Release Schedule

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We are interested in ideas/classes/code/etc. to be included in future Bioperl releases, specifically the next developer release (1.5.2), the next stable release (1.6), and beyond. Please keep the ideas/comments as short as possible, and leave a signature using '~~~~'. --Chris Fields 12:34, 8 August 2006 (EDT)

Use the discussion page for questions and answers. --Senduran 16:16, 14 August 2006 (EDT)

Contents

Bioperl-core

Changes noted here reflect the planned 'roadmap' for the future direction of the main BioPerl distribution (bioperl-core).

Bioperl 1.6

  • 'Stable' Release
  • Release ASAP
  • Requires perl 5.8.1 or later (perl 5.6 no longer supported)
    • Late Nov-Dec 2008
    • The remainder of the issues on the Project priority list not covered here or in 1.5.2 to be pushed to 1.7-1.8
  • Have regular 'maintenance' releases for bug fixes only (no additional modules, no API changes).
  • API 'locked in', i.e. no API changes are allowed in the 1.6 release series which will break user scripts. All such changes must wait until 1.7.

The following issues/bugs need to be addressed prior to 1.6. Please voice opinions on the discussion page (this will be edited to reflect changes).

  • Should GBrowse-related modules (Bio::Graphics, Bio::DB::GFF, Bio::DB::SeqFeature-related, etc) be split off into a separate distribution for 1.6?
  • Split and rename related tests (SearchIO.t and hmmer.t, for instance) into smaller test files (SearchIO_blast.t, SearchIO_hmmer.t, SearchIO_infernal.t, etc). This same theme could be used for Bio::SeqIO, Bio::AlignIO, and other 'pluginable' parsers.
    • The tests should be as focused as possible, the end result hopefully being that these changes are geared towards...
      • post-1.6 releases when splitting up BioPerl into their respective smaller distributions, and...
      • will probably help tremendously when bugfixing, targeting modules for deprecation, etc.
    • Related to the above: we probably can group related tests with similar themes together (Variation_*.t, Coordinate_*.t, etc).
  • Bio::LocatableSeq has issues with translated nucleotide sequences derived from BLAST/FASTA reports. This has been partially fixed by using a mapping() method, but TFASTX/Y frameshifts aren't yet supported.
  • OTHER BUGS TO BE ADDED

The following are now pushed to later releases (the below are much easier to accomplish once we split bioperl into set subdistributions, so should wait until after 1.6):

  • Determine who is available to maintain modules
  • Assign orphaned modules to new maintainers
  • Each maintainer, for their set of modules:
    • Uses Devel::Cover (with Pod::Coverage) via Module::Build to:
      • Check and complete POD documentation for all methods
      • Improve test coverage: try to ensure that all methods are fully tested in t/module.t
    • Reports which modules are complete and which are not
  • For incomplete or unmaintained modules introduced since 1.4, move, remove, or revert

What are the main impediments/issues we need to resolve for a 1.6 release?

Need tests

The existing tests were moved over to Bio::Root::Test which makes dealing with them easier, but they are still completely inadequate in terms of code coverage.

As I (Senduran) see it, we can't claim a 'stable' release by either sense of the word. We don't know if its sufficiently bug free, not has the API been given a thorough work-out to see if it makes enough sense for us to recommend and support it for years to come.

Moving toward complete test coverage will also make clear the modules that can't go into 1.6 because they're only partially developed or non-functional.

This is the major work that needs to be done vs. the 1.5.2 release, and it is a substantial job requiring organization and a dedicated team.

SeqFeature/Annotation changes: Keep or roll back?

Note: SeqFeature/Annotation changes have been rolled back.

Bug fixes

We need to identify bugs that are blocking and prioritize bugs as needed for 1.6 (or beyond).

Bioperl 1.7

  • A proposal is queued for dividing up modules based on test coverage, development status, etc.
  • Next release, Fall 2009-Spring 2008. Will need to go through some extensive alpha testing.

Bioperl 1.8

  • Achieve a state of Zen completeness
  • Due date: 2012

Bioperl-run

These are the proposed plans for the bioperl-run distribution:

  • Flesh up the Bio::Tools::Run::Phylo::PAML::Evolver
    • Should create a MC<control>.dat file and execute evolver under the guise of bioperl-run::Bio::Tools::Run::Phylo::PAML::Codeml
    • Preferably have a [prepare]-[execute] structure instead of a [prepare+execute] structure like bioperl-run::Bio::Tools::Run::Phylo::PAML::Codeml CVS 1.38
    • Preferably take the empirical codon frequencies of a Results.pm and stash them somehow in the MC<control>.dat (Jason: how do you see this being done?)
  • A wrapper for Mumsa [1]:
    • MUMSA compares multiple sequence alignments. My idea would be to put the module in Bio::Tools::Run::Alignment::Utils::Mumsa.pm
  • A wrapper for seqgen:
    • Should call seqgen with the basics
    • Should ease the way of a codon rates/usage from a Bio::Tools::Phylo::PAML codonusage to a seqgen <CODON_POSITION_RATES> string.
  • Some RNA tool wrappers (Vienna RNA, Infernal, RNAMotif, UNAfold)
  • More?

References

  1. Lassmann T and Sonnhammer EL. Automatic assessment of alignment quality. Nucleic Acids Res. 2005;33(22):7120-8. DOI:10.1093/nar/gki1020 | PubMed ID:16361270 | HubMed [mumsa]
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