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Core commits

Recent Commits to bioperl-live:master

small test fix for taxonomy woes (stop-gap, need a better long-term solution)
Moved optimized \n and \r removal subroutine from Bio::DB::Fasta
Merge branch 'topic/issue86'
fixing issue 86
Merge pull request #96 from rocky/Inline-C-Fasta
Handle Structured Comments correctly by keeping them 'tabular', i.e. don't remove the returns
Faster, more idiomatic C code. Use stiop_crln() in the other place it is used. Add my variable in strip_crnl and rename from strip_nlcr. Document better
Fixed a typo from my previous commit
If we have Inline::C around, use that to speed up remove carriage returns and
nexml.t: Added a missing XML::Twig requirement.
Sopma.t: Added -requires_networking requirement up front (in case
Another regular expression which benefits from compiling
Inactivated tests for GOR4.t, HNN.t and Sopma.t, since their server Fixed a bug where the server is not responding but the
Using compiled regexps in s/// speeds up seq/subseq() by about 7% from 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data.
Fixed small typo
Updated Changes and included myself in AUTHORS after Chris suggestion Fix for issue #90. Added new codon tables 24 & 25 and
Coveralls report finally worked but only some jobs can finish on time,
Run commits

Recent Commits to bioperl-run:master

Raxml: use File::Spec->devnull() instead of our own code and do not import extra stuff into namespace
Merge pull request #13 from hettling/master
convert to markdown for consistency
convert to markdown for consistency
removed obsolete whitespace
StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,
Added MYMETA.json to .gitignore
Added -d option (random starting tree) to raxml run, because raxml
(1) when -w option was provided with a custom directory, 'run' always
WBCommandExts.t: Fixed a pending TODO related to
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
Ext commits

Recent Commits to bioperl-ext:master

markdown-ize README
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?
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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