Pybel

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Added
~~~~~
- Bytes IO of BEL Graphs
- Graph caching and Graph Cache Manager

Fixed
~~~~~
- Annotations weren't getting cached because *somebody* forgot to add the urls. Fixed.
- Removed typos in default namespace list

Changed
~~~~~~~
- More explicit tests and overall test case refactoring
- Better handling of BEL script metadata

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Added
~~~~~
- OWL namespace support and caching
- Full support for BEL canonicalization and output

Fixed
~~~~~
- Rewrote namespace cache and SQLAlchemy models

Removed
~~~~~~~
- Removed unnecessary pandas and matplotlib dependencies

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Added
~~~~~
- Canonical BEL terms added to nodes on parsing
- Fragment parsing
- Support for alternative names for evidence (SupportingText)
- More explicit support of unqualified edges
- Created top-level constants file

Fixed
~~~~~
- Fix incorrect HGVS protein truncation parsing
- Fix missing location option in abundance tag parsing
- Fix json input/output

Removed
~~~~~~~
- Deleted junk code from mapper and namespace cache manager

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Added
~~~~~
- Nested statement parsing support
- Fusion parsing support

Fixed
~~~~~
- Fixed graphml input/output
- Changed encodings of python files to utf-8
- Fixed typos in language.py

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Added
~~~~~
- Neo4J CLI output
- Edge and node filtering
- Assertions of document metadata key
- Added BEL 2.0 protein modification default mapping support

Changed
~~~~~~~
- Rewrite HGVS parsing
- Updated canonicalization

Fixed
~~~~~
- Typo in amino acid dictionary
- Assertion of citation

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Changed
~~~~~~~
- Made logging lazy and updated logging codes
- Update rewriting of old statements
- Explicitly streamlined MatchFirst statements; huge speed improvements