From: tla <tla@mit.edu>
Date: Tue, 10 Jan 2012 12:15:52 +0000 (+0100)
Subject: remove path hackery for pars exe
X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=commitdiff_plain;h=457b1620fd58822d243cb43d538fdf6f228585c8;p=scpubgit%2Fstemmatology.git

remove path hackery for pars exe
---

diff --git a/lib/Text/Tradition/Stemma.pm b/lib/Text/Tradition/Stemma.pm
index 9a53812..70fd634 100644
--- a/lib/Text/Tradition/Stemma.pm
+++ b/lib/Text/Tradition/Stemma.pm
@@ -4,6 +4,7 @@ use Bio::Phylo::IO;
 use Encode qw( decode_utf8 );
 use File::chdir;
 use File::Temp;
+use File::Which;
 use Graph;
 use Graph::Reader::Dot;
 use IPC::Run qw/ run binary /;
@@ -303,13 +304,9 @@ sub run_phylip_pars {
     close CMD;
 
     # And then we run the program.
-    ### HACKY HACKY
-    my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe';
-    my $program = "pars";
-    if( $^O eq 'darwin' ) {
-        $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program";
-    } else {
-        $program = "$PHYLIP_PATH/$program";
+    my $program = File::Which::which( 'pars' );
+    unless( -x $program ) {
+	return( undef, "Phylip pars not found in path" );
     }
 
     {
diff --git a/t/stemma.t b/t/stemma.t
index 95b25e3..7f3bc7d 100644
--- a/t/stemma.t
+++ b/t/stemma.t
@@ -1,6 +1,7 @@
 #!/usr/bin/perl
 
 use strict; use warnings;
+use File::Which;
 use Test::More;
 use lib 'lib';
 use Text::Tradition;
@@ -47,16 +48,19 @@ foreach my $i ( 0 .. $#wits ) {
 }
 
 # Test that pars runs
-my( $status, $tree ) = $stemma->run_phylip_pars();
-ok( $status, "pars ran successfully" );
-print STDERR "Error was $tree\n" unless $status;
-
-# Test that we get a tree
-is( scalar @{$stemma->distance_trees}, 1, "Got a single tree" );
-# Test that the tree has all our witnesses
-$tree = $stemma->distance_trees->[0];
-my @leaves = grep { $tree->degree( $_ ) == 1 } $tree->vertices;
-is( scalar @leaves, 3, "All witnesses in the tree" );
+SKIP: {
+    skip "pars not installed", 3 unless File::Which::which('pars');
+    my( $status, $tree ) = $stemma->run_phylip_pars();
+    ok( $status, "pars ran successfully" );
+    print STDERR "Error was $tree\n" unless $status;
+    
+    # Test that we get a tree
+    is( scalar @{$stemma->distance_trees}, 1, "Got a single tree" );
+    # Test that the tree has all our witnesses
+    $tree = $stemma->distance_trees->[0];
+    my @leaves = grep { $tree->degree( $_ ) == 1 } $tree->vertices;
+    is( scalar @leaves, 3, "All witnesses in the tree" );
+}
 
 # Test our dot output
 my $display = $stemma->as_dot();
@@ -67,4 +71,4 @@ my $editable = $stemma->editable();
 ok( $editable =~ /digraph/, "Got a dot edit graph" );
 ok( $editable =~ /hypothetical/, "Graph contains an edit class" );
 
-done_testing();
\ No newline at end of file
+done_testing();