the Package in a more-or-less customary fashion, plus the right to make
+reasonable modifications.
Definitions:
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- Holder, and derivatives of that collection of files created through
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+you may distribute this Package in aggregate with other (possibly
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+9. The name of the Copyright Holder may not be used to endorse or promote
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.
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-The End
+ The End
=====================================
MANIFEST
=====================================
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Changes
LICENSE
MANIFEST
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class: Dist::Zilla::Plugin::AutoMetaResources
name: '@BioPerl/AutoMetaResources'
@@ -169,15 +169,15 @@ x_Dist_Zilla:
-
class: Dist::Zilla::Plugin::MetaResources
name: '@BioPerl/MetaResources'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::Encoding
name: '@BioPerl/Encoding'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::NextRelease
name: '@BioPerl/NextRelease'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::Git::Check
config:
@@ -190,10 +190,10 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: '2.39.2 (Apple Git-143)'
repo_root: .
name: '@BioPerl/Git::Check'
- version: '2.047'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Git::Commit
config:
@@ -208,12 +208,12 @@ x_Dist_Zilla:
allow_dirty_match: []
changelog: Changes
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: '2.39.2 (Apple Git-143)'
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:
@@ -221,16 +221,16 @@ x_Dist_Zilla:
branch: ~
changelog: Changes
signed: 0
- tag: Bio-DB-NCBIHelper-v1.7.7
+ tag: Bio-DB-NCBIHelper-v1.7.8
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
- git_version: 2.28.0
+ git_version: '2.39.2 (Apple Git-143)'
repo_root: .
Dist::Zilla::Role::Git::StringFormatter:
time_zone: local
name: '@BioPerl/Git::Tag'
- version: '2.047'
+ version: '2.048'
-
class: Dist::Zilla::Plugin::Prereqs
config:
@@ -238,52 +238,52 @@ x_Dist_Zilla:
phase: runtime
type: requires
name: Prereqs
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':InstallModules'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':IncModules'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':TestFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExtraTestFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ExecFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':PerlExecFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':ShareFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':MainModule'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':AllFiles'
- version: '6.017'
+ version: '6.031'
-
class: Dist::Zilla::Plugin::FinderCode
name: ':NoFiles'
- version: '6.017'
+ version: '6.031'
zilla:
class: Dist::Zilla::Dist::Builder
config:
is_trial: '0'
- version: '6.017'
-x_generated_by_perl: v5.33.1
-x_serialization_backend: 'YAML::Tiny version 1.73'
+ version: '6.031'
+x_generated_by_perl: v5.34.0
+x_serialization_backend: 'YAML::Tiny version 1.74'
x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'
=====================================
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 v6.031.
use strict;
use warnings;
@@ -55,7 +55,7 @@ my %WriteMakefileArgs = (
"Test::Most" => 0,
"Test::RequiresInternet" => 0
},
- "VERSION" => "1.7.7",
+ "VERSION" => "1.7.8",
"test" => {
"TESTS" => "t/*.t"
}
=====================================
dist.ini
=====================================
@@ -1,5 +1,5 @@
name = Bio-DB-NCBIHelper
-version = 1.7.7
+version = 1.7.8
author = Aaron Mackey <amackey at virginia.edu>
author = Brian Osborne <bosborne at alum.mit.edu>
author = Jason Stajich <jason at bioperl.org>
=====================================
lib/Bio/DB/EntrezGene.pm
=====================================
@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::DB::EntrezGene;
-$Bio::DB::EntrezGene::VERSION = '1.7.7';
+$Bio::DB::EntrezGene::VERSION = '1.7.8';
use strict;
use vars qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING);
=====================================
lib/Bio/DB/GenBank.pm
=====================================
@@ -165,7 +165,7 @@ preceded with a _
# Let the code begin...
package Bio::DB::GenBank;
-$Bio::DB::GenBank::VERSION = '1.7.7';
+$Bio::DB::GenBank::VERSION = '1.7.8';
use strict;
use vars qw(%PARAMSTRING $DEFAULTFORMAT $DEFAULTMODE);
=====================================
lib/Bio/DB/GenPept.pm
=====================================
@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::DB::GenPept;
-$Bio::DB::GenPept::VERSION = '1.7.7';
+$Bio::DB::GenPept::VERSION = '1.7.8';
use strict;
use vars qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING);
=====================================
lib/Bio/DB/NCBIHelper.pm
=====================================
@@ -85,7 +85,7 @@ preceded with a _
# Let the code begin...
package Bio::DB::NCBIHelper;
-$Bio::DB::NCBIHelper::VERSION = '1.7.7';
+$Bio::DB::NCBIHelper::VERSION = '1.7.8';
use strict;
use Bio::DB::Query::GenBank;
=====================================
lib/Bio/DB/Query/GenBank.pm
=====================================
@@ -96,7 +96,7 @@ preceded with a _
# Let the code begin...
package Bio::DB::Query::GenBank;
-$Bio::DB::Query::GenBank::VERSION = '1.7.7';
+$Bio::DB::Query::GenBank::VERSION = '1.7.8';
use strict;
use URI::Escape 'uri_unescape';
use Bio::DB::NCBIHelper;
=====================================
lib/Bio/DB/Taxonomy/entrez.pm
=====================================
@@ -101,7 +101,7 @@ Internal methods are usually preceded with a _
# Let the code begin...
package Bio::DB::Taxonomy::entrez;
-$Bio::DB::Taxonomy::entrez::VERSION = '1.7.7';
+$Bio::DB::Taxonomy::entrez::VERSION = '1.7.8';
use vars qw($EntrezLocation $UrlParamSeparatorValue %EntrezParams
$EntrezGet $EntrezSummary $EntrezFetch %SequenceParams
$XMLTWIG $DATA_CACHE $RELATIONS);
=====================================
t/Taxonomy.t
=====================================
@@ -45,7 +45,6 @@ if (defined $ENV{BIOPERLEMAIL}) {
my %common_names = map { $_ => 1 } $n->common_names;
cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
ok exists $common_names{human};
- ok exists $common_names{man};
is $n->division, 'Primates';
is $n->genetic_code, 1;
@@ -99,7 +98,7 @@ if (defined $ENV{BIOPERLEMAIL}) {
sleep(3);
ok $n = $db->get_Taxonomy_Node('1760');
- is $n->scientific_name, 'Actinomycetia';
+ is $n->scientific_name, 'Actinomycetes';
sleep(3);
@@ -165,8 +164,8 @@ if (defined $ENV{BIOPERLEMAIL}) {
# 'Chlorella vulgaris' | 3077 | 3077
# 'Phygadeuon solidus' | 1763951 | 1763951
# 'Ovatus' | 666060 | 666060
- # 'Phygadeuon ovatus' | "No hit" | 666060
- # 'Trimorus ovatus' | "No hit" | 666060
+ # 'Phygadeuon ovatus' | 2890685 | 2890685
+ # 'Zaphod Beeblebrox' | "No hit" | "No hit"
my @ids;
@ids = $db->get_taxonids('Lissotriton vulgaris');
@@ -178,8 +177,8 @@ if (defined $ENV{BIOPERLEMAIL}) {
@ids = $db->get_taxonids('Ovatus');
is $ids[0], 666060, 'Correct: Ovatus';
@ids = $db->get_taxonids('Phygadeuon ovatus');
- is $ids[0], 'No hit', 'Correct: No hit';
- @ids = $db->get_taxonids('Trimorus ovatus');
+ is $ids[0], '2890685', 'Correct: 2890685';
+ @ids = $db->get_taxonids('Zaphod Beeblebrox');
is $ids[0], 'No hit', 'Correct: No hit';
}
View it on GitLab: https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/-/commit/89ce83c5630d00fda86e8e87c0e1e6c81af05284
--
View it on GitLab: https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/-/commit/89ce83c5630d00fda86e8e87c0e1e6c81af05284
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