Tracking SVN commits

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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 14839 - Fixed bug: not using gapped length to calculate LocatableSeq->end in _overlap... Fixed bug: not using gapped length to calculate LocatableSeq->end in _overlap_alignment. Letting the default behavior use ungapped length instead 14838 - Fixed bug: all LocatableSeq->end specified based on gapped length (instead of... Fixed bug: all LocatableSeq->end specified based on gapped length (instead of ungapped) now not specified 14837 - Fixed bug for add_seq: $seq->end now based on ungapped length Fixed bug for add_seq: $seq->end now based on ungapped length 14836 - Fixed bug for set_consensus_sequence->end: end needs to take into account seq... Fixed bug for set_consensus_sequence->end: end needs to take into account sequence gaps 14835 - [bug 2576] explicitly leave hit table block if a blank line is encountered ... [bug 2576] * explicitly leave hit table block if a blank line is encountered after the hit table (passes all SearchIO.t tests) 14834 - Fix a typo in pod doc Fix a typo in pod doc 14833 - grep not needed (check for ontology is in Ontology::get_predicate_terms) grep not needed (check for ontology is in Ontology::get_predicate_terms) 14832 - [bug 2573] only work with Bio::Ontology::Relationship instances with a set ... [bug 2573] * only work with Bio::Ontology::Relationship instances with a set Bio::Ontology::Ontology 14831 - Update documentation Update documentation 14830 - complete sentence complete sentence 14829 - _build_nt_matrix() now uses $self->warn rather than straight print to report... _build_nt_matrix() now uses $self->warn rather than straight print to report on ambiguous residues (suggested by Dominic Rose on the bioperl mailing list) 14828 - quashed an uninit variable warning quashed an uninit variable warning 14827 - set the mysql autoreconnect flag set the mysql autoreconnect flag 14826 - Add some print_* methods for einfo, esummary, etc. Add some print_* methods for einfo, esummary, etc. 14825 - added an option to bp_seqfeature_load to ignore ##sequence-region directives ... added an option to bp_seqfeature_load to ignore ##sequence-region directives in the gff3 file 14823 - added a background color fallback option added a background color fallback option 14821 - don't complain if there's no scripts directory don't complain if there's no scripts directory 14820 - added get_feature_by_primary_id() method added get_feature_by_primary_id() method 14817 - added a get_feature_by_id() method to Bio::DB::SeqFeature::Store as an alias ... added a get_feature_by_id() method to Bio::DB::SeqFeature::Store as an alias for the non-intuitive fetch() method that does the same thing 14816 - * write PROJECT support test case round-trip tests WGS, similar should ... * write PROJECT support * test case * round-trip tests * WGS, similar should conform with other annotation tag names (all lc) * bring handler-based parser up-to-date

Run commits
RSS
Revision Log - /bioperl-run/trunk 14824 - * add_sequences option (adds sequences to an alignment) - bug 2562 * add_sequences option (adds sequences to an alignment) - bug 2562 14796 - Closed 3 filehandles that were not Closed 3 filehandles that were not 14785 - Warn user when some sequences are discarded because they are too short Warn user when some sequences are discarded because they are too short 14773 - patching the correct Primer3.pm (not Bio::Tools::Primer3.pm) patching the correct Primer3.pm (not Bio::Tools::Primer3.pm) 14743 - AAML parsing was failing on runmode=0 data (usertree) AAML parsing was failing on runmode=0 data (usertree) 14742 - bug 2523 bug 2523 14717 - Added version() method. Tests pass on latest exonerate version 2.0.0. Testing... Added version() method. Tests pass on latest exonerate version 2.0.0. Testing for hit locations might not be worth the trouble in the long run! 14715 - silence warnings silence warnings 14714 - All tests pass now even if no binaries are installed. More testing is needed ... All tests pass now even if no binaries are installed. More testing is needed with binaries in place. 14713 - POD fixes POD fixes 14711 - POD fixes POD fixes 14709 - fixing POD whitespace issues fixing POD whitespace issues 14686 - Added forgotten -data_format attribute. Now uses -longid to format the MSA to... Added forgotten -data_format attribute. Now uses -longid to format the MSA to phylip sequential format for phyml input. 14681 - wrapper around phyml wrapper around phyml 14680 - fix typo in docs fix typo in docs 14661 - Update to 0.81 params. Need to set up tests for this, ERPIN, RNAMotif. Update to 0.81 params. Need to set up tests for this, ERPIN, RNAMotif. 14644 - recently seems to need comma-separated values for the header in the results -... recently seems to need comma-separated values for the header in the results -- not sure if this was a problem at the very beginning 14636 - correction now that B::SF::Annotated behaves more like Generic correction now that B::SF::Annotated behaves more like Generic 14634 - added POD warnings for coordinate issues; added automatic correction for resu... added POD warnings for coordinate issues; added automatic correction for result feature coordinates 14631 - paml 4b now accepts more codon frequency models paml 4b now accepts more codon frequency models

Ext commits
RSS
Revision Log - /bioperl-ext/trunk 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 677 - added bit about VERSION issues added bit about VERSION issues 676 - Uses io_lib 1.8.11 or 1.8.12; newer versions don't seem to work correctly Uses io_lib 1.8.11 or 1.8.12; newer versions don't seem to work correctly 675 - Updated bug reporting Updated bug reporting 674 - Fixed spaces Fixed spaces 673 - Fixed spaces and URL's Fixed spaces and URL's 672 - Updating mailing lists URL Updating mailing lists URL 671 - fixed some memory issues fixed some memory issues 670 - Now we allocate memory for the emission matrix rows in HMM_new Now we allocate memory for the emission matrix rows in HMM_new 669 - support for ends-free alignment support for ends-free alignment 668 - Looks like all version numbers must match for 'make' Looks like all version numbers must match for 'make'

Bioperl-DB
RSS
Revision Log - /bioperl-db/trunk 14776 - Fixed inconsistencies in the PODs of the loading scripts. Fixed errors and in... Fixed inconsistencies in the PODs of the loading scripts. Fixed errors and inconsistencies in the INSTALL document. 14602 - get rid of undefined string warnings in verbose output get rid of undefined string warnings in verbose output 14601 - bug 2226 bug 2226 14599 - Throw if no primary key defined (cases where the persistent object is not cre... Throw if no primary key defined (cases where the persistent object is not created and one attempts to remove in same run). 617 - bug 2387 bug 2387 616 - added GPL License added GPL License 615 - changed license to "perl", ie. artistic or GPL changed license to "perl", ie. artistic or GPL 614 - bug 2287 bug 2287 613 - more similar to original test more similar to original test 612 - some fixes related to bioperl-live Ontology fixes some fixes related to bioperl-live Ontology fixes 611 - removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new" removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new" 610 - Adding support for schemas in PostgreSQL. Though I think this should work, it... Adding support for schemas in PostgreSQL. Though I think this should work, it is not tested yet. 609 - Documenting that in theory location() should always be present. Documenting that in theory location() should always be present. 608 - Patch by Bryan Cardillo to fix the issue in http://lists.open-bio.org/piperma... Patch by Bryan Cardillo to fix the issue in http://lists.open-bio.org/pipermail/biosql-l/2006-August/001048.html 607 - latest version from core latest version from core 606 - now just a warning to use Build.PL now just a warning to use Build.PL 605 - auto-generate Makefile.PL auto-generate Makefile.PL 604 - now auto-generated now auto-generated 603 - latest version from core latest version from core 601 - mention the wiki for instructions, corrections mention the wiki for instructions, corrections

BioSQL schema changes
RSS
Revision Log - /biosql-schema 294 - Fixed to work with the latest phylodb schema. Added ability to download from ... Fixed to work with the latest phylodb schema. Added ability to download from ITIS website automatically. Simplified DSN construction and driver recognition. 293 - Checking success of updating parent_taxon_IDs. Somewhat simplifying driver re... Checking success of updating parent_taxon_IDs. Somewhat simplifying driver recognition and DSN construction. 292 - Fixed cardinality direction for columns and OTUs. Fixed cardinality direction for columns and OTUs. 291 - Small typo (forgot to add the Pg version#). Not nice. Small typo (forgot to add the Pg version#). Not nice. 290 - Tagging release v1.0.1. Tagging release v1.0.1. 289 - Merging changes for v1.0.1 from the main trunk to the 1.0 branch. Merging changes for v1.0.1 from the main trunk to the 1.0 branch. 288 - Fixed documentation in load_ncbi_taxonomy script. Added Changes items for thi... Fixed documentation in load_ncbi_taxonomy script. Added Changes items for this release. 287 - Fixed to no longer require the primary key for taxon nodes to be equal to the... Fixed to no longer require the primary key for taxon nodes to be equal to the NCBI taxonID. 286 - Widened bioentry.accession and dbxref.accession to 128 chars. Added migration... Widened bioentry.accession and dbxref.accession to 128 chars. Added migration scripts for v1.0.1 (which this will constitute). 285 - Fixing inconsistencies in how the biosql database is named. Added a note abou... Fixing inconsistencies in how the biosql database is named. Added a note about compatibility (i.e., lack thereof) with Pg v8.3+. 284 - Adding scripts for adding back the automatic typecasts in PostgreSQL v8.3+, f... Adding scripts for adding back the automatic typecasts in PostgreSQL v8.3+, from Peter Eisentrauts blog. 283 - Caught up with the latest additions to the PhyloDB module so those get delete... Caught up with the latest additions to the PhyloDB module so those get deleted too. 282 - Added foreign key constraints for tree_dbxref and node_dbxref. Added foreign key constraints for tree_dbxref and node_dbxref. 281 - Added diagrams for possible models for the components of a phylogenetic anal... Added diagrams for possible models for the components of a phylogenetic analysis and for expressing an evolutionary transition model. 280 - Adding PNG format as exported format in addition to PDF. Updated the diagram ... Adding PNG format as exported format in addition to PDF. Updated the diagram to the latest changes from the 2008 BioHackathon and regenerated all exports. 279 - Release notes for v1.0.0. Release notes for v1.0.0. 278 - Tagging the 1.0.0 release. Closing in ... Tagging the 1.0.0 release. Closing in ... 277 - Removed phyloDB changes as they do not pertain to this release. Removed phyloDB changes as they do not pertain to this release. 276 - Apparently this wasn't auto-recognized as mimetype text/html. Apparently this wasn't auto-recognized as mimetype text/html. 275 - Merged updates from main trunk (#274). Merged updates from main trunk (#274).