Changes

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0.06400   2010-10-20 20:54:37 PST8PDT

 * added naama's stock_dbxrefprop from upstream chado

0.06302   2010-10-20 09:58:19 PST8PDT

 * corrected homepage url in CPAN upload

0.06301   2010-10-19 17:49:41 PST8PDT

 * corrected missing DBIx::Class::Tree::NestedSet dep

0.06300   2010-10-18 17:38:29 PST8PDT

 * converted build system to Dist::Zilla
 * applied nmenda's type_id corrections from chado trunk
 * fix permission denied test failure caused by shipping a
   t/var/BCS.db file by accident

0.06200

 * removed erroneous duplicate General/Project.pm module
 * Updated natdiv module from Chado upstream (fixed upstream by nmenda).
 * Added create_stockprops method to stock module (nmenda).

0.06001

 * Corrected missing stuff in the manifest.

0.06000

 * Added DBIx::Class::Tree::NestedSet support to for Phylonodes.
 * Added Natural Diversity and Project module support.

0.05801

 * Fix bugs and add tests for child_features and parent_features on
   Sequence::Feature
 * Added parent_relationships and child_relationships rels to
   Sequence::Feature as more intuitive aliases for
   feature_relationship_*

0.05800
 
 * New aliases on Sequence::Feature
    child_features  -> featureloc_features
    parent_features -> featureloc_srcfeatures
 * Added a function for creating cvtermsynonyms ($cvterm->add_synonym)
 * Added a function for creating new cvtermprops ($cvterm->create_cvtermprops) 
 * Test suite can now deploy a Chado schema to a SQLite database
   if BCS_TEST_DSN is not defined. This means that smokers can
   now run these tests without setting up any databases.
        -- leto

0.05703

 * relaxed dependency on Carp 1.08

0.05702

 * that upload was a bit TOO clean, was missing the Build.PL!

0.05701

  * corrected a dirty cpan upload

0.05700

  * re-dumped with latest schema loader devel version
  * stripped _id suffixes for a number of relationships that still had
    them.  Hopefully the schema loader patch used for this will make
    it into schema loader releases.  List of changed relationship names:

     lib/Bio/Chado/Schema/CellLine/CellLine.pm
      cell_line_relationship_subject_ids -> cell_line_relationship_subjects
      cell_line_relationship_object_ids  -> cell_line_relationship_objects

     lib/Bio/Chado/Schema/Contact/Contact.pm
      contact_relationship_object_ids -> contact_relationship_objects
      contact_relationship_subject_ids -> contact_relationship_subjects

     lib/Bio/Chado/Schema/Cv/Cvterm.pm
      arraydesign_platformtype_ids -> arraydesign_platformtypes
      arraydesign_substratetype_ids -> arraydesign_substratetypes
      cvtermpath_type_ids -> cvtermpath_types
      cvtermpath_object_ids -> cvtermpath_objects
      cvtermpath_subject_ids -> cvtermpath_subjects
      cvtermprop_type_ids -> cvtermprop_types
      cvtermprop_cvterm_ids -> cvtermprop_cvterms
      cvterm_relationship_type_ids -> cvterm_relationship_types
      cvterm_relationship_object_ids -> cvterm_relationship_objects
      cvterm_relationship_subject_ids -> cvterm_relationship_subjects
      cvtermsynonym_type_ids -> cvtermsynonym_types
      cvtermsynonym_cvterm_ids -> cvtermsynonym_cvterms
      expression_cvterm_cvterm_ids -> expression_cvterm_cvterms
      expression_cvterm_cvterm_type_ids -> expression_cvterm_cvterm_types
      phenotype_assay_ids -> phenotype_assays
      phenotype_attr_ids -> phenotype_attrs
      phenotype_observable_ids -> phenotype_observables
      phenotype_cvalue_ids -> phenotype_cvalues
      protocolparam_unittype_ids -> protocolparam_unittypes
      protocolparam_datatype_ids -> protocolparam_datatypes

     lib/Bio/Chado/Schema/Genetic/Environment.pm
      phenotype_comparison_environment2_ids -> phenotype_comparison_environment2s
      phenotype_comparison_environment1_ids -> phenotype_comparison_environment1s

     lib/Bio/Chado/Schema/Genetic/Genotype.pm
      phenotype_comparison_genotype1_ids -> phenotype_comparison_genotype1s
      phenotype_comparison_genotype2_ids -> phenotype_comparison_genotype2s

     lib/Bio/Chado/Schema/Mage/Acquisition.pm
      acquisition_relationship_subject_ids -> acquisition_relationship_subjects
      acquisition_relationship_object_ids -> acquisition_relationship_objects

     lib/Bio/Chado/Schema/Mage/Biomaterial.pm
      biomaterial_relationship_subject_ids -> biomaterial_relationship_subjects
      biomaterial_relationship_object_ids -> biomaterial_relationship_objects

     lib/Bio/Chado/Schema/Mage/Element.pm
      element_relationship_object_ids -> element_relationship_objects
      element_relationship_subject_ids -> element_relationship_subjects

     lib/Bio/Chado/Schema/Mage/Elementresult.pm
      elementresult_relationship_subject_ids -> elementresult_relationship_subjects
      elementresult_relationship_object_ids -> elementresult_relationship_objects

     lib/Bio/Chado/Schema/Mage/Quantification.pm
      quantification_relationship_subject_ids -> quantification_relationship_subjects
      quantification_relationship_object_ids -> quantification_relationship_objects

     lib/Bio/Chado/Schema/Phenotype/Phenotype.pm
      phenotype_comparison_phenotype1_ids -> phenotype_comparison_phenotype1s
      phenotype_comparison_phenotype2_ids -> phenotype_comparison_phenotype2s

     lib/Bio/Chado/Schema/Phylogeny/Phylonode.pm
      phylonode_relationship_object_ids -> phylonode_relationship_objects
      phylonode_relationship_subject_ids -> phylonode_relationship_subjects

     lib/Bio/Chado/Schema/Pub/Pub.pm
      pub_relationship_object_ids -> pub_relationship_objects
      pub_relationship_subject_ids -> pub_relationship_subjects

     lib/Bio/Chado/Schema/Sequence/Feature.pm
      feature_genotype_feature_ids -> feature_genotype_features
      feature_genotype_chromosome_ids -> feature_genotype_chromosomes
      featureloc_feature_ids -> featureloc_features
      featureloc_srcfeature_ids -> featureloc_srcfeatures
      featurepos_feature_ids -> featurepos_features
      featurepos_map_feature_ids -> featurepos_map_features
      featurerange_leftendf_ids -> featurerange_leftendfs
      featurerange_rightstartf_ids -> featurerange_rightstartfs
      featurerange_rightendf_ids -> featurerange_rightendfs
      featurerange_leftstartf_ids -> featurerange_leftstartfs
      featurerange_feature_ids -> featurerange_features
      feature_relationship_subject_ids -> feature_relationship_subjects
      feature_relationship_object_ids -> feature_relationship_objects

     lib/Bio/Chado/Schema/Stock/Stock.pm
      stock_relationship_subject_ids -> stock_relationship_subjects
      stock_relationship_object_ids -> stock_relationship_objects

  * new create_with() function for creating new cvterms
  * more POD tweaking to improve CPAN indexing

0.05501

  * tweaked per-chado-module POD for better CPAN indexing

0.05500

  * much better POD, added autogenerated links from Schema.pm to
    per-chado-module POD files, and links to chado module pod files
    in Schema.pm
  * improved slide presentation to the version given at January 2010
    GMOD meeting

0.05001

  * test count bugfix

0.05000

  * Added DBICSL-generated POD
  * Turned off DBIC's cascade_delete and cascade_copy on all relations
    (thanks to Siddhartha Basu for troubleshooting).  Things break if
    these are on and you don't have every part of the schema installed.

0.04300

  * Corrected a rather dirty CPAN upload, Util.pod file was in the
    wrong place.

0.04200

  * removed Util.pm, replaced with Util.pod for documentation, moved
    the actual Util methods into a separate package inside Schema.pm.
    Thanks to Aure Bombarely.

0.04100

  * added missing dependency on BioPerl

0.04000

  * added new modules and relationships for the newly released
    cell_line module in Chado

0.03100

  * added $VERSION to Bio::Chado::Schema to support CPAN indexer,
    bumped version by several numbers to force CPAN reindexing

0.022

  * update to schema dumping script now finds many more inter-module
    relationships
  * added the new inter-module relationships found by the dumping
    script

0.01_03

  * changed namespace to Bio::Chado instead of Chado

0.01_01

  * Initial release.