Pybel

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Added
~~~~~
- Serialization functions can be accessed directly from the BELGraph class (https://github.com/pybel/pybel/pull/344)
- Added several useful node filter functions (Thanks ddomingof; https://github.com/pybel/pybel/pull/347)
- Add a function for removing extraneous citation metadata

Changed
~~~~~~~
- pybel.struct.graph.BELgraph.summarize() now prints the number of warnings, even if it is zero

Fixed
~~~~~
- Platform specificity for requirements in setup.py (Thanks scolby33; https://github.com/pybel/pybel/pull/346)
- Print statement problem (Thanks smoe; https://github.com/pybel/pybel/pull/351)
- Import paths for INDRA (Thanks bgyori; https://github.com/pybel/pybel/pull/339
- Improvements on flake8 status (Thanks tehw0lf; https://github.com/pybel/pybel/pull/353)
- Ensure complexes have at least one member (Thanks 10mubeen for pointing this out)
- Make "Other" as the default namespace domain for generating BEL namespace files

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Fixed
~~~~~
- Wrong names in CLI
- Add missing star import for pybel.dsl.ListAbundance

Changed
~~~~~~~
- Update iteration over BEL files to read in one pass

Added
~~~~~
- More summary functions in pybel.struct

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Changed
~~~~~~~
- Update edge hashing algorithm (this invalidates old hashes)
- Edge hashes are now used as keys instead of being put inside edge data dictionaries
- Improved graph operations with new location of edge hashes
- Update Node/Link JSON schema
- Improve __contains__ and has_node functions to handle DSL objects
- Require usage of DSL when creating BELGraph instances
- Use DSL completely in ORM
- Add SHA512 to authors to avoid issues with MySQL's collation

Removed
~~~~~~~
- Remove ``pybel.tokens.node_to_tuple`` function and ``pybel.tokens.node_to_bel`` functions
- All tuple-related functions in the DSL (AKA the tupleectomy)

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Added
~~~~~
- Automatic generation of CLI documentation with ``sphinx-click``
- Several edge creation convenience functions to the ``BELGraph``
- Graph summary functions

Changed
~~~~~~~
- Improve Drop networks (Thanks scolby33) (https://github.com/pybel/pybel/pull/319)
- Huge improvements to documentation and code style reccomended by flake8

Fixed
~~~~~
- Fixed handling of tuples (64d0685)

Removed
~~~~~~~
- Remove function ``BELGraph.iter_data``

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Added
~~~~~
- Several subgraph functions (https://github.com/pybel/pybel/pull/315)

Changed
~~~~~~~
- Better SQL implementation of get_recent_networks (https://github.com/pybel/pybel/pull/312)

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Removed
~~~~~~~
- Removed CX and NDEx IO in favor of https://github.com/pybel/pybel-cx

Changed
~~~~~~~
- Better (less annoying) logging for deprecated transformations
- Turn off SQL echoing by default
- Update getting annotation entries
- Better options for using TQDM while parsing

Added
~~~~~
- Flag to INDRA machine to run locally
- Add require annotations option to parser (https://github.com/pybel/pybel/issues/255)
- Data missing key node predicate builder