Refactor Bio::Species tests into modular files

t/AnnotationI.t

@@ -0,0 +1,30 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Test::More tests => 4;
+
+BEGIN {
+    use_ok('Bio::AnnotationI');
+}
+
+{
+    package MyAnnotation;
+    use base qw(Bio::AnnotationI);
+
+    sub new {
+        my $class = shift;
+        return bless {}, $class;
+    }
+
+    sub tagname  { return "mock_tag"; }
+    sub as_text  { return "Mock annotation as text"; }
+    sub hash_tree { return {}; }
+}
+
+my $a = MyAnnotation->new();
+
+isa_ok($a, 'Bio::AnnotationI');
+is($a->tagname, 'mock_tag', 'tagname returns expected value');
+is($a->as_text, 'Mock annotation as text', 'as_text returns expected value');
+

t/SeqI.t

@@ -0,0 +1,31 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Test::More tests => 4;
+
+BEGIN {
+    use_ok('Bio::SeqI');
+}
+
+{
+    package MySeq;
+    use base qw(Bio::SeqI);
+
+    sub new {
+        my $class = shift;
+        return bless {}, $class;
+    }
+
+    sub display_id { return "test_id"; }
+    sub seq        { return "ATGC"; }
+    sub desc       { return "Test sequence"; }
+    sub alphabet   { return "dna"; }
+}
+
+my $seq = MySeq->new();
+
+isa_ok($seq, 'Bio::SeqI');
+is($seq->display_id, 'test_id', 'display_id returns correct value');
+is($seq->seq, 'ATGC', 'seq returns correct sequence');
+

t/Species/basic.t

@@ -0,0 +1,25 @@
+#!/usr/bin/env perl
+use strict;
+use warnings;
+use Test::More tests => 8;
+
+use_ok('Bio::Species');
+
+my $sps = Bio::Species->new();
+$sps->classification(qw(sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota));
+
+is $sps->binomial, 'Homo sapiens';
+
+$sps->sub_species('sapiensis');
+is $sps->binomial, 'Homo sapiens';
+is $sps->binomial('FULL'), 'Homo sapiens sapiensis';
+
+is $sps->sub_species, 'sapiensis';
+
+my $species = Bio::Species->new(
+    -classification => [qw(sapiens Homo Hominidae Catarrhini Primates Eutheria Mammalia Vertebrata Chordata Metazoa Eukaryota)],
+    -common_name    => 'human'
+);
+is $species->binomial, 'Homo sapiens';
+is $species->genus, 'Homo';
+

t/Species/memory.t

@@ -0,0 +1,57 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Bio::Root::Test;
+use Bio::Species;
+
+eval { require Test::Memory::Cycle; 1; };
+my $CYCLE = $@ ? 0 : 1;
+eval { require Test::Weaken; 1; };
+my $WEAKEN = $@ ? 0 : 1;
+
+test_begin(-tests => 6);
+
+SKIP: {
+    skip("Test::Memory::Cycle not installed", 3) if !$CYCLE;
+
+    # Intentional circular ref (should leak)
+    my ($a, $b); $a = \$b; $b = \$a;
+    ok(Test::Memory::Cycle::memory_cycle_exists($a), "Intentional circular reference leaks");
+
+    # Bio::Species should not leak
+    my $species = Bio::Species->new(
+        -classification => [qw(sapiens Homo)],
+        -common_name    => 'human'
+    );
+    ok(!Test::Memory::Cycle::memory_cycle_exists($species), "Bio::Species does not leak");
+
+    # GitHub issue #81 regression
+    ok(!Test::Memory::Cycle::memory_cycle_exists(Bio::Species->new(-classification => ['A'])), "Regression test for #81");
+}
+
+SKIP: {
+    skip("Test::Weaken not installed", 3) if !$WEAKEN;
+
+    # Deliberate leak
+    ok(Test::Weaken::leaks({
+        constructor => sub { my ($a, $b); $a = \$b; $b = \$a; }
+    }), "Deliberate circular ref detected by Test::Weaken");
+
+    # Bio::Species should not leak
+    ok(!Test::Weaken::leaks({
+        constructor => sub {
+            Bio::Species->new(
+                -classification => [qw(sapiens Homo)],
+                -common_name    => 'human'
+            )
+        }
+    }), "Bio::Species passes Test::Weaken");
+
+    # Regression test for #81
+    ok(!Test::Weaken::leaks({
+        constructor => sub { Bio::Species->new(-classification => ['A']) }
+    }), "Regression check for #81 via Test::Weaken");
+}
+

t/Species/taxonomy_db.t

@@ -0,0 +1,25 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use Bio::Root::Test;
+use Bio::Species;
+use Bio::DB::Taxonomy;
+
+test_begin(-tests => 5,
+           -requires_module     => 'Bio::DB::Taxonomy::entrez',
+           -requires_networking => 1);
+
+my $species = Bio::Species->new(-id => 51351);
+my $taxdb   = Bio::DB::Taxonomy->new(-source => 'entrez');
+
+eval { $species->db_handle($taxdb); };
+skip("Unable to connect to Entrez database; no network or server busy?", 5) if $@;
+
+is $species->binomial, 'Brassica rapa subsp.';
+is $species->binomial('FULL'), 'Brassica rapa subsp. pekinensis';
+is $species->genus, 'Brassica';
+is $species->species, 'rapa subsp.';
+is $species->sub_species, 'pekinensis';
+