Tracking Git commits

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Core commits
RSS

Recent Commits to bioperl-live:master

Minor POD edits
Standardized URL to "https://github.com/bioperl/bioperl-live/issues"
changes all issue tracking in preparation for switch to github issues
Minor edits
allowing lines with species label ($seq) without $rest, as comes with yn00
spellink
Merge pull request #66 from nathanweeks/sqlite_collate_nocase
Used quoted strings in Bio::Species to avoid a 'Invalid [] range in regex' error, Species.t and genbank.t pass
SeqIO/embl.pm: At 'next_seq' subroutine, added a little more
Add the COLLATE NOCASE constraint to the name.name,
SeqIO/Genbank: Complete elimination of the use of '$_',
Unflattener: Fix for Bug #3458. Incorporated Bastien Chevreux
SeqIO/Tinyseq.pm: Fixed an uninitialized value warning from
SearchResultEventBuilder: Simplified calculation of 'HSP-query_length'
Bio/Ontology/InterProTerm: Fixed an uninitialized warning in
SeqFeatureDB Postgres: Changed the use of system("cp") command
Massive check of file open lines. Changed bareword filehandles
Merge pull request #65 from MartinMcGrath/master
Fixed filename in test
Fixed bad filename
Run commits
RSS

Recent Commits to bioperl-run:master

I'm not sure if these programs will run on Windows now
Windows use 'NUL' instead of '/dev/null', so added the option
Added a way to find the required files in Windows using "dir"
Hmmer: Prevent errors caused by the presence of whitespace
Bowtie.t: "qx/ulimit -n 3>&-/" does not work as intended on Windows;
AssemblerBase.pm: In "reset_parameters", added an intermediary hash
BWA.t, Bowtie.t, Maq.t & Samtools.t: Moved tests using
AnalysisFactory_soap.t & Analysis_soap.t: Changed tests to 0.
Build.PL & MYMETA.json: Added SOAP::Lite v0.716 in
SoapEU-function.t: Updated expected version of a genome to current
StandAloneBlastPlus.pm: Some temporal files were not deleted
SABlastPlus.t: Added an additional $fac->cleanup for
SABlastPlus.t: Some bl2seq tests were giving hits even when the
Vista.t: The 'java Vista 2>&1' command to determine if Vista
FastTree.t & Neighbor.t: Fixed number of skipped tests and removed
BEDTools.t: Moved the file-finding lines inside the SKIP block,
Blat.t: Fixed skipped tests number and removed "$blat_present",
Hyphy/BatchFile.pm: Changed @validvals[$i] to $validvals[$i].
MAFFT.pm: Fixed an uninitialized warning from
POD update
Ext commits
RSS

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)
RSS

Recent Commits to bioperl-db:master

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
[bug 2092]
moved Bio into lib to make Module::Build installation more normal
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