Merge pull request #138 from dozy/build_deps_master_patch

update dependencies in Build.pl
wtsi-npg · Feb 25, 2016 · 5dddc41 · 5dddc41
2 parents 4ff1ece + 4fb7254
commit 5dddc41
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Showing 6 changed files with 20 additions and 27 deletions.
diff --git a/Build.PL b/Build.PL
@@ -60,8 +60,6 @@ my $builder = $class->new(
 
   'build_requires' => {
     'English'               => 0,
-  },
-  'test_requires' => {
     'Test::More'            => 0,
     'Test::Compile'         => 0,
     'Test::Cmd'             => 0,
@@ -72,7 +70,10 @@ my $builder = $class->new(
     'Carp'                  => 0,
     'Cwd'                   => 0,
     'Data::Dumper'          => 0,
+    'Fcntl'                 => 0,
+    'File::Basename'        => 0,
     'File::Slurp'           => 0,
+    'File::Spec'            => 0,
     'File::Temp'            => 0,
     'File::Which'           => 0,
     'Getopt::Long'          => 0,

diff --git a/Changes b/Changes
@@ -1,6 +1,9 @@
 CHANGES LOG
 -----------
 
+release 0.17.3
+ - update Build.PL and tests to have correct and full set of requirements
+
 release 0.17.2
  - turn off compression of AlignmentFilter output
  - changes to merge_final_output_prep to use tears to stream data into iRODS, generate extra stats,

diff --git a/t/10-vtfp-array_expansion.t b/t/10-vtfp-array_expansion.t
@@ -1,9 +1,7 @@
 use strict;
 use warnings;
 use Test::More tests => 1;
-use Test::Deep;
 use Perl6::Slurp;
-use Data::Dumper;
 use JSON;
 
 my $template = q[t/data/10-vtfp-array_expansion.json];
@@ -13,6 +11,6 @@ my $template = q[t/data/10-vtfp-array_expansion.json];
 
 my $vtfp_results = from_json(slurp "bin/vtfp.pl $template |");
 my $c = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~1A~,q~1B~,q~2A~,q~3A~,q~3B~,q~3C~,q~3D~,q~4A~,q~5A~,q~5B~], type => q~EXEC~, id => q~n1~}]};
-cmp_deeply ($vtfp_results, $c, 'first array element expansion test');
+is_deeply ($vtfp_results, $c, 'first array element expansion test');
 }
 
diff --git a/t/10-vtfp-param_ring.t b/t/10-vtfp-param_ring.t
@@ -1,9 +1,7 @@
 use strict;
 use warnings;
 use Test::More tests => 3;
-use Test::Deep;
 use Perl6::Slurp;
-use Data::Dumper;
 use JSON;
 
 my $template = q[t/data/10-vtfp-param_ring.json];
@@ -14,28 +12,25 @@ my $template = q[t/data/10-vtfp-param_ring.json];
 #  p1 - p4 will appear in the resulting cmd attribute (if they are set).
 
 my $vtfp_results = from_json(slurp "bin/vtfp.pl -keys p3 -vals break $template |");
-#print "\n\n\n", q[Dump1: ], Dumper($vtfp_results), "\n\n\n";
 my $c = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~one~,q~break~,q~break~,q~break~], type => q~EXEC~, id => q~n1~}]};
-cmp_deeply ($vtfp_results, $c, 'first parameter ring test');
+is_deeply ($vtfp_results, $c, 'first parameter ring test');
 }
 
 {
 # this is a slightly more complicated version of the previous test. It sets two parameter values in the ring, and one
 #  not involved the ring (p1)
 
 my $vtfp_results = from_json(slurp "bin/vtfp.pl -keys p1,p2,p4 -vals first,second,fourth $template |");
-#print "\n\n\n", q[Dump2: ], Dumper($vtfp_results), "\n\n\n";
 my $c = {edges => [], nodes => [ {cmd => [q~/bin/echo~,q~first~,q~second~,q~fourth~,q~fourth~], type => q~EXEC~, id => q~n1~}]};
-cmp_deeply ($vtfp_results, $c, 'second parameter ring test');
+is_deeply ($vtfp_results, $c, 'second parameter ring test');
 }
 
 {
 # another variant of the first previous test. It nullifies the first parameter, then sets the value for p5 (in the ring,
 # but not referenced directly in the node cmd) to confirm that the value propagates through the defaults to p2, p3, and p4
 
 my $vtfp_results = from_json(slurp "bin/vtfp.pl -nullkeys p1 -keys p5 -vals fifth $template |");
-#print "\n\n\n", q[Dump3: ], Dumper($vtfp_results), "\n\n\n";
 my $c = {edges => [], nodes => [ {cmd => [q~/bin/echo~,q~fifth~,q~fifth~,q~fifth~], type => q~EXEC~, id => q~n1~}]};
-cmp_deeply ($vtfp_results, $c, 'third parameter ring test');
+is_deeply ($vtfp_results, $c, 'third parameter ring test');
 }
 
diff --git a/t/10-vtfp-pv.t b/t/10-vtfp-pv.t
@@ -2,9 +2,7 @@ use strict;
 use warnings;
 use Carp;
 use Test::More tests => 3;
-use Test::Deep;
 use Perl6::Slurp;
-use Data::Dumper;
 use JSON;
 use File::Temp qw(tempdir);
 
@@ -20,13 +18,13 @@ subtest 'pv0' => sub {
 	system(qq[bin/vtfp.pl -verbosity_level 0 -o $processed_template -export_param_vals $pv_file $template]) == 0 or croak q[Failed to export params];
 	my $pv_data = from_json(slurp $pv_file);
 	my $expected = {assign_local => {} ,param_store => [], assign => []};
-	cmp_deeply ($pv_data, $expected, '(ts1) exported parameter values as expected');
+	is_deeply ($pv_data, $expected, '(ts1) exported parameter values as expected');
 
 	my $vtfp_results = from_json(slurp "bin/vtfp.pl -verbosity_level 0 -param_vals $pv_file $template |");
 	my $c = from_json(slurp $processed_template);
 	$expected = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~The~,q~funeral~,q~ends~,q~with~,q~a~,q~mournful~,q~fireworks~,q~display~], type => q~EXEC~, id => q~n1~}]};
-	cmp_deeply ($vtfp_results, $c, '(ts1) json config generated using pv file matches original generated config');
-	cmp_deeply ($vtfp_results, $expected, '(ts1) json config generated using pv file as expected');
+	is_deeply ($vtfp_results, $c, '(ts1) json config generated using pv file matches original generated config');
+	is_deeply ($vtfp_results, $expected, '(ts1) json config generated using pv file as expected');
 };
 
 # export parameter values from a template, overriding default for parameter "subject" from the command-line. Reimport the parameter values.
@@ -36,13 +34,13 @@ subtest 'pv1' => sub {
 	system(qq[bin/vtfp.pl -verbosity_level 0 -o $processed_template -export_param_vals $pv_file -keys subject,adj -vals party,deafening $template]) == 0 or croak q[Failed to export params];
 	my $pv_data = from_json(slurp $pv_file);
 	my $expected = {assign_local => {} ,param_store => [], assign => [ {subject => q~party~, adj =>q~deafening~, }]};
-	cmp_deeply ($pv_data, $expected, '(ts2) exported parameter values as expected');
+	is_deeply ($pv_data, $expected, '(ts2) exported parameter values as expected');
 
 	my $vtfp_results = from_json(slurp "bin/vtfp.pl -verbosity_level 0 -param_vals $pv_file $template |");
 	my $c = from_json(slurp $processed_template);
 	$expected = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~The~,q~party~,q~ends~,q~with~,q~a~,q~deafening~,q~fireworks~,q~display~], type => q~EXEC~, id => q~n1~}]};
-	cmp_deeply ($vtfp_results, $c, '(ts2) json config generated using pv file matches original generated config');
-	cmp_deeply ($vtfp_results, $expected, '(ts2) json config generated using pv file as expected');
+	is_deeply ($vtfp_results, $c, '(ts2) json config generated using pv file matches original generated config');
+	is_deeply ($vtfp_results, $expected, '(ts2) json config generated using pv file as expected');
 };
 
 # export parameter values from a template, overriding defaults for parameters "subject" and "prepobj" from the command-line. Reimport the parameter values.
@@ -52,13 +50,13 @@ subtest 'pv2' => sub {
 	system(qq[bin/vtfp.pl -verbosity_level 0 -o $processed_template -export_param_vals $pv_file -keys subject,prepobj -vals world,whimper -nullkeys adj $template]) == 0 or croak q[Failed to export params];
 	my $pv_data = from_json(slurp $pv_file);
 	my $expected = {assign_local => {} ,param_store => [], assign => [ {subject => q~world~, prepobj => q~whimper~, adj => undef}]};
-	cmp_deeply ($pv_data, $expected, '(ts3) exported parameter values as expected');
+	is_deeply ($pv_data, $expected, '(ts3) exported parameter values as expected');
 
 	my $vtfp_results = from_json(slurp "bin/vtfp.pl -verbosity_level 0 -param_vals $pv_file $template |");
 	my $c = from_json(slurp $processed_template);
 	$expected = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~The~,q~world~,q~ends~,q~with~,q~a~,q~whimper~], type => q~EXEC~, id => q~n1~}]};
-	cmp_deeply ($vtfp_results, $c, '(ts4) json config generated using pv file matches original generated config');
-	cmp_deeply ($vtfp_results, $expected, '(ts4) json config generated using pv file as expected');
+	is_deeply ($vtfp_results, $c, '(ts4) json config generated using pv file matches original generated config');
+	is_deeply ($vtfp_results, $expected, '(ts4) json config generated using pv file as expected');
 };
 
 1;
diff --git a/t/10-vtfp-subst_directive.t b/t/10-vtfp-subst_directive.t
@@ -1,9 +1,7 @@
 use strict;
 use warnings;
 use Test::More tests => 1;
-use Test::Deep;
 use Perl6::Slurp;
-use Data::Dumper;
 use JSON;
 
 my $template = q[t/data/10-vtfp-array_expansion.json];
@@ -13,6 +11,6 @@ my $template = q[t/data/10-vtfp-array_expansion.json];
 
 my $vtfp_results = from_json(slurp "bin/vtfp.pl $template |");
 my $c = {edges=> [], nodes => [ {cmd => [q~/bin/echo~,q~1A~,q~1B~,q~2A~,q~3A~,q~3B~,q~3C~,q~3D~,q~4A~,q~5A~,q~5B~], type => q~EXEC~, id => q~n1~}]};
-cmp_deeply ($vtfp_results, $c, 'first array element expansion test');
+is_deeply ($vtfp_results, $c, 'first array element expansion test');
 }