[Bioperl-l] Happy Christmasl; More testing please!

[Ewan Birney]

New tar file is up:

  ftp.bioperl.org - pub/birney/bioperl-1.2-alpha-2.tar.gz

OR

  http://bioperl.org/ftp/birney/




Peter has updated bptutorial.pl, Jason and I have fixed some more things,
Lincoln has been tweaking Bio::Graphics. RemoteBlast is now back in the
core, and Bio::Perl has some easy routes to using it, meaning the
following 3 line script will work:


use Bio::Perl;

$result =
blast_sequence('FEKWGNIVDVVVMKDPRTKRSRGFGFITYSHSSMIDEAQKSRPHKIDGRV');

write_blast(">result.blast",$result);


(cool huh!)



This abuses NCBI Blast servers, so we probably need to put a delay loop in
remote blast to make sure abuse is limited.


Open question about whether StandAloneBlast should also migrate back - i
think yes, because then we give people a good way to get standalone blast
to work and stop abusing NCBI. (one day I should write a service that
works against EBI to abuse EBI... Hmmmm)


Tests:

I run tests regularly on:

   uname   Perl Version

   Darwin   5.6.0
   SunOS    5.5 patch level 3
   OSF1     5.6.1


All tests pass for me. SearchIO is still spewing warnings liberally which
someone will get to before it is released.



For other OS's and other Perl versions (notice I don't test against Perl
5.8) i don't test.


PLEASE PLEASE PLEASE ---- TEST

  - download bioperl-1.2-alpha-2.tar.gz
  - simply run perl Makefile.PL
  - make test

  - NO NEED to download all the supporting modules - just the "out of the
box" Bioperl tests will be fine. i don't care about "side" modules which
require half of CPAN installed before they work (eg, the XML set). I worry
about the "standard" Bioperl set.

  - report back to the list the uname (type uname on the command line) and
the perl -v commands, and either
    (a) all tests pass (don't worry about skipping tests or the warnings
on searchio)

   Or

  (b) tests don't pass - in which case, tell us which one and run the test
by hand, going

      perl t/XXXXXX.t


and include the output.


YOU NOW WAIVE YOUR RIGHTS TO MOAN ABOUT YOUR SYSTEM NOT WORKING IF YOU
DONT TEST THE ALPHA AND RELEASE CANDIDATE TAR FILES



--- finally - Happy Christmas to all.




ewan