Release Schedule

From BioPerl

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)

1 Bioperl-core
2 Bioperl-run
- 2.1 References

Bioperl-core

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

Bioperl 1.5.3 and up

UCSC genome browser tables interface for easy genomic sequence retrieval
New Bio::DB* interface classes for non-sequence-related data
Clean up Bio::DB::EUtilities

Bioperl 1.6

Stable Release
Release ASAP
- Late Spring-Summer 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
Clean-up and polish
- 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
  - Feature/Annotation rollback complete. Still need to check oddities with SwissProt/UniProt parsing.
Have regular 'maintenance' releases for bug fixes only (no additional modules, no API changes).
It has been proposed to separate out less-developed modules from the core. Here is a first take on such a division. Dave Messina 06:04, 13 February 2008 (EST)

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

Need tests

The existing tests were moved over to BioperlTest 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.

Not sure how feasible this is. It would be easier to vet modules when coming in, probably by pushing new ones into a separate 'dev' or 'extras' distribution prior to rigorous testing. --Chris Fields 13:15, 12 February 2008 (EST)

SeqFeature/Annotation changes: Keep or roll back?

Note: SeqFeature/Annotation changes have been rolled back.

Serious issues are still present re: Bio::SeqFeatureI's use of Bio::Annotation::Collection for tag values, a controversial change added to the main core trunk prior to the 1.5 release which makes tags in SeqFeatures Annotation objects. This primarily affects Bioperl-db and Bio::SeqFeature::Generic/Bio::SeqFeature::Annotated and is now used in the latest GMOD and GBrowse releases.

These issues must be addressed and resolved prior to a stable 1.6 release. Furthermore, any changes must be coordinated along with the GMOD project, which relies on the current implementation from the main trunk.

Several posts over the last two years detail the issues involved.

The original thread (with responses) detailing SeqFeature/Annotation changes: http://thread.gmane.org/gmane.comp.lang.perl.bio.general/6924
Further posts

Several developers have offered possible solutions:

Ewan's solution : http://thread.gmane.org/gmane.comp.lang.perl.bio.general/9101
Chris Mungall's suggestion : http://thread.gmane.org/gmane.comp.lang.perl.bio.general/6924/focus=6950

Bioperl 1.7

Next developer release, Fall 2007-Spring 2008?
Perl6 should be out by this time, maybe sooner. Yikes!

Bioperl 1.8

Stable release, release date unknown
Completion of ideas on the Project priority list
- Starting with parsing code as the main priority

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?