Enabling tests to make sure we never allow a warning test to succeed

modules/t/attributeAdaptor.t

@@ -17,6 +17,7 @@ use strict;
 use Bio::EnsEMBL::Test::TestUtils;
 
 use Test::More;
+use Test::Warnings;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Attribute;

modules/t/dbConnection.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Test::Exception;
 use Test::MockObject::Extends;
 use Time::HiRes qw/usleep/;

modules/t/dbEntries.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;

modules/t/exon.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;

modules/t/fullIdCaching.t

@@ -40,6 +40,7 @@ package main;
 use strict;
 use warnings;
 use Test::More;
+use Test::Warnings;
 use Test::Exception;
 use Bio::EnsEMBL::DBSQL::GeneAdaptor;
 use Bio::EnsEMBL::DBSQL::Support::FullIdCache;

modules/t/gene.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Test::Exception;
 use Data::Dumper;
 use Bio::EnsEMBL::Registry;

modules/t/gtfSerialiser.t

@@ -23,6 +23,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Test::Differences;
 use IO::String;
 

modules/t/intronSupportingEvidence.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Test::Exception;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;
@@ -61,11 +62,11 @@ my $assert_ise_vs_intron = sub {
   my $intron_from_exons = Bio::EnsEMBL::Intron->new($e1, $e2);
   
   note 'Asserting Intron tests';
-  capture_std_streams(sub {
-    my($stdout_ref, $stderr_ref) = @_;
-    Bio::EnsEMBL::Intron->new($e1, $exon_adaptor->fetch_by_dbID(162033));
-    like($$stderr_ref, qr/Exons have different slice references/, 'Intron must warn if a different reference slice is used');
-  });
+  warns_like 
+    { Bio::EnsEMBL::Intron->new($e1, $exon_adaptor->fetch_by_dbID(162033)); }
+    qr/Exons have different slice references/, 
+    'Intron must warn if a different reference slice is used';
+
   ok($intron_from_exons->is_splice_canonical(), 'Checking Intron is canonical in its splicing');
   
   note 'Starting IntronSupportingEvidence tests';

modules/t/objectLoad.t

@@ -15,6 +15,7 @@
 use strict;
 use warnings;
 use Test::More;
+use Test::Warnings;
 #use Test::Differences qw/eq_or_diff/;
 use Bio::EnsEMBL::Test::MultiTestDB;
 

modules/t/operon.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Bio::EnsEMBL::DBEntry;
 use Bio::EnsEMBL::Operon;
 use Bio::EnsEMBL::Test::MultiTestDB;

modules/t/operon_transcript.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;
 use Bio::EnsEMBL::Operon;

modules/t/proteinAlignFeatureAdaptor.t

@@ -13,6 +13,7 @@
 # limitations under the License.
 
 use Test::More;
+use Test::Warnings;
 
 use strict;
 use warnings;

modules/t/proteinFeatureAdaptor.t

@@ -17,6 +17,7 @@ use strict;
 use Bio::EnsEMBL::Test::TestUtils;
 
 use Test::More;
+use Test::Warnings;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
 

modules/t/repeatConsensusAdaptor.t

@@ -15,6 +15,7 @@
 use strict;
 
 use Test::More;
+use Test::Warnings;
 use Bio::EnsEMBL::Test::TestUtils;
 
 use Bio::EnsEMBL::Test::MultiTestDB;

modules/t/schemaPatches.t

@@ -19,6 +19,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 use Test::Differences;
 
 use Bio::EnsEMBL::ApiVersion qw/software_version/;
@@ -46,10 +47,6 @@ SKIP: {
     }
   }, $sql_dir);
 
-  if(-d catdir($project_dir, '.git')) {
-    note 'This was bad. Project is a Git project';
-  }
-
   # Get the last SQL schema
   my $last_table_sql = get_table_sql($last_release);
 
@@ -241,11 +238,10 @@ sub load_sql {
 # Get table.sql for a given Ensembl release
 sub get_table_sql {
   my $release = shift;
+  $release = $release == software_version() ? 'master' : "release/${release}";
   
-  my $git_url = 
-    "https://raw2.github.com/Ensembl/ensembl/release/${release}/sql/table.sql";
-  
-  return get_url($git_url);
+  my $url = "https://raw2.github.com/Ensembl/ensembl/${release}/sql/table.sql";
+  return get_url($url);
 }
 
 # Assume if ensembl.org is down then there is no point in continuing with the tests (1 shot)
@@ -261,19 +257,6 @@ sub test_ensembl {
 
 sub get_url {
   my ($url) = @_;
-
-  # Here we check the installation of IO::Socket::SSL,
-  # as HTTP::Tiny or LWP will need it to download from
-  # github using https
-  my $IO_Socket_SSL = 0;
-  eval {
-    require IO::Socket::SSL;
-    $IO_Socket_SSL = 1;
-  };
-
-  fail "Unable to download from $url, need IO::Socket::SSL"
-    unless $IO_Socket_SSL;
-
   my $content = eval { do_GET($url, 5, 0.5); };
   return $content if defined $content;
   diag $@;

modules/t/transcript.t

@@ -16,6 +16,7 @@ use strict;
 use warnings;
 
 use Test::More;
+use Test::Warnings;
 
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;

modules/t/translation.t

@@ -20,6 +20,7 @@ use Bio::EnsEMBL::Translation;
 use Bio::EnsEMBL::Exon;
 
 use Test::More;
+use Test::Warnings;
 
 my $loaded = 0;
 END { print "not ok 1\n" unless $loaded; }

modules/t/unmappedObject.t

@@ -16,6 +16,7 @@
 use strict;
 
 use Test::More;
+use Test::Warnings;
 use Bio::EnsEMBL::Test::MultiTestDB;
 use Bio::EnsEMBL::Test::TestUtils;
 use Bio::EnsEMBL::UnmappedObject;