Pybel

---------------------------------------------------------------------------------
Added
~~~~~
- Added several IO functions and convenience functions (gzipped wrappers, etc.)

---------------------------------------------------------------------------------
Fixed
~~~~~
- Fixed autoflushing in manager

---------------------------------------------------------------------------------
Added
~~~~~
- Add metagraph for nested statements
- Add xrefs to DSL model
- Add OBO-style identifier parsing and export
- Add TSV exporter that does reasoning over edges (originally from BioKEEN)

Changed
~~~~~~~
- DSL format now stores all data in a 'concept' entry
- Try looking up namespace to identifiers mapping by default
- Changed name of pybel.to_bel_path to pybel.to_bel_script
- Used magic to combine ``to_*_file`` and ``to_*_path`` functions

---------------------------------------------------------------------------------
Added
~~~~~
- BELGraph class now has built-in summaries for authors and citations
- Added first Jupyter notebook into documentation. More to come!

Changed
~~~~~~~
- Authors are always stored as lists inside edges
- Nodes in node-link JSON always have the BEL string included
- Updated documentation for data model and DSL
- Enforce keyword argument usage in BELGraph.add_qualified_edge
- Use iterator in pybel.union so graphs can be lazily loaded and combine

Removed
~~~~~~~
- Remove remaining traces of namespace hierarchy table

Fixed
~~~~~
- Union function also takes union of locally defined annotations now
- Handling of special translocations (sec, surf; https://github.com/pybel/pybel/issues/377)
- Fixed public header in pybel.to_web
- Fixed public interface to pipeline and queries
- Fixed parsing of gene methylations/modifications

---------------------------------------------------------------------------------
Fixed
~~~~~
- Fix handling of node JSON with identifier but not name (https://github.com/pybel/pybel/issues/375)
- Fix handling of isolated nodes in `pybel.union` (https://github.com/pybel/pybel/issues/373)

---------------------------------------------------------------------------------
Added
~~~~~
- Add JSON to node and edge SQL models (https://github.com/pybel/pybel/pull/358)
- Add more properties to the Fragment class
- Node pruning command to CLI
- Type hints (https://github.com/pybel/pybel/issues/369)

Changed
~~~~~~~
- Use a declarative setup (https://github.com/pybel/pybel/issues/360)
- Pass flake8 (https://github.com/pybel/pybel/issues/363)
- Change handling of locally defined namespaces in parser
- Excise `pybel.resources` module to new package [`bel_resources`](https://github.com/cthoyt/bel-resources)

Fixed
~~~~~
- Add sha512 to JSON of edges' nodes when retrieving from the database
- Add nested sha512 identifiers when outputting node-link (https://github.com/pybel/pybel/issues/370)
- Fixed handling of invalid entities in the BEL parser (https://github.com/pybel/pybel/issues/368)
- Fixed merging of locally defined annotations when using `pybel.union` (https://github.com/pybel/pybel/issues/372)

Removed
~~~~~~~
- Dropped Python 2.7 support (https://github.com/pybel/pybel/issues/285)
- Dropped Python 3.4 support (https://github.com/pybel/pybel/issues/286)