Merge branch 'feature/perlversioninvariance': Make core API compatible with Perl 5.26

.travis.yml

 language: perl
 
+os:
+  - linux
+
+
 perl:
   - '5.14'
-  - '5.12'
-  - '5.10'
+  - '5.26'
 
 env:
   matrix:
@@ -24,7 +27,7 @@ before_install:
   - git clone --branch master --depth 1 https://github.com/Ensembl/ensembl-test.git
   - git clone --branch master --depth 1 https://github.com/Ensembl/ensembl-variation.git
   - git clone --branch master --depth 1 https://github.com/Ensembl/ensembl-compara.git
-  - git clone -b bioperl-release-1-6-1 --depth 1 https://github.com/bioperl/bioperl-live.git
+  - git clone -b release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
 
 install:
   - cpanm -v --installdeps --notest .
@@ -43,16 +46,14 @@ jobs:
 
 matrix:
   exclude:
-  - perl: '5.10'
-    env: COVERALLS=false DB=mysql
-  - perl: '5.12'
-    env: COVERALLS=false DB=sqlite
-  - perl: '5.12'
-    env: COVERALLS=true  DB=mysql
   - perl: '5.14'
-    env: COVERALLS=false DB=sqlite
+    env: COVERALLS=false DB=mysql
   - perl: '5.14'
     env: COVERALLS=true  DB=mysql
+  - perl: '5.26'
+    env: COVERALLS=false DB=sqlite
+  - perl: '5.26'
+    env: COVERALLS=false DB=mysql
 
 notifications:
   email:

cpanfile

@@ -8,6 +8,7 @@ test_requires 'Test::Warnings';
 test_requires 'Test::Differences';
 test_requires 'Test::Exception';
 test_requires 'Test::MockObject';
+test_requires 'Test::Deep';
 test_requires 'Test::More';
 test_requires 'Devel::Peek';
 test_requires 'Devel::Cycle';

misc-scripts/cloud/EnsCloud/Cmd/Command/SpeciesToVolumes.pm

@@ -287,7 +287,7 @@ sub make_image {
     foreach my $i (@$existing_images) {
         if ( $i->{description} eq $tag ) {
             $self->log->warn( "Image " . $i->{image_id} . " already exists for " . $tag );
-            return undef;
+            return;
         }
     }
     my $create_image = $self->ec2->register_image(
@@ -573,7 +573,7 @@ sub build_queue {
         my ( $db_species, $db_release, $db_type );
         if ( ( $db_species, $db_type, $db_release ) = $db_name =~ /^([a-z]+_[a-z]+)_([a-z]+)_(\d+)_\w+$/ ) {
             next unless $db_species =~ /$species_filter/;
-            next unless $db_type ~~ @$wanted_dbs;
+            next unless grep {$_ eq $db_type} @$wanted_dbs;
             push @{ $db_hash->{$db_species} }, [ $db_size, $db_path, $db_type, $db_release, $db_name ];
         }
         elsif ( $db_name =~ /ensembl_compara_(\d+)/ && 'compara' ~~ @$wanted_dbs ) {

modules/t/gene.t

@@ -974,6 +974,15 @@ $multi->restore;
 
 SKIP: {
   skip 'No registry support for SQLite yet', 1 if $db->dbc->driver() eq 'SQLite';
+  
+  # Time to get dirty: ENSCORESW-2595
+  # With specific compiled Perls, run under specific circumstances, disconnect_if_idle() gives rise
+  # to a seg fault. This is out of the scope of Perl, and not obviously the fault disconnect_if_idle()
+  # For the purposes of unit tests only, we can disable that behaviour by short-circuiting disconnect_if_idle()
+  # Unfortunately the problem manifests through TravisCI and the Perl they deploy, so we are forced to
+  # implement a workaround for the sake of testing harmony.
+  no warnings 'redefine';
+  local *Bio::EnsEMBL::DBSQL::DBConnection::disconnect_if_idle = sub { return 1};
 
   #test the get_species_and_object_type method from the Registry
   my $registry = 'Bio::EnsEMBL::Registry';

modules/t/subSliceFeature.t

@@ -17,6 +17,7 @@ use strict;
 use warnings;
 use Test::More;
 use Test::Warnings;
+use Test::Deep;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::SubSlicedFeature;
 
@@ -56,8 +57,13 @@ foreach (@$exon_list) {
     note($_->start);
     note($_->end);
 }
+
 ok(scalar(@$exon_list) == 4, "Correct Exons for subsliced Gene");
-is($exon_list->[0]->stable_id,'ENSE00001048819', "Correct Exon returned for subsliced Gene");
+
+cmp_bag([map { $_->stable_id} @$exon_list] ,['ENSE00000661210',
+          'ENSE00001048819',
+          'ENSE00000859928',
+          'ENSE00000859927'],'Correct Exon IDs returned');
 
 $fake_gene = Bio::EnsEMBL::SubSlicedFeature->new(-feature => $gene, -start => 1, -end => 2);
 $transcript_list = $fake_gene->get_all_Transcripts;