Changes

 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@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

+libbio-db-refseq-perl (1.7.4-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe@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

 name = Bio-DB-RefSeq
-version = 1.7.3
+version = 1.7.4
 author = Heikki Lehvaslaiho <heikki@bioperl.org>
 copyright_holder = Heikki Lehvaslaiho <heikki@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

-# -*-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();