Changes

 Summary of important user-visible changes for BioPerl
 -----------------------------------------------------
 
+1.7.4     2019-02-05 16:23:53+00:00 Europe/London
+
+    * Fix Bio::Root::Test, and the testuite, to properly check for
+      internet connection and the NO_NETWORK_TESTING environment
+      variable.  Previously, tests that required internet connection
+      were not being skipped, causing tests to fail.
+
+
 1.7.3     2019-01-30 13:30:34+00:00 Europe/London
 
     * The following modules have been removed from the BioPerl

MANIFEST

@@ -1431,5 +1431,3 @@ t/data/version3.scf
 t/data/wellcome_tol.nhx
 t/data/worm_fam_2785.cdna
 t/data/yeast.tRNAscanSE
-travis_scripts/dependency_installs
-travis_scripts/trigger-dockerhub.sh

META.json

@@ -127,16 +127,16 @@
    "resources" : {
       "bugtracker" : {
          "mailto" : "bioperl-l@bioperl.org",
-         "web" : "https://github.com/bioperl/bioperl/issues"
+         "web" : "https://github.com/bioperl/bioperl-live/issues"
       },
       "homepage" : "https://metacpan.org/release/BioPerl",
       "repository" : {
          "type" : "git",
-         "url" : "git://github.com/bioperl/bioperl.git",
-         "web" : "https://github.com/bioperl/bioperl"
+         "url" : "git://github.com/bioperl/bioperl-live.git",
+         "web" : "https://github.com/bioperl/bioperl-live"
       }
    },
-   "version" : "1.7.3",
+   "version" : "1.7.4",
    "x_Dist_Zilla" : {
       "perl" : {
          "version" : "5.028001"
@@ -276,11 +276,6 @@
             "name" : "@BioPerl/AutoPrereqs",
             "version" : "6.012"
          },
-         {
-            "class" : "Dist::Zilla::Plugin::AutoMetaResources",
-            "name" : "@BioPerl/AutoMetaResources",
-            "version" : "1.21"
-         },
          {
             "class" : "Dist::Zilla::Plugin::MetaResources",
             "name" : "@BioPerl/MetaResources",
@@ -351,7 +346,7 @@
                   "branch" : null,
                   "changelog" : "Changes",
                   "signed" : 0,
-                  "tag" : "BioPerl-v1.7.3",
+                  "tag" : "BioPerl-v1.7.4",
                   "tag_format" : "%N-v%v",
                   "tag_message" : "%N-v%v"
                },
@@ -524,6 +519,16 @@
             "name" : "PodWeaver",
             "version" : "4.008"
          },
+         {
+            "class" : "Dist::Zilla::Plugin::MetaResources",
+            "name" : "MetaResources",
+            "version" : "6.012"
+         },
+         {
+            "class" : "Dist::Zilla::Plugin::PruneFiles",
+            "name" : "PruneFiles",
+            "version" : "6.012"
+         },
          {
             "class" : "Dist::Zilla::Plugin::FinderCode",
             "name" : ":InstallModules",

META.yml

@@ -96,10 +96,10 @@ requires:
   version: '0'
   warnings: '0'
 resources:
-  bugtracker: https://github.com/bioperl/bioperl/issues
+  bugtracker: https://github.com/bioperl/bioperl-live/issues
   homepage: https://metacpan.org/release/BioPerl
-  repository: git://github.com/bioperl/bioperl.git
-version: 1.7.3
+  repository: git://github.com/bioperl/bioperl-live.git
+version: 1.7.4
 x_Dist_Zilla:
   perl:
     version: '5.028001'
@@ -210,10 +210,6 @@ x_Dist_Zilla:
       class: Dist::Zilla::Plugin::AutoPrereqs
       name: '@BioPerl/AutoPrereqs'
       version: '6.012'
-    -
-      class: Dist::Zilla::Plugin::AutoMetaResources
-      name: '@BioPerl/AutoMetaResources'
-      version: '1.21'
     -
       class: Dist::Zilla::Plugin::MetaResources
       name: '@BioPerl/MetaResources'
@@ -268,7 +264,7 @@ x_Dist_Zilla:
           branch: ~
           changelog: Changes
           signed: 0
-          tag: BioPerl-v1.7.3
+          tag: BioPerl-v1.7.4
           tag_format: '%N-v%v'
           tag_message: '%N-v%v'
         Dist::Zilla::Role::Git::Repo:
@@ -400,6 +396,14 @@ x_Dist_Zilla:
               version: '0.163250'
       name: PodWeaver
       version: '4.008'
+    -
+      class: Dist::Zilla::Plugin::MetaResources
+      name: MetaResources
+      version: '6.012'
+    -
+      class: Dist::Zilla::Plugin::PruneFiles
+      name: PruneFiles
+      version: '6.012'
     -
       class: Dist::Zilla::Plugin::FinderCode
       name: ':InstallModules'

Makefile.PL

@@ -145,7 +145,7 @@ my %WriteMakefileArgs = (
     "Test::More" => 0,
     "Test::Weaken" => 0
   },
-  "VERSION" => "1.7.3",
+  "VERSION" => "1.7.4",
   "test" => {
     "TESTS" => "t/*.t t/Align/*.t t/AlignIO/*.t t/Annotation/*.t t/LocalDB/*.t t/LocalDB/Index/*.t t/LocalDB/Taxonomy/*.t t/Matrix/*.t t/Matrix/IO/*.t t/Ontology/*.t t/Ontology/IO/*.t t/RemoteDB/*.t t/Root/*.t t/SearchIO/*.t t/SearchIO/Writer/*.t t/Seq/*.t t/SeqFeature/*.t t/SeqIO/*.t t/SeqTools/*.t t/Tools/*.t t/Tools/Alignment/*.t t/Tools/EMBOSS/*.t t/Tools/Phylo/*.t t/Tools/Phylo/Phylip/*.t t/Tools/Signalp/*.t t/Tools/Spidey/*.t t/Tree/*.t t/Tree/TreeIO/*.t"
   }

debian/changelog

-bioperl (1.7.3-1) UNRELEASED; urgency=medium
+bioperl (1.7.4-1) UNRELEASED; urgency=medium
 
-  * Drop broken uversionmangle from watch file
   * New upstream version
+  * Drop broken uversionmangle from watch file
   * debhelper 12
   * Standards-Version: 4.3.0
   * Build-Depends: libyaml-perl, libtest-requiresinternet-perl
-  * Skip t/Root/HTTPget.t in test suite
 
- -- Andreas Tille <tille@debian.org>  Tue, 05 Feb 2019 09:35:06 +0100
+ -- Andreas Tille <tille@debian.org>  Tue, 05 Feb 2019 21:51:10 +0100
 
 bioperl (1.7.2-3) unstable; urgency=medium
 

debian/tests/pkg-perl/smoke-skip

 t/Perl.t
 t/Species.t
-t/Root/HTTPget.t

dist.ini

 name = BioPerl
-version = 1.7.3
+version = 1.7.4
 author = See individual modules
 copyright_holder = See individual modules
 license = Perl_5
@@ -10,6 +10,9 @@ license = Perl_5
 -remove = PodWeaver
 -remove = Test::EOL
 -remove = Test::NoTabs
+;; [AutoMetaResources] is not suitable for us because our repo name
+;; is different from the distribution name.
+-remove = AutoMetaResources
 
 ;; This is a dependency for Windows only
 AutoPrereqs.skips[0] = ^Win32$
@@ -43,3 +46,17 @@ file = lib/BioPerl.pm
 [PodWeaver]
 config_plugin = @BioPerl
 finder = PodWeaver-Ready
+
+;; The distribution name is different from the repository name so we
+;; can't use [AutoMetaResources] that comes from [@BioPerl].
+[MetaResources]
+homepage = https://metacpan.org/release/BioPerl
+bugtracker.web = https://github.com/bioperl/bioperl-live/issues
+bugtracker.mailto = bioperl-l@bioperl.org
+repository.url = git://github.com/bioperl/bioperl-live.git
+repository.web = https://github.com/bioperl/bioperl-live
+repository.type = git
+
+[PruneFiles]
+filename = .travis.yml
+match = ^travis_scripts

lib/Bio/Align/AlignI.pm

@@ -93,7 +93,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::AlignI;
-$Bio::Align::AlignI::VERSION = '1.7.3';
+$Bio::Align::AlignI::VERSION = '1.7.4';
 use strict;
 
 

lib/Bio/Align/DNAStatistics.pm

@@ -335,7 +335,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::DNAStatistics;
-$Bio::Align::DNAStatistics::VERSION = '1.7.3';
+$Bio::Align::DNAStatistics::VERSION = '1.7.4';
 use vars qw(%DNAChanges @Nucleotides %NucleotideIndexes
 	    $GapChars $SeqCount $DefaultGapPenalty %DistanceMethods
             $CODONS %synchanges $synsites $Precision $GCChhars);

lib/Bio/Align/PairwiseStatistics.pm

@@ -76,7 +76,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::PairwiseStatistics;
-$Bio::Align::PairwiseStatistics::VERSION = '1.7.3';
+$Bio::Align::PairwiseStatistics::VERSION = '1.7.4';
 use vars qw($GapChars);
 use strict;
 

lib/Bio/Align/ProteinStatistics.pm

@@ -86,7 +86,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::ProteinStatistics;
-$Bio::Align::ProteinStatistics::VERSION = '1.7.3';
+$Bio::Align::ProteinStatistics::VERSION = '1.7.4';
 use vars qw(%DistanceMethods $Precision $DefaultGapPenalty);
 use strict;
 

lib/Bio/Align/StatisticsI.pm

@@ -69,7 +69,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Align::StatisticsI;
-$Bio::Align::StatisticsI::VERSION = '1.7.3';
+$Bio::Align::StatisticsI::VERSION = '1.7.4';
 use strict;
 
 

lib/Bio/Align/Utilities.pm

 package Bio::Align::Utilities;
-$Bio::Align::Utilities::VERSION = '1.7.3';
+$Bio::Align::Utilities::VERSION = '1.7.4';
 use strict;
 use warnings;
 use Carp;

lib/Bio/AlignIO.pm

@@ -274,7 +274,7 @@ methods. Internal methods are usually preceded with a _
 # 'Let the code begin...
 
 package Bio::AlignIO;
-$Bio::AlignIO::VERSION = '1.7.3';
+$Bio::AlignIO::VERSION = '1.7.4';
 use strict;
 
 use Bio::Seq;

lib/Bio/AlignIO/Handler/GenericAlignHandler.pm

 # Let the code begin...
 
 package Bio::AlignIO::Handler::GenericAlignHandler;
-$Bio::AlignIO::Handler::GenericAlignHandler::VERSION = '1.7.3';
+$Bio::AlignIO::Handler::GenericAlignHandler::VERSION = '1.7.4';
 use strict;
 use warnings;
 

lib/Bio/AlignIO/arp.pm

@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::AlignIO::arp;
-$Bio::AlignIO::arp::VERSION = '1.7.3';
+$Bio::AlignIO::arp::VERSION = '1.7.4';
 use strict;
 use base qw(Bio::AlignIO);
 

lib/Bio/AlignIO/bl2seq.pm

@@ -103,7 +103,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::AlignIO::bl2seq;
-$Bio::AlignIO::bl2seq::VERSION = '1.7.3';
+$Bio::AlignIO::bl2seq::VERSION = '1.7.4';
 use strict;
 
 use Bio::SearchIO;

lib/Bio/AlignIO/clustalw.pm

@@ -71,7 +71,7 @@ methods. Internal methods are usually preceded with a _
 # Let the code begin...
 
 package Bio::AlignIO::clustalw;
-$Bio::AlignIO::clustalw::VERSION = '1.7.3';
+$Bio::AlignIO::clustalw::VERSION = '1.7.4';
 use vars qw($LINELENGTH $CLUSTALPRINTVERSION);
 use strict;
 

lib/Bio/AlignIO/emboss.pm

@@ -77,7 +77,7 @@ Internal methods are usually preceded with a _
 
 
 package Bio::AlignIO::emboss;
-$Bio::AlignIO::emboss::VERSION = '1.7.3';
+$Bio::AlignIO::emboss::VERSION = '1.7.4';
 use vars qw($EMBOSSTitleLen $EMBOSSLineLen);
 use strict;