Pybel

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Changed
~~~~~~~
- ``pybel.post_graphdati()`` has been renamed to ``pybel.to_biodati()``
- ``pybel.to_web()`` has been renamed to ``pybel.to_bel_commons()``
- ``pybel.from_web()`` has been renamed to ``pybel.from_bel_commons()``

Added
~~~~~
- Content importers from GraphDati format with ``pybel.from_graphdati()`` and ``pybel.from_graphdati()``
and enable usage of respective extensions ``*.bel.graphdati.json`` and ``*.bel.graphdati.json.gz`` with
``pybel.load()`` (https://github.com/pybel/pybel/pull/425)
- Content importer from BioDati with ``pybel.from_biodati()`` (https://github.com/pybel/pybel/pull/425)
- Add direct function for loading CBN files (so you don't have to load the JSON first) with
``pybel.from_cbn_jgif_file()``
- Added ``pybel.grounding.ground()`` function that uses the unlisted Python 3.7+ dependency, ``pyobo
to ground/normalize entities in a given BEL graph. This also takes care of upgrading legacy namespace
names and mapping SCOMP/SFAM via FamPlex. (https://github.com/pybel/pybel/pull/426)

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Added
~~~~~
- Support for transcription factor relationships in TSV (machine learning) output

Fixed
~~~~~
- Fixed incorrect parsing of OBO-style identifiers (https://github.com/pybel/pybel/pull/421)
- Make sure pop() works in translocations (https://github.com/pybel/pybel/pull/421)
- None and non-empty string checks in DSL (3156d519)
- Fixed Jupyter export (the interface changed in Jinja2; d6e7e619)

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Added
~~~~~
- Add PyKEEN import hooks, so you can automatically load up a BEL file for machine learning with
`PyKEEN <https://pykeen.readthedocs.io>`_.
- Update TSV exporter for better ML-ready triples for PyKEEN
- Added INDRA I/O options and `pybel.from_bel_script_gz` option
- Add HiPathia Exporter (https://github.com/pybel/pybel/pull/414)
- Add PyNPA Exporter (https://github.com/pybel/pybel/pull/413)
- Add universal I/O functions `pybel.load` and `pybel.dump` (https://github.com/pybel/pybel/pull/417)

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Added
~~~~~
- Gzip variant of umbrella nodelink exporter
- More entry points for exporting

Fixed
~~~~~
- OBO-style export was broken if name and identifier weren't available. This works with whatever is available now
- If CURIE is requested and both identifier and name are available, defaults to identifier.

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Added
~~~~~
- Added support for BEP-0005
- Added BEP-0001 support (population abundance; https://github.com/pybel/pybel/issues/402)
- Added BEP-0003 support (noCorrelation relation; https://github.com/pybel/pybel/issues/403)
- Added BEP-0012 support (correlation relation; https://github.com/pybel/pybel/issues/403)
- Added BEP-0011 support (binds relation; https://github.com/pybel/pybel/issues/403)
- Add GraphDati exporter and BioDati uploader (https://github.com/pybel/pybel/issues/407)
- Add Hetionet importer (https://github.com/pybel/pybel/issues/406)
- Add several more I/O functions (``pybel.to_bel_script_gz``, etc.)

Removed
~~~~~~~
- Removed support for ``label`` relation
- Removed support for node attributes and description

Updated
~~~~~~~
- Updated programmatic citation handling. Now a tuple of strings (database, identifier) can
be passed anywhere a citation is needed.

Fixed
~~~~~
- Fixed output of BEP-0008 (OBO-style identifiers)
- Fixed convenience functions for ``BELGraph.add_inhibits`` and ``BELGraph.add_activates`` (there was a typo
and it was adding the opposite relation in both)
- Fixed that graph edge adder functions don't add two-way edges (https://github.com/pybel/pybel/issues/409)

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Added
~~~~~
- Umbrella node-link JSON exporter(https://github.com/pybel/pybel/pull/400)
- GraphML exporter with umbrella nodes (https://github.com/pybel/pybel/pull/400)