Tracking Git commits

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Core commits

Recent Commits to bioperl-live:master

Fixed a typo from my previous commit
nexml.t: Added a missing XML::Twig requirement.
Sopma.t: Added -requires_networking requirement up front (in case
Inactivated tests for GOR4.t, HNN.t and Sopma.t, since their server Fixed a bug where the server is not responding but the
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,
Last try failed probably because I did not specify one of
In the last try 3 builds almost finished. This last tweak removes
Argument worked but "-subs_only" actually took longer than
This argument order should work
Make Devel::Cover ignore external module 'prove' and checking
Unfortunately, the complete coverage test could not complete
Good news! Reducing the output made it finish much faster,
I found that the extra verbosity was caused by 'prove',
Failed try. Even testing coverage of only subroutines was
Second try at test coverage, this time only covering 'subroutine'
The first attempt of test coverage was working but resulted
Run commits

Recent Commits to bioperl-run:master

StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,
Added MYMETA.json to .gitignore
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
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
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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