Pybel

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Added
~~~~~
- Added equivalentTo relation
- Added OWL annotation support
- Version integrity checking
- Dump cache functionality

Changed
~~~~~~~
- Merged GENE, GENE_VARIANT, and GENE_FUSION

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Changed
~~~~~~~
- Switch ontospy dependency to onto2nx for Windows support

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Added
~~~~~
- Add thorough testing of BEL document

Changed
~~~~~~~
- Improved string externalization
- Update to data model for fusions
- Improved parser performance

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Added
~~~~~
- Codec support for opening files by path

Changed
~~~~~~~
- Protein modifications, gene modifications, and variants are now stored as dictionaries in the latent data structure
- Many constants have been externalized
- BEL default names, like kinaseActivity are automatically assigned a sentinel value as a namespace

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Added
~~~~~
- Make HGVS parsing less complicated by storing as strings
- add warning tracking

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Added
~~~~~
- Gene modification support
- Namespace equivalence mapping data models and manager
- Extension loading

Changed
~~~~~~~
- Better testing (local files only with mocks)
- Better names for exceptions and warnings