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

14858 - Document that get_tag_values() return variable is context sensitive (array of...
Document that get_tag_values() return variable is context sensitive (array of scalar)

14857 - fixed bugs that interfered with the display of stranded features defined usin...
fixed bugs that interfered with the display of stranded features defined using the FeatureFile format
14856 - essential ideogram glyph base class missing
essential ideogram glyph base class missing
14855 - remove a spurious line creating an unneeded object
remove a spurious line creating an unneeded object
14854 - small documentation typo fix
small documentation typo fix
14853 - small documentation typo and grammar fix
small documentation typo and grammar fix
14852 - small documentation typo fix
small documentation typo fix
14851 - small documentation typo fix
small documentation typo fix
14850 - small documentation fix
small documentation fix
14849 - testing translation between nhx and phyloxml
testing translation between nhx and phyloxml
14840 - Allow other Bio::SeqFeature::CollectionI
Allow other Bio::SeqFeature::CollectionI
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]

[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]

[bug 2573]
* only work with Bio::Ontology::Relationship instances with a set Bio::Ontology::Ontology

14831 - Update documentation
Update documentation

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

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
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

Bioperl-DB
RSS

Revision Log - /bioperl-db/trunk

14848 - Added test for inserting, updating, and constraining char columns using numer...
Added test for inserting, updating, and constraining char columns using numeric
values (which can be an issue in PostgreSQL v8.3+).

14847 - Made sure that the persistence driver's prepare() and bind_param() front-ends...
Made sure that the persistence driver's prepare() and bind_param() front-ends
are actually being used.
14846 - Migrated code to capabilities of more modern DBI and DBD versions.
Migrated code to capabilities of more modern DBI and DBD versions.
14845 - Mostly cosmetic change in how the config file is written to silence a warning.
Mostly cosmetic change in how the config file is written to silence a warning.
14844 - Fixed to use placeholders and a named query, rather than doing the quoting it...
Fixed to use placeholders and a named query, rather than doing the quoting
itself (which would have also been a security hole if the parameter came from
user or web form input). This also gets rid of the incompatibility with
PostgreSQL v8.3+!
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

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).

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