fix deprecated code

cjfields · May 30, 2015 · 2be83c3 · 2be83c3
1 parent 995168b
commit 2be83c3
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Showing 7 changed files with 32 additions and 32 deletions.
diff --git a/t/PrimarySeq.t b/t/PrimarySeq.t
@@ -4,7 +4,7 @@ use Test;
 
 use lib './lib';
 
-eval_lives_ok 'use Bio::PrimarySeq', 'Can use Bio::PrimarySeq';
+eval-lives-ok 'use Bio::PrimarySeq', 'Can use Bio::PrimarySeq';
 
 use Bio::PrimarySeq;
 

diff --git a/t/Range.t b/t/Range.t
@@ -70,7 +70,7 @@ for @spans -> $s {
 }
 
 ok(@ranges[0] ~~ Bio::Role::Range, 'Range role');
-isa_ok(@ranges[0], MyRange, 'MyRange class');
+isa-ok(@ranges[0], MyRange, 'MyRange class');
 ok(!@ranges[0].^isa(Bio::Role::Range), 'Role consumed by class');
 is(@ranges[0].start, 1);
 is(@ranges[0].end, 100);

diff --git a/t/Role/IO.t b/t/Role/IO.t
@@ -19,7 +19,7 @@ my $in = MyIO.new( file => $*SPEC.catfile('t','data','test.fasta'), :r);
 ok($in ~~ Bio::Role::IO, 'does Bio::Role::IO');
 is($in.file, $*SPEC.catfile('t','data','test.fasta')); # De-UNIX this
 
-isa_ok($in.fh, 'IO::Handle');
+isa-ok($in.fh, 'IO::Handle');
 
 todo('Mode NYI', 1);
 is($in.mode, 'r');

diff --git a/t/Role/Temp.t b/t/Role/Temp.t
@@ -27,15 +27,15 @@ my ($tfh,$tfile);
 {
     ok my $obj = MyTemp.new();
 
-    isa_ok $obj, 'MyTemp';
+    isa-ok $obj, 'MyTemp';
 
     ok $obj ~~ Bio::Role::Temp;
 
     my $TEST_STRING = "Bioperl rocks!\n";
     ($tfile, $tfh) = $obj.tmpfile();
 
     # check write
-    isa_ok $tfh, 'IO::Handle';
+    isa-ok $tfh, 'IO::Handle';
     $tfh.print($TEST_STRING);
     $tfh.close;
 
@@ -76,7 +76,7 @@ my ($tfh,$tfile);
 {
     my $obj = MyTemp.new();
     ($tfile, $tfh) = $obj.tmpfile(:!unlink);
-    isa_ok $tfh, 'IO::Handle';
+    isa-ok $tfh, 'IO::Handle';
     $tfh.close;
     ok $tfile.IO ~~ :e, ':e' ;
     $obj = Nil; 
@@ -91,14 +91,14 @@ my ($tfh,$tfile);
 
     # check suffix is applied
     my ($tfile, $tfh) = $obj.tmpfile(:suffix<.bioperl>);
-    isa_ok $tfh, 'IO::Handle';
+    isa-ok $tfh, 'IO::Handle';
     #like $tfh, rx/\.bioperl$/, 'tempfile suffix';
     ok close $tfh;
     @cleaned.push: $tfile;
 
     ## check single return value mode of File::Temp
     #my $fh2 = $obj->tempfile;
-    #isa_ok $fh2, 'GLOB';
+    #isa-ok $fh2, 'GLOB';
     #ok $fh2, 'tempfile() in scalar context';
     #ok close $fh2;
     #}

diff --git a/t/Root.t b/t/Root.t
@@ -12,16 +12,16 @@ use Bio::Root::Root;
 my $s = Bio::Root::Root.new();
 
 ok($s.isa(Bio::Root::Root));
-eval_dies_ok('$s.throw("foo")','throw');
-lives_ok {$s.warn("foo")},'warn() does not die';
+eval-dies-ok('$s.throw("foo")','throw');
+lives-ok {$s.warn("foo")},'warn() does not die';
 $s.warn("foo");
-lives_ok {$s.debug("foo"),'debug() does not die'};
+lives-ok {$s.debug("foo"),'debug() does not die'};
 
 # test strictness
 $s.strict = 2;   # convert warn to throw
-eval_dies_ok('$s.throw("foo")');
-eval_dies_ok('$s.warn("foo")');
-lives_ok {$s.debug("foo")};
+eval-dies-ok('$s.throw("foo")');
+eval-dies-ok('$s.warn("foo")');
+lives-ok {$s.debug("foo")};
 
 # check inheritance
 class Foo is Bio::Root::Root {};
@@ -30,12 +30,12 @@ my $n = Foo.new();
 
 ok($n.isa(Foo));
 ok($n.isa(Bio::Root::Root));
-eval_dies_ok('$n.throw("foo")');
-lives_ok {$n.warn("foo")};
-lives_ok {$n.debug("foo")};
+eval-dies-ok('$n.throw("foo")');
+lives-ok {$n.warn("foo")};
+lives-ok {$n.debug("foo")};
 $s.strict = 2;   # convert warn to throw
-eval_dies_ok('$n.throw("foo")');
-eval_dies_ok('$n.warn("foo")');
-lives_ok {$n.debug("foo")};
+eval-dies-ok('$n.throw("foo")');
+eval-dies-ok('$n.warn("foo")');
+lives-ok {$n.debug("foo")};
 
 done();
diff --git a/t/SeqIO.t b/t/SeqIO.t
@@ -12,7 +12,7 @@ my $in = Bio::SeqIO.new(format  => 'fasta');
 
 is($in.format, 'fasta', 'format');
 
-dies_ok { $in.format = 'fastq' }, 'readonly';
+dies-ok { $in.format = 'fastq' }, 'readonly';
 
 # no version or variant (these are optional)
 ok($in.format-version ~~ Any, 'version');
@@ -25,8 +25,8 @@ $in = Bio::SeqIO.new(format  => 'fasta',
 
 is($in.format, 'fasta', 'format');
 is($in.format-version, 1.0, 'version');
-dies_ok { $in.format-version = 2.0 }, 'readonly';
-dies_ok { $in.format-variant = 'new'}, 'readonly';
+dies-ok { $in.format-version = 2.0 }, 'readonly';
+dies-ok { $in.format-variant = 'new'}, 'readonly';
 
 is($in.format-variant, 'old', 'variant');
 
@@ -38,6 +38,6 @@ is($in.format, 'fasta', 'format');
 is($in.format-version, 1.0, 'version');
 is($in.format-variant, 'old', 'variant');
 
-dies_ok {Bio::SeqIO.new(format  => "foo")}, 'dies with an unknown format';
+dies-ok {Bio::SeqIO.new(format  => "foo")}, 'dies with an unknown format';
 
 done();
diff --git a/t/Tools/IUPAC.t b/t/Tools/IUPAC.t
@@ -4,8 +4,8 @@ use lib './lib';
 
 use Test;
 plan 10;
-eval_lives_ok 'use Bio::Tools::IUPAC', 'Can use Bio::Tools::IUPAC';
-eval_lives_ok 'use Bio::PrimarySeq', 'Can use Bio::PrimarySeq';
+eval-lives-ok 'use Bio::Tools::IUPAC', 'Can use Bio::Tools::IUPAC';
+eval-lives-ok 'use Bio::PrimarySeq', 'Can use Bio::PrimarySeq';
 
 use Bio::Tools::IUPAC;
 use Bio::PrimarySeq; 
@@ -88,13 +88,13 @@ my $stream  = Bio::Tools::IUPAC.new(seq => $ambiseq);
 is $stream.count(), 4;
 
 #this is pretty useless but still test it anyway. Probably get rid of this api later
-is_deeply($stream.iupac_iub(),%IUB,'Can access IUB hash from method call');
-is_deeply($stream.iupac_rev_iub(),%REV_IUB,'Can access REV_IUB hash from method call');
-is_deeply($stream.iupac_iup(),%IUP,'Can access IUP hash from method call');
+is-deeply($stream.iupac_iub(),%IUB,'Can access IUB hash from method call');
+is-deeply($stream.iupac_rev_iub(),%REV_IUB,'Can access REV_IUB hash from method call');
+is-deeply($stream.iupac_iup(),%IUP,'Can access IUP hash from method call');
 
-is_deeply(%Bio::Tools::IUPAC::IUB,%IUB,'Can access IUB hash as a class variable');
-is_deeply(%Bio::Tools::IUPAC::REV_IUB,%REV_IUB,'Can access REV_IUB hash as a class variable');
-is_deeply(%Bio::Tools::IUPAC::IUP,%IUP,'Can access IUP hash as a class variable');
+is-deeply(%Bio::Tools::IUPAC::IUB,%IUB,'Can access IUB hash as a class variable');
+is-deeply(%Bio::Tools::IUPAC::REV_IUB,%REV_IUB,'Can access REV_IUB hash as a class variable');
+is-deeply(%Bio::Tools::IUPAC::IUP,%IUP,'Can access IUP hash as a class variable');
 
 my $b = 1; 
 while (my $uniqueseq = $stream.next_seq()) {