[Bioperl-guts-l] bioperl-live/maintenance modules.pl,1.19,1.20

[Heikki Lehvaslaiho]

Update of /home/repository/bioperl/bioperl-live/maintenance
In directory pub.open-bio.org:/tmp/cvs-serv13765

Modified Files:
	modules.pl 
Log Message:
improve untested() to take into account syntax to import methods, e.g.
    use Bio::Align::Utilities qw(aa_to_dna_aln bootstrap_replicates);


Index: modules.pl
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/maintenance/modules.pl,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** modules.pl	15 Dec 2005 21:14:35 -0000	1.19
--- modules.pl	16 Jan 2006 17:02:38 -0000	1.20
***************
*** 377,388 ****
  sub untested {
      foreach (`find ../t -name "*.t" -print | xargs grep -hs "[ur][se][eq]"`) {
- #        print "1-$_\n" if /OntologyT/; 
- #        s/^\s*//;
          s/.*use +//;
          s/.*require +//;
          next unless /^Bio/;
          s/[\W;]+$//;
          my $name = $_;
! #        print "2-$name\n" if /OntologyT/; 
          next unless $MODULES{$_};
          $MODULES{$_}->tested(1) 
--- 377,388 ----
  sub untested {
      foreach (`find ../t -name "*.t" -print | xargs grep -hs "[ur][se][eq]"`) {
          s/.*use +//;
          s/.*require +//;
          next unless /^Bio/;
+ 
          s/[\W;]+$//;
+         s/([\w:]+).*/$1/;
          my $name = $_;
! 
          next unless $MODULES{$_};
          $MODULES{$_}->tested(1) 
***************
*** 399,412 ****
          _used_and_super($name);
  
- #        foreach ($MODULES{$name}->each_superclass) {
- ##            print $MODULES{$name}->name, "\n";
- #            $MODULES{$name}->tested(1)
- #                unless defined $MODULES{$name} or $MODULES{$name}->tested;
- #        }
- #        foreach ($MODULES{$name}->each_used_class) {
- #            $MODULES{$name}->tested(1)
- #                unless defined $MODULES{$name} and $MODULES{$name}->tested;
- #        }
- 
      }
  
--- 399,402 ----
***************
*** 415,419 ****
          # skip some name spaces 
          next  if /^Bio::Search/; # Bio::Search and Bio::SearchIO are extensively tested 
!                                 # but classes are used by attribute naming 
  
          print "$_\n" if
--- 405,409 ----
          # skip some name spaces 
          next  if /^Bio::Search/; # Bio::Search and Bio::SearchIO are extensively tested 
!                                  # but classes are used by attribute naming 
  
          print "$_\n" if