Tracking Git commits

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Core commits

Recent Commits to bioperl-live:master

Remove modules and tests (StandAloneBlast and WrapperBase) that now reside in bioperl-run
Removed empty file Bio/Tools/Run/, which seems
Bio/DB/Taxonomy/ Fix for issue #80, changed DESTROY
Add travis-ci badge
Bio/Location/ Removed the "$loc->is_remote" condition Fixed a long-standing issue at "from_string()" Adjusted from_string() subroutine to
hmmmer2 & hmmer3: Complete elimination of the use of '$_'
hmmer.t: Fixed minor mistake Fixed a bug where an homology line ending in CS or RF Fix for issue #70, removed the line at write_seq()
Bio/SeqFeature/ Fix for issue #76, adjusted "seq"
all "": Fixed subroutines calling "Bio::Phylo::IO->parse".
t/Tree/TreeIO/nexml.t: A close function was being used on
hmmer.t: Added tests to document "$hit->bits"
HMMERHSP: For HMMer report parsing, changed "$hsp->bits" to
Merge branch 'master' of
giving new meaning to the term "git", moving back where it belongs Another tweak to "_read_GenBank_Species" regex
memory adapter does not expect fasta database to be closed after initial load, so leave it open
Run commits

Recent Commits to bioperl-run:master

Update Build.PL, MYMETA.json with build dependencies
no dependencies on any of the Test::* or Sub::Uplevel in any test (except maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
Update Build.PL with config_requires and build_requires; add MANIFEST
Merge branch 'master' into topic/move_WrapperBase
fixed translate_params tests according to discussion at commit a6d0dc2; removed TODO around translate_params test
move StandAloneBlast* and WrapperBase* from root/Bio... to root/lib/Bio...
Merge branch 'master' of ../move_WrapperBase/bioperl-wb into topic/move_WrapperBase
test parameters independent of their order as issued on command line
Removed empty file Bio/Tools/Run/, which seems
Merge branch 'master' of
giving new meaning to the term "git", moving back where it belongs
adding back -DOH
loosened validation for outfmt in BlastMethods to allow quoted multiple values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
fix parsing edge case
issue 12: changes to _translate_params that allow quoted option values
POD updates
Really die if EMBOSS is not found
Merge branch 'master' of
Merge pull request #71 from nathanweeks/issue/bio-seqfeature-lite-strand
Merge pull request #67 from stu2/master
Ext commits

Recent Commits to bioperl-ext:master

moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
bug 2074
Bioperl-DB (BioSQL)

Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
update Changes
fix empty POD section
some pod cleaning
main trunk version is wrong
* 02species.t now compared to similarly behaving instance, also creates comparable array
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