[med-svn] [Git][med-team/libbio-db-refseq-perl][master] 4 commits: New upstream version 1.7.4
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Dec 30 20:28:24 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / libbio-db-refseq-perl
Commits:
6e579f8a by Michael R. Crusoe at 2019-12-30T20:21:25Z
New upstream version 1.7.4
- - - - -
863884d8 by Michael R. Crusoe at 2019-12-30T20:21:25Z
routine-update: New upstream version
- - - - -
9907bd71 by Michael R. Crusoe at 2019-12-30T20:21:26Z
Update upstream source from tag 'upstream/1.7.4'
Update to upstream version '1.7.4'
with Debian dir ba4f011b137361744bf0e16ca34e7c2fc86da3a7
- - - - -
74bc1451 by Michael R. Crusoe at 2019-12-30T20:24:09Z
release 1.7.4-1
- - - - -
9 changed files:
- Changes
- META.json
- META.yml
- Makefile.PL
- debian/changelog
- debian/control
- dist.ini
- lib/Bio/DB/RefSeq.pm
- t/RefSeq.t
Changes:
=====================================
Changes
=====================================
@@ -1,6 +1,9 @@
Summary of important user-visible changes for Bio-DB-RefSeq
-----------------------------------------------------------
+1.7.4 2019-12-07 16:09:01-06:00 America/Chicago
+ * Fixes for issues related to using Bio::Root::Test (issue #3)
+
1.7.3 2019-11-28 00:44:59-06:00 America/Chicago
* First release after split from bioperl-live
* Address database connection failures (issue #2). Works for nucleotide
=====================================
META.json
=====================================
@@ -37,12 +37,14 @@
},
"test" : {
"requires" : {
- "Bio::Root::Test" : "0",
"File::Spec" : "0",
"IO::Handle" : "0",
"IPC::Open3" : "0",
"Test::More" : "0",
+ "Test::Needs" : "0",
+ "Test::RequiresInternet" : "0",
"perl" : "5.006",
+ "utf8" : "0",
"warnings" : "0"
}
}
@@ -60,7 +62,7 @@
"web" : "https://github.com/bioperl/bio-db-refseq"
}
},
- "version" : "1.7.3",
+ "version" : "1.7.4",
"x_Dist_Zilla" : {
"perl" : {
"version" : "5.028001"
@@ -280,7 +282,7 @@
"branch" : null,
"changelog" : "Changes",
"signed" : 0,
- "tag" : "Bio-DB-RefSeq-v1.7.3",
+ "tag" : "Bio-DB-RefSeq-v1.7.4",
"tag_format" : "%N-v%v",
"tag_message" : "%N-v%v"
},
=====================================
META.yml
=====================================
@@ -3,12 +3,14 @@ abstract: 'Database object interface for RefSeq retrieval'
author:
- 'Heikki Lehvaslaiho <heikki at bioperl.org>'
build_requires:
- Bio::Root::Test: '0'
File::Spec: '0'
IO::Handle: '0'
IPC::Open3: '0'
Test::More: '0'
+ Test::Needs: '0'
+ Test::RequiresInternet: '0'
perl: '5.006'
+ utf8: '0'
warnings: '0'
configure_requires:
ExtUtils::MakeMaker: '0'
@@ -28,7 +30,7 @@ resources:
bugtracker: https://github.com/bioperl/bio-db-refseq/issues
homepage: https://metacpan.org/release/Bio-DB-RefSeq
repository: git://github.com/bioperl/bio-db-refseq.git
-version: 1.7.3
+version: 1.7.4
x_Dist_Zilla:
perl:
version: '5.028001'
@@ -201,7 +203,7 @@ x_Dist_Zilla:
branch: ~
changelog: Changes
signed: 0
- tag: Bio-DB-RefSeq-v1.7.3
+ tag: Bio-DB-RefSeq-v1.7.4
tag_format: '%N-v%v'
tag_message: '%N-v%v'
Dist::Zilla::Role::Git::Repo:
=====================================
Makefile.PL
=====================================
@@ -23,14 +23,16 @@ my %WriteMakefileArgs = (
"vars" => 0
},
"TEST_REQUIRES" => {
- "Bio::Root::Test" => 0,
"File::Spec" => 0,
"IO::Handle" => 0,
"IPC::Open3" => 0,
"Test::More" => 0,
+ "Test::Needs" => 0,
+ "Test::RequiresInternet" => 0,
+ "utf8" => 0,
"warnings" => 0
},
- "VERSION" => "1.7.3",
+ "VERSION" => "1.7.4",
"test" => {
"TESTS" => "t/*.t"
}
@@ -39,13 +41,15 @@ my %WriteMakefileArgs = (
my %FallbackPrereqs = (
"Bio::DB::DBFetch" => 0,
- "Bio::Root::Test" => 0,
"File::Spec" => 0,
"IO::Handle" => 0,
"IPC::Open3" => 0,
"Test::More" => 0,
+ "Test::Needs" => 0,
+ "Test::RequiresInternet" => 0,
"base" => 0,
"strict" => 0,
+ "utf8" => 0,
"vars" => 0,
"warnings" => 0
);
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+libbio-db-refseq-perl (1.7.4-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 30 Dec 2019 21:21:28 +0100
+
libbio-db-refseq-perl (1.7.3-2) unstable; urgency=medium
* Be explicit about libhttp-message-perl dependency.
=====================================
debian/control
=====================================
@@ -10,6 +10,7 @@ Build-Depends-Indep: libbio-perl-perl,
libhttp-message-perl,
libwww-perl,
libtest-requiresinternet-perl,
+ libtest-needs-perl,
perl
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-refseq-perl
=====================================
dist.ini
=====================================
@@ -1,5 +1,5 @@
name = Bio-DB-RefSeq
-version = 1.7.3
+version = 1.7.4
author = Heikki Lehvaslaiho <heikki at bioperl.org>
copyright_holder = Heikki Lehvaslaiho <heikki at bioperl.org>
license = Perl_5
=====================================
lib/Bio/DB/RefSeq.pm
=====================================
@@ -116,7 +116,7 @@ methods. Internal methods are usually preceded with a _
# Let the code begin...
package Bio::DB::RefSeq;
-$Bio::DB::RefSeq::VERSION = '1.7.3';
+$Bio::DB::RefSeq::VERSION = '1.7.4';
use strict;
use vars qw($MODVERSION %HOSTS %FORMATMAP $DEFAULTFORMAT);
=====================================
t/RefSeq.t
=====================================
@@ -1,35 +1,27 @@
-# -*-Perl-*- Test Harness script for Bioperl
-# $Id$
+#!/usr/bin/env perl
+use utf8;
use strict;
+use warnings;
-BEGIN {
- use Bio::Root::Test;
+use Test::More;
+use Test::Needs qw(LWP::UserAgent HTTP::Request::Common Data::Stag);
+use Test::RequiresInternet;
- test_begin(-tests => 7,
- -requires_modules => [qw(IO::String
- LWP::UserAgent
- HTTP::Request::Common)]);
- use_ok('Bio::DB::RefSeq');
-}
+use Bio::DB::RefSeq;
-my $verbose = test_debug() || -1;
+my $verbose = $ENV{'BIOPERLDEBUG'} || -1;
my ($db,$seq,$seqio);
# get a single seq
$seq = $seqio = undef;
-SKIP: {
- test_skip(-tests => 6, -requires_networking => 1);
-
- eval {
- ok defined($db = Bio::DB::RefSeq->new(-verbose=>$verbose));
- ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
- is( $seq->length, 3775);
- ok defined ($db->request_format('fasta'));
- ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
- is( $seq->length, 3775);
- };
- skip "Warning: Couldn't connect to RefSeq with Bio::DB::RefSeq.pm!", 6 if $@;
-}
+ok defined($db = Bio::DB::RefSeq->new(-verbose=>$verbose));
+ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
+is( $seq->length, 3775);
+ok defined ($db->request_format('fasta'));
+ok(defined($seq = $db->get_Seq_by_acc('NM_006732')));
+is( $seq->length, 3775);
+
+done_testing();
View it on GitLab: https://salsa.debian.org/med-team/libbio-db-refseq-perl/compare/0ac18e13487b7b835541b37f8952c21a0fd23fe7...74bc14510930a9ff477224a9b989fa60c2fc6525
--
View it on GitLab: https://salsa.debian.org/med-team/libbio-db-refseq-perl/compare/0ac18e13487b7b835541b37f8952c21a0fd23fe7...74bc14510930a9ff477224a9b989fa60c2fc6525
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