Talk:Release 1.5.2

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New Bio::DB* interface classes for non-sequence-related data


  • Is the new Bio::DB::SeqFeature implementation sufficiently stable? This is a replacement for Bio::DB::GFF for explicit GFF3 support.
    • We need to contact Lincoln and Scott Cain about this. --Chris Fields 10:22, 14 August 2006 (EDT)
    • Will you do that Chris? Senduran 15:58, 14 August 2006 (EDT)
    • I have emailed GMOD-GBrowse (cc'd to bioperl-l) and hope to hear back soon. I think Lincoln may still be on vacation. --Chris Fields 17:47, 14 August 2006 (EDT)
    • Looks like the decision is to keep this in for further testing. --Chris Fields 23:47, 21 August 2006 (EDT)

Unimplemented/undocumented modules

  • Begin checking modules for unimplemented/undocumented methods, full tests, etc.
    • I will have a page set up to keep track of these, linked from the Developer Information page --Chris Fields 10:22, 14 August 2006 (EDT)
    • Might be useful to include instructions/guidelines/examples on ways to find these things, eg. Devel::Cover & Pod::Coverage mini-tutorial. Senduran 15:58, 14 August 2006 (EDT)
    • I'm initially using a simple regex to look for throw/warn_not _implemented, but will expand out from there. --Chris Fields 17:47, 14 August 2006 (EDT)

Update URLs and emails

  • Check that URLs (and e-mail addresses?) in modules/documentation are valid/updated.
    • Mauricio was working on this. I don't know if all BioPerl modules were changed. --Chris Fields 10:22, 14 August 2006 (EDT)
    • Mauricio, to what extent does further work need to be done on this? Senduran 15:58, 14 August 2006 (EDT)
    • What I did for URLs was a general batch processing of everything in the CVS tree. Need to do a deep "by module" revision. What do you think about validating/updating e-mails? --Mauricio 17:01, 14 August 2006 (EDT)
    • E-mail check is good, but you'll have to keep track of who likes to obfuscate their address and who doesn't, and make sure it is consistent across all files. --Senduran 17:28, 14 August 2006 (EDT)

Updating INSTALL and other distribution docs

  • Converting INSTALL and other related wiki pages for distributions
    • Should these be converted to text (per previous distributions) or change over to HTML, PDF, other format?
    • It would be easier to have the full installation instructions on the wiki and a general truncated text version in the distribution.--Chris Fields 10:22, 14 August 2006 (EDT)
    • INSTALL document in the distribution must remain a plain text file and must contain all the information necessary to complete install without further lookups. The user's ease of installation matters more than our ease of maintainance. Senduran 15:58, 14 August 2006 (EDT)
      • Brian agrees with you on that point. The problem we face is the different OS variations when installing Bioperl (see Installing Bioperl on Windows and Installing Bioperl for Unix) and the logistics of converting to text from the most up-to-date versions on the wiki. Saying that, I don't think that it be just 'perl Makefile.PL; make; make install;' either. Brian and I had talked about this before, so I'll look into it to see if there is an easy solution that can be used for all future distributions. --Chris Fields 17:47, 14 August 2006 (EDT)

Updating Change log

  • Ensure that the Change log is complete (as well as the CHANGES distribution file)
    • Need to work out what has changed since 1.5.1 that needs mentioning Senduran 16:05, 14 August 2006 (EDT)
      • Might be easier to start with bug fixes, then look at CVS commits. I don't think it's absolutly necessary to add every single small commit, but ones that fix code would be nice --Chris Fields 17:47, 14 August 2006 (EDT)

Other BioPerl packages

  • Can a message be displayed after "make test" to tell the user to update any software they may have and that failed?
    • They can look at the test results --Senduran 10:21, 25 October 2006 (EDT)
      • I agree they can, but often errors due to old software result in obscure fails. -- Nath 13:31, 25 October 2006 (EDT)

Other discussion

Do we need to have all tests for all distributions passing, or just bioperl core? --Chris Fields 00:16, 20 October 2006 (EDT)

  • For -run, -network and -db, since I'm aiming for a unified release. --Senduran 06:09, 21 October 2006 (EDT)
    • We'll need to make an exception for the ActivePerl/WinXP/bioperl-db combo since it requires changes to core modules that break other functionality (so we can't implement those for all OS's). The problems there, I think, primarily lie with the perl version (ActiveState). I may try another Win perl implementation or CygWin. I know the perl version with CygWin and bioperl-db work, but DBD::mysql is a pain to install. --Chris Fields 12:00, 21 October 2006 (EDT)
    • For -run, it can be hard to fix all tests since each of us have a different set of available programs for testing (because of different OSs). -- Mauricio 12:58, 21 October 2006 (EDT)
    • Not everything in -run has to work, but at least we should try to fix the most agregious problems we actually know about.
    • I now have a linux box that has a large chunk of software installed for which there are Bioperl-run tests -- Nath 09:31, 25 October 2006 (EDT)
  • t/protgraph.t needs v1.01 of Class::AutoClass. I (Chris) have a WinXP PPM for Class::AutoClass specifically for ActiveState Perl 5.8 that we could place on the BioPerl server if needed (though you could use nmake to install). I will also put in a request with ActiveState to update their version to the latest so hopefully this won't be a major problem.
    • Can Chris/Nathan make that PPM available on the BioPerl server? Whilst Bio::Graph may get deprecated, we still need it working in 1.5.2. --Senduran
      • Nathan has set up a separate directory for the release candidates (, which contains the Windows Class::AutoClass PPM, among others. I think the best option is to move the PPM dependency archives to a permanent directory since they aren't dependent on a particular BioPerl PPM version. Then we can modify the relevant XML files to grab the archives there. Nathan? --Chris Fields 10:13, 8 November 2006 (EST)
        • The directory was only setup for the short term while I was figuring out how best to version the RC releases for PPM, the files will be moved over to the standard directory with the official 1.5.2 release. I'll but all the dependencies in a seperate directory and update the XML file accordingly. --Nath 02:57, 13 November 2006 (EST)
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