[Bioperl-l] test suite upgrade

[Jason Stajich]

A Smarter test suite and some code corrections to make perl 5.00404 happy
have been checked in.  

Please checkout the live version and give it a try.  

Notes: 

- This involved copying Test.pm version 1.15 I believe, removing the line
  that required Test::Harness of a certain version (which won't install on
  5.00404) and doing some fun use lib stuff in the BEGIN block of t test.  
  Unfortunately my first hope of just pushing the 't' dir on the @INC
  stack did not work under 5.00404 - it was not being recognized.  I'm not
  sure if that was not available in earlier versions of perl or what.  At
  ant rate it was solved by our good friend eval...

BEGIN {     
    # to handle systems with no installed Test module
    # we include the t dir (where a copy of Test.pm is located)
    # as a fallback
    eval { require Test; };
    if( $@ ) {
        use lib 't';
    }
    use Test;
    plan tests => 35 }

All new test modules should follow this format or they won't be able to
use Test.pm on platforms with Test.pm not installed.  

- The LiveSeq test is still not working, but that's probably because I
  haven't really dug much to find out why it is failing.

- I get strange errors (the ever cryptic 'dubious' message) in 5.00404
  when exit is called in the BEGIN block which is necessary for tests
  where all the necessary modules are not installed on the system.

- Things to deal with platform compatibility have not been addressed
  (alarm still called,index.t).  I tried to work on the Index.t problem
  but didn't get the general solution to work (because we can't depend on
  File::Spec to be installed,grrr) so I will have to probably rely on the
  suggested fix by Shailesh.

-Jason

Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/