Set environment variables in the module t/env.pm, not in makefile

fortune9 · May 17, 2015 · 4c9900a · 4c9900a
1 parent 0fb1fd0
commit 4c9900a
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Showing 9 changed files with 122 additions and 99 deletions.
diff --git a/MANIFEST b/MANIFEST
@@ -28,6 +28,7 @@ t/pod-coverage.t
 t/pod.t
 t/tai.out
 t/test.fa
+t/env.pm
 TODO
 xt/boilerplate.t
 Makefile.PL
diff --git a/Makefile.PL b/Makefile.PL
@@ -2,6 +2,7 @@ use 5.006;
 use strict;
 use warnings;
 use ExtUtils::MakeMaker;
+use File::Spec;
 
 WriteMakefile(
     NAME             => 'Bio::CUA',
@@ -55,13 +56,21 @@ package MY; # other content MakeMaker can't produce
 sub postamble
 {
 	# The return will be directly write to makefile
-	my $postamble = <<POST;
-export expected_file = t/expected.tsv
-export seq_file = t/test.fa
-export tRNA_file = t/dmel_r5_apr2006.tRNA_copy
-POST
 
-	return $postamble;
+	# get the command to set environment variables
+#	my $os = $^O;
+#	my $set = $os =~ /MSWin/i? 'set' : 'export';
+#	my $expFile  = File::Spec->catfile('t', 'expected.tsv');
+#	my $seqFile  = File::Spec->catfile('t', 'test.fa');
+#	my $tRNAFile = File::Spec->catfile('t', 'dmel_r5_apr2006.tRNA_copy');
+#
+#	my $postamble = <<POST;
+#export expected_file = $expFile
+#export seq_file = $seqFile
+#export tRNA_file = $tRNAFile
+#POST
+
+#	return $postamble;
 }
 
 # put subroutines here
diff --git a/t/01-seqio.t b/t/01-seqio.t
@@ -3,6 +3,8 @@ use 5.006;
 use strict;
 use warnings;
 use Test::More;
+use lib 't';
+use env;
 
 # variables
 my $sep = "\t";

diff --git a/t/02-codontable.t b/t/02-codontable.t
@@ -3,6 +3,8 @@ use 5.006;
 use strict;
 use warnings;
 use Test::More;
+use lib 't';
+use env;
 
 # variables
 my $sep = "\t";

diff --git a/t/03-summarizer.t b/t/03-summarizer.t
@@ -10,6 +10,8 @@ use 5.006;
 use strict;
 use warnings;
 use Test::More;
+use lib 't';
+use env;
 
 #unless ( $ENV{RELEASE_TESTING} ) {
 #    plan( skip_all => "Author tests not required for installation" );

diff --git a/t/04-builder.t b/t/04-builder.t
@@ -4,6 +4,9 @@ use strict;
 use warnings;
 use Test::More;
 use File::Basename;
+use File::Spec;
+use lib 't';
+use env;
 
 # variables
 my $sep = "\t";
@@ -13,8 +16,8 @@ my $tRNAFile = $ENV{'tRNA_file'};
 BAIL_OUT("environment variables NOT found")
 unless($expectedFile and $seqFile and $tRNAFile);
 my $dir = dirname(__FILE__);
-my $caiFile = "$dir/cai.out";
-my $taiFile = "$dir/tai.out";
+my $caiFile = File::Spec->catfile($dir,"cai.out");
+my $taiFile = File::Spec->catfile($dir,"tai.out");
 
 my $module;
 BEGIN {

diff --git a/t/05-calculator.t b/t/05-calculator.t
@@ -4,15 +4,19 @@ use strict;
 use warnings;
 use Test::More;
 use File::Basename;
+use Bio::CUA::SeqIO;
+use File::Spec;
+use lib 't';
+use env;
 
 my $sep = "\t";
 my $seqFile = $ENV{'seq_file'};
 my $expectedFile = $ENV{'expected_file'};
 BAIL_OUT("environment variables NOT found")
 unless($expectedFile and $seqFile);
 my $dir = dirname(__FILE__);
-my $caiFile = "$dir/cai.out";
-my $taiFile = "$dir/tai.out";
+my $caiFile = File::Spec->catfile($dir, "cai.out");
+my $taiFile = File::Spec->catfile($dir, "tai.out");
 
 my $module;
 BEGIN {

diff --git a/t/cai.out b/t/cai.out
@@ -1,59 +1,59 @@
-GAG	1
-ACG	0.744186046511628
-CAC	1
-CGG	0.540540540540541
-CAA	0.380352644836272
-CTG	1
-ATC	1
-ATT	0.414225941422594
-CCC	1
-TAC	1
-GCT	0.309734513274336
 CAT	0.537688442211055
+TCC	0.845018450184502
 TTC	1
-AAA	0.398576512455516
-TCA	0.254612546125461
+ACA	0.469767441860465
 GAA	0.394927536231884
-AAC	1
-CCG	0.878306878306878
-CTC	0.386058981233244
-TAT	0.537634408602151
+ACG	0.744186046511628
+CGC	1
+GAT	0.892857142857143
+ATA	0.284518828451883
+CGT	0.371621621621622
+ATC	1
 AGT	0.450184501845018
-GGA	0.537671232876712
+CGA	0.364864864864865
+TGT	0.23
+CAG	1
+GCA	0.274336283185841
+CCC	1
+TTG	0.329758713136729
+CTG	1
+GTC	0.565610859728507
+GTA	0.194570135746606
+CTA	0.190348525469169
+TAT	0.537634408602151
+ATT	0.414225941422594
+AGA	0.243243243243243
+CTT	0.142091152815013
 AGC	1
-GTG	1
+TCG	0.712177121771218
+AAA	0.398576512455516
+CCA	0.587301587301587
 GCC	1
-AGA	0.243243243243243
+GGC	1
+AAG	1
+GAG	1
+TCA	0.254612546125461
+TGC	1
 GCG	0.47787610619469
-ACC	1
-ATA	0.284518828451883
 GTT	0.330316742081448
+GAC	1
+GCT	0.309734513274336
+CTC	0.386058981233244
+AAC	1
+CGG	0.540540540540541
+CAA	0.380352644836272
 TTA	0.0857908847184987
-TTG	0.329758713136729
-CGT	0.371621621621622
-CTA	0.190348525469169
-CTT	0.142091152815013
 GGT	0.335616438356164
-TCG	0.712177121771218
-TGT	0.23
+ACC	1
+CCG	0.878306878306878
 GGG	0.174657534246575
-GTA	0.194570135746606
-GTC	0.565610859728507
-TGC	1
 AGG	0.310810810810811
 AAT	0.604477611940298
-GGC	1
-CAG	1
-TCC	0.845018450184502
+GGA	0.537671232876712
 TTT	0.450261780104712
+ACT	0.288372093023256
+CAC	1
 TCT	0.191881918819188
-CGA	0.364864864864865
+TAC	1
+GTG	1
 CCT	0.407407407407407
-CGC	1
-GAT	0.892857142857143
-GCA	0.274336283185841
-AAG	1
-CCA	0.587301587301587
-ACA	0.469767441860465
-ACT	0.288372093023256
-GAC	1
diff --git a/t/tai.out b/t/tai.out
@@ -1,60 +1,60 @@
+TGC	0.334608030592734
+GCG	0.173996175908222
 TCA	0.095640535372849
-AAA	0.286806883365201
-AAC	0.573613766730402
-GAA	0.286806883365201
-CTC	0.17208413001912
-CCG	0.315487571701721
-AGC	0.286806883365201
-TAT	0.253824091778203
-GGA	0.286806883365201
-AGT	0.169216061185469
-GTG	0.365200764818356
+AAG	0.713193116634799
+GAG	1
+GGC	0.669216061185469
+CCA	0.239039196940727
 GCC	0.413001912045889
+AAA	0.286806883365201
+TCG	0.221797323135755
+CTT	0.239005736137667
 AGA	0.1434034416826
-GCG	0.173996175908222
+AGC	0.286806883365201
+AGG	0.189292543021033
+GGG	0.0917782026768642
+CCG	0.315487571701721
 ACC	0.309751434034417
-ACG	0.235181644359465
-GAG	1
-CAC	0.239005736137667
-CGG	0.152963671128107
+GGT	0.394837476099426
 CAA	0.191204588910134
-CTG	0.413001912045889
-ATC	0.309751434034417
-ATT	0.430210325047801
-CCC	0.240917782026769
-TAC	0.430210325047801
+TTA	0.191204588910134
+CGG	0.152963671128107
+AAC	0.573613766730402
+CTC	0.17208413001912
 GCT	0.573613766730402
-CAT	0.141013384321224
-TTC	0.382409177820268
+GAC	0.669216061185469
+GTT	0.286806883365201
 TTT	0.225621414913958
-CGA	0.478059273422562
+GGA	0.286806883365201
+AAT	0.338432122370937
+GTG	0.365200764818356
+CCT	0.334608030592734
+TAC	0.430210325047801
 TCT	0.382409177820268
+CAC	0.239005736137667
+ACT	0.430210325047801
 CGC	0.344168260038241
-CCT	0.334608030592734
-GAT	0.394837476099426
-CCA	0.239039196940727
-AAG	0.713193116634799
-GCA	0.09565965583174
+GAA	0.286806883365201
 ACA	0.286849904397706
-ACT	0.430210325047801
-GAC	0.669216061185469
-ATA	0.0956453154875717
-GTT	0.286806883365201
-TTA	0.191204588910134
+ACG	0.235181644359465
+TTC	0.382409177820268
+TCC	0.275334608030593
+CAT	0.141013384321224
+AGT	0.169216061185469
+ATC	0.309751434034417
+TGG	0.397705544933078
 CGT	0.478011472275335
-TTG	0.252390057361377
-CTT	0.239005736137667
-CTA	0.0956261950286807
-GGT	0.394837476099426
-TCG	0.221797323135755
-GTA	0.0956309751434034
-GGG	0.0917782026768642
+ATA	0.0956453154875717
+GAT	0.394837476099426
+CGA	0.478059273422562
 TGT	0.197418738049713
-TGG	0.397705544933078
+ATT	0.430210325047801
+TAT	0.253824091778203
+CTG	0.413001912045889
 GTC	0.206500956022945
-TGC	0.334608030592734
-AGG	0.189292543021033
-AAT	0.338432122370937
+GTA	0.0956309751434034
+CTA	0.0956261950286807
+TTG	0.252390057361377
+CCC	0.240917782026769
+GCA	0.09565965583174
 CAG	0.443594646271511
-TCC	0.275334608030593
-GGC	0.669216061185469