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Core commits
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Recent Commits to bioperl-live:master

even better DOI
add DOI badge from Zenodo
Merge pull request #106 from lairdm/master
A test to ensure Bio::PrimarySeqI->trunc() doesn't use clone() for a Bio::Seq::RichSeq type object
Darn you, emacs, putting tab characters in. Sorry, didn't realize I hadn't changed my configs after reinstalling my laptop last month.
Merge branch 'master' of https://github.com/lairdm/bioperl-live
Added Bio::Seq::RichSeq as a seq object type that will cause Bio::PrimarySeqI->trunc() not to do a clone of the original object first. The clone was cloning features of the rich sequence object outside the requested range in trunc()
Remove cruft (soz)
Merge branch 'topic_105'
fix #105 - find the real "first orf"
skip tests when using perl < 5.12
Merge branch master of github.com:bioperl/bioperl-live
remove test file
Merge branch 'master' of github.com:bioperl/bioperl-live
Fix #103
a bit more doc; getting about 1000 full lineage lookups in 2 sec
small profiling improvement w/index files
bit more docs on todo items
all key tests pass (only a few haven't been checked), but likely needs optimization
all but two tests passing
Run commits
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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/hmmer3.pm, which seems
Merge branch 'master' of https://github.com/bioperl/bioperl-live
Ext commits
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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)
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Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
add MANIFEST.SKIP
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
remove MANIFEST.SKIP
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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