[Bioperl-l] New testing base: BioperlTest.pm

Sendu Bala bix at sendu.me.uk
Wed Jun 20 15:38:20 UTC 2007

In considering updating all the test scripts to take advantage of the 
new network option, and/or reimplementing them in Test::More, I thought 
now would be a good time to standardize all the test scripts and reduce 
the possibility of having to alter them all in the future if something 

For example we could decide on an alternate way of choosing to run 
network tests, or a new way of deciding to output debug information. 
There are also some inconsistencies in the messages produced by tests 
skipping all, and even an unfortunate mistake that has been copy/pasted 
through a lot of test scripts.

My solution is t/lib/BioperlTest.pm (documented with perldoc)

We go from this:

use strict;
our $DEBUG;

   eval { require Test::More; };
   if( $@ ) {
     use lib 't/lib';
   use Test::More; # the mistake!
   use Module::Build;
   my $build = Module::Build->current();
   my $do_network_tests = $build->notes('network');

   eval {
     require IO::String;
     require LWP;
     require LWP::UserAgent;
   if ($@) {
     plan skip_all => 'IO::String or LWP or LWP::UserAgentnot installed.
This means Bio::Tools::Run::RemoteBlast is not usable. Skipping tests';
   elsif (!$do_network_tests) {
     plan skip_all => 'Network tests have not been requested, skipping
   else {
     plan tests => 21;


my $obj = Bio::Object->new(-verbose => $DEBUG);

To this:

use strict;

   use lib 't/lib';
   use BioperlTest;

   test_begin(-requires_modules => [qw(IO::String LWP LWP::UserAgent)],
              -requires_networking => 1,
              -tests => 21);


my $obj = Bio::Object->new(-verbose => test_debug());

Can anyone identify problems with this approach? Is the interface 
presented by BioperlTest flexible enough that any changes would only be 
additions for new functionality (and therefore all test scripts wouldn't 
need to be altered)? Is BioperlTest missing anything you'd like?

Are there any objections to me updating all tests in this manner? For an 
example, see t/RemoteBlast.t


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