Tracking SVN commits

From BioPerl

Tracking SVN commits

You can track code development in BioPerl by RSS feeds or the bioperl-guts Mailing list. There is a list of all BioPerl RSS feeds as well.

Core commits
RSS
Revision Log - /bioperl-live/trunk 16983 - [bug 3076] Fix bad catch of strand information. Tested data was wrong, corre... [bug 3076] Fix bad catch of strand information. Tested data was wrong, corrected to match expected output. Patch courtesy Ha X. Dang 16982 - [bug 3058] now bypasses exec string in output [bug 3058] * now bypasses exec string in output 16981 - [bug 3073] now with RDP species-parsing goodness. Yum! [bug 3073] * now with RDP species-parsing goodness. Yum! 16980 - rework assembly tests to be more modular, should make it easier to add more a... rework assembly tests to be more modular, should make it easier to add more as needed, turn others off, etc 16979 - commenting out a section of code fixes test crashes from improperly munged da... commenting out a section of code fixes test crashes from improperly munged data. Needs the author to take a look, but it seems the related code wasn't doing anything but somehow changing data in-place 16978 - 1170 -> 1770 (matches data) 1170 -> 1770 (matches data) 16977 - remote change in ensembl, make a little less prone to future changes remote change in ensembl, make a little less prone to future changes 16976 - load Bio::DB::Fasta (this fails with SQLite tests) load Bio::DB::Fasta (this fails with SQLite tests) 16975 - remote database update, local dump file needed to be updated to match remote ... remote database update, local dump file needed to be updated to match remote database change 16974 - HSP n defaults to 1 (must have at least one HSP used for score/e-val/p-val) HSP n defaults to 1 (must have at least one HSP used for score/e-val/p-val) 16973 - use settable n, fall back to num_hsps (more consistent with recent changes) use settable n, fall back to num_hsps (more consistent with recent changes) 16972 - make test less prone to volatile changes make test less prone to volatile changes 16971 - missing test file missing test file 16970 - Razi's patch for parsing out the algorithm reference, gets tests working again Razi's patch for parsing out the algorithm reference, gets tests working again 16969 - Bio::Assembly::IO::ace addendum to write quality scores for contigs that don'... Bio::Assembly::IO::ace addendum to write quality scores for contigs that don't have any Bio::Assembly::Contig POD clarification 16968 - Added serious tests of Bio::Assembly::Singlet, changes in Bio::Assembly::Sing... Added serious tests of Bio::Assembly::Singlet, changes in Bio::Assembly::Singlet and Contig 16967 - Bio::Assembly::Tools::ContigSpectrum cleaning, POD update and checking that t... Bio::Assembly::Tools::ContigSpectrum cleaning, POD update and checking that the module Graph::Undirected is installed 16966 - Added BioPerl recommended dependency: Sort::Naturally Bio::Assembly::IO::ace ... Added BioPerl recommended dependency: Sort::Naturally Bio::Assembly::IO::ace and tigr write contig IDs in natural order when possible POD and test updates 16965 - Some cleaning of Bio::Assembly::ContigSpectrum Some cleaning of Bio::Assembly::ContigSpectrum 16964 - Main change: Added write_assembly method for ACE assembly file format in Bio:... Main change: Added write_assembly method for ACE assembly file format in Bio::Assembly::IO::ace Satellite changes: Fixes with the way Bio::Assembly::IO::ace reads and records singlets Bio::Assembly::IO::ace now records base segments (BS tag) and read description (DS tag) as features of the contig feature collection Bio::Assembly::Singlet seqref method updated so that the reference sequence has coordinates in the singlet POD revisions, typo fixing, update of the tests...

Run commits
RSS
Revision Log - /bioperl-run/trunk 16949 - cwd call not used (and can produce error), so I'm removing it. cwd call not used (and can produce error), so I'm removing it. 16942 - Some extra variables were on the left side of the _rearrange, causing imprope... Some extra variables were on the left side of the _rearrange, causing improper assignment of parameters. 16922 - fix _fastize changing sequence alphabet upon gap-stripping fix _fastize changing sequence alphabet upon gap-stripping 16907 - duh, thanks Ben duh, thanks Ben 16906 - alias -program_dir to -prog_dir (thanks Ben) alias -program_dir to -prog_dir (thanks Ben) 16891 - [bug 3002] add a bit o' code for email address prompting for tests requiring ... [bug 3002] add a bit o' code for email address prompting for tests requiring them 16888 - use safe_parse (deafferret++); tests now run, but fail with EMBOSS 6.2.0 use safe_parse (deafferret++); tests now run, but fail with EMBOSS 6.2.0 16887 - throw error if XML::Twig borks on a parse throw error if XML::Twig borks on a parse 16886 - skipping wrong number of tests skipping wrong number of tests 16882 - redundant sub redundant sub 16878 - make overwrite behavior work make overwrite behavior work 16873 - Follow the bowtie environment variable index location behaviour definition fr... Follow the bowtie environment variable index location behaviour definition from bowtie manual 16870 - Remove unix command from constructor. Remove unix command from constructor. 16869 - bug fix bugzilla #3014 bug fix bugzilla #3014 16834 - handle multiple results: next_result, rewind_results handle multiple results: next_result, rewind_results 16829 - ease off on throws; let bl2seq work without a db being specified (as it should) ease off on throws; let bl2seq work without a db being specified (as it should) 16822 - yikes--this was a baddie. Fixed now. yikes--this was a baddie. Fixed now. 16805 - File::Temp::filename is full path--fix File::Temp::filename is full path--fix 16784 - tests for bug#3003 tests for bug#3003 16783 - more informative msg more informative msg

Ext commits
RSS
Revision Log - /bioperl-ext/trunk 15966 - moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compi... moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet 15948 - use UPPPER_TOL to catch the case when the expectation maximization step appea... use UPPPER_TOL to catch the case when the expectation maximization step appears to be decreasing. This should make it very unlikely to throw exception 15947 - fixed Vitebi typo fixed Vitebi typo 15942 - Fixed the typemap and also a memory bug in viterbi function in HMM.xs Fixed the typemap and also a memory bug in viterbi function in HMM.xs 15553 - adding FEEDBACK:Support section to pod adding FEEDBACK:Support section to pod 15297 - Bump to 1.007 (similar to trunk) Bump to 1.007 (similar to trunk) 15030 - ext patches (courtesy Thomas Jahns) ext patches (courtesy Thomas Jahns) 14843 - get rid of some unended comment warnings from C compiler get rid of some unended comment warnings from C compiler 14842 - -fPIC needed for lib construction -fPIC needed for lib construction 14841 - include errno definition include errno definition 14781 - removed DEBUG=1 removed DEBUG=1 14779 - IUPAC DNA support IUPAC DNA support 14778 - IUPAC DNA test case IUPAC DNA test case 14492 - Add some helper code and tests to demo evalue oddities (bug 1857); casting is... Add some helper code and tests to demo evalue oddities (bug 1857); casting issue? 14476 - Add cast to correct pointer type (get rid of warnings) Add cast to correct pointer type (get rid of warnings) 682 - update version to last bioperl release update version to last bioperl release 681 - bug 2329 bug 2329 680 - bug 2074/2329 bug 2074/2329 679 - Removed Aaron's old test script (now in t/staden_read.t). Do we modify maste... Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this? 678 - bug 2074 bug 2074

Bioperl-DB
RSS
Revision Log - /bioperl-db/trunk 16448 - weird duplication removed weird duplication removed 16447 - committing patch for bug #2958 committing patch for bug #2958 16310 - test commit to check SVN::Notify test commit to check SVN::Notify 16309 - Build.PL now checks for DBD drivers and attempts to DTRT Build.PL now checks for DBD drivers and attempts to DTRT 16224 - remove MANIFEST.SKIP remove MANIFEST.SKIP 16214 - update Changes update Changes 16206 - fix empty POD section fix empty POD section 16205 - some pod cleaning some pod cleaning 16157 - main trunk version is wrong main trunk version is wrong 15998 - * 02species.t now compared to similarly behaving instance, also creates compa... * 02species.t now compared to similarly behaving instance, also creates comparable array * remove debugging lines 15997 - [bug 2092] commit Sendu's patch comment out lines in SpeciesAdaptor that ... [bug 2092] * commit Sendu's patch * comment out lines in SpeciesAdaptor that munge genus/species names (old behavior) * 02species.t tests now failing, checking to see what the problem is 15910 - moved Bio into lib to make Module::Build installation more normal moved Bio into lib to make Module::Build installation more normal 15906 - fixed up capitalisation; allowed --accept; improved script install; will inst... fixed up capitalisation; allowed --accept; improved script install; will install modules from lib 15904 - fix up shebang lines so they can be converted during install fix up shebang lines so they can be converted during install 15903 - remove Data::Dumper remove Data::Dumper 15902 - * scripts now convert over properly. should probably consider actually go... * scripts now convert over properly. * should probably consider actually going through the scripts and adding the 'bp_foo.PLS' directly instead of working around this * not sure why we are going through the trouble of running the conversion just prior to installation, anyone know? 15900 - * get scripts working, module installation from Bio as well these need to b... * get scripts working, module installation from Bio as well * these need to be mapped to their bp_*.PLS counterparts 15899 - * convert over to Module::Build add concrete MANIFEST.SKIP (no point on gen... * convert over to Module::Build * add concrete MANIFEST.SKIP (no point on generating this for only one file) 15601 - [bug 2757] patch for error handling, per Mark Johnson [bug 2757] * patch for error handling, per Mark Johnson 15552 - adding FEEDBACK:Support section to pod adding FEEDBACK:Support section to pod

BioSQL schema changes
RSS
Revision Log - /biosql-schema 317 - load_taxonomy.pl script was renamed load_ncbi_taxonomy.pl. load_taxonomy.pl script was renamed load_ncbi_taxonomy.pl. 316 - Fixed to point to the currently valid download URL. Fixed documentation which... Fixed to point to the currently valid download URL. Fixed documentation which said we don't support this when in reality we do! Added command line arguments to control download URL and print the default. 315 - Adding logo versions to repository. Adding logo versions to repository. 314 - Fixed statement about Bioperl-db and Pg v8.3+ - we are fully compatible. Fixed statement about Bioperl-db and Pg v8.3+ - we are fully compatible. 313 - These aren't needed anymore - Bioperl-db is pretty much Pg 8.3 compatible. These aren't needed anymore - Bioperl-db is pretty much Pg 8.3 compatible. 312 - Fixing the comment characters. Fixing the comment characters. 311 - Fixed missing primary key definitions (the lack of those upsets SQLAlchemy in... Fixed missing primary key definitions (the lack of those upsets SQLAlchemy in Python). 310 - Fixed missing primary key definitions (this upsets SQLAlchemy in Python). Cha... Fixed missing primary key definitions (this upsets SQLAlchemy in Python). Changed attribute_value to qualifier_value convention to stay consistent with the core schema. 309 - Added some association tables that were added to the schema module. Added some association tables that were added to the schema module. 308 - Updated the comment about what this is all inspired by. Updated the comment about what this is all inspired by. 307 - Added comments throughout, fixed syntax and renaming errors, changed parent/c... Added comments throughout, fixed syntax and renaming errors, changed parent/child to object/subject. This instantiates error-free on Pg 8.3. 306 - Added cross-references for character states and characters. Added ontology te... Added cross-references for character states and characters. Added ontology term annotations for matrix cells, characters, and character states. Added foreign key constraints for those. 305 - Added tag/value annotation for characters, and a table for connecting trees a... Added tag/value annotation for characters, and a table for connecting trees and character matrices. 304 - Added foreign key constraints for what we have so far. Added foreign key constraints for what we have so far. 303 - Fix the documentation to say more precisely what is being dropped. Fix the documentation to say more precisely what is being dropped. 302 - Fixed typos and other syntactical errors. Schema instantiates now w/o error. Fixed typos and other syntactical errors. Schema instantiates now w/o error. 301 - Fixed typo left over from copying and pasting. Fixed typo left over from copying and pasting. 300 - Replaced partitions with a hierarchy of character matrices. Replaced partitions with a hierarchy of character matrices. 299 - Fixed documentation typos. Fixed documentation typos. 298 - Enable svn keyword expansion. Enable svn keyword expansion.