Pybel

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Added
~~~~~
- Exposed transitivities parsed via nested statements through ``pybel.BELGraph.transitivities``
(https://github.com/pybel/pybel/issues/490).

Fixed
~~~~~
- Some dependencies updated their interfaces (https://github.com/pybel/pybel/pull/491)

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Added
~~~~~
- Support for direct regulations via ``pybel.constants.DIRECTLY_REGUALTES`` and
``pybel.BELGraph.add_directly_regulates``

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- Add support for named reactions (https://github.com/pybel/pybel/pull/485)
- Switch to GitHub Actions
- Use `PyStow <https://github.com/cthoyt/pystow>`_ for file management
- Use `Bioregistry <https://github.com/bioregistry/bioregistry>`_ for prefix normalization

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Added
~~~~~
- Support for homomultimers in ML triples export
- Graph dispatches allow quick access to PyBEL functionality (https://github.com/pybel/pybel/pull/449)
- Add "Streamable" BEL I/O (https://github.com/pybel/pybel/pull/451)
- ``pybel.to_triples`` allows direct export of ML-ready triples to a numpy ndarray.
- ``pybel.parse`` function allows for quick parsing of BEL strings
- Add JSON Schema for validating nodes and edges (https://github.com/pybel/pybel/pull/450) thanks aman527
- Add BEL Repository functionality, previously located in https://github.com/pybel/bel-repository
- Pickling can be done with gzip to greatly reduce size both on files (https://github.com/pybel/pybel/commit/d90578cb)
and on bytes (https://github.com/pybel/pybel/commit/fcc99952)

Changed
~~~~~~~
- PyBEL now supports Python 3.6+ only.
- ``pybel.to_tsv`` renamed to ``pybel.to_triples_file``
- The citation entry in PyBEL JSON datastructure now uses ``namespace``/``identifier``/``name`` instead
of ``db``/``db_id``. The corresponding constants ``pybel.constants.CITATION_DB``/``pybel.constants.CITATION_DB_ID``/
``pybel.constants.CITATION_DB_NAME`` have been removed (https://github.com/pybel/pybel/pull/453).
- The citation entry now relies on a subclass of ``pybel.language.Entity``, which means empty strings are
no longer allowed.
- The inconsistent usage of ``subject``/``source`` as well as ``object``/``target`` has been normalized everywhere.
This means the constants ``pybel.constants.SUBJECT``/``pybel.constants.OBJECT`` were removed and
new constants ``pybel.constants.SOURCE_MODIFIER``/``pybel.constants.TARGET_MODIFIER`` were added
(https://github.com/pybel/pybel/pull/453).
- Remove the BEL default namespace. All usages get normalized to controlled vocabularies (mostly GO) automatically
(https://github.com/pybel/pybel/pull/455).
- Improve namespace/annotation database insertion with Pandas (https://github.com/pybel/pybel/pull/454)
- Pickling now uses protocol 5 by default assisted by the ``pickle5`` backport on Python 3.6 (https://github.com/pybel/pybel/commit/679dcab7)
- Database now stores graphs in gzipped pickles (https://github.com/pybel/pybel/commit/9ee9bf21)
- Unspecified molecular activities now use the top-level GO term (https://github.com/pybel/pybel/commit/d56993e6)
- New annotation storage format using lists of annotations instead of dictionaries (https://github.com/pybel/pybel/pull/461)
- Citations now wrapped in dedicated data structure (https://github.com/pybel/pybel/pull/468)

Fixed
~~~~~
- Parser now correctly supports dashes and dots in namespaces as well as in names without quoting (https://github.com/pybel/pybel/pull/460)
- Bug in creating list abundances with name and list definition (https://github.com/pybel/pybel/pull/465)

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Added
~~~~~
- Importer from `EMMAA <https://emmaa.indra.bio>`_ (https://github.com/pybel/pybel/pull/432)
- I/O for Amazon S3 (https://github.com/pybel/pybel/pull/431)
- Improve TSV exporter (d7d12878, 74d51c1c, e1082523, 6ffc1df6)
- Add identifier-based entity remapper (ba8aa933)
- Add annotation grounding (https://github.com/pybel/pybel/pull/435, https://github.com/pybel/pybel/pull/443)
- Add HiPathia export examples (https://github.com/pybel/pybel/pull/422)

Changed
~~~~~~~
- Updated default BEL Commons instance from https://bel-commons.scai.fraunhofer.de to
https://bel-commons-dev.scai.fraunhofer.de
- Add more namespaces for JGIF parsing to support CBN and BioDati import (9f74122d and
https://github.com/pybel/pybel/pull/435; thanks djinnome)
- Make Jupyter notebook export accessible from top level at ``pybel.to_jupyter`` (4d76faad)

Fixed
~~~~~
- Fix bug in display of nice labels in Jupyter notebook (775bdc30)

Removed
~~~~~~~
- Remove default service URL for BEL Commons exporter. The Fraunhofer instance was taken
down (a9a540fb).

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Changed
~~~~~~~
- Updated GraphDati and BioDati exports (https://github.com/pybel/pybel/commit/c9f95344b72ff86239c8987d6b534000ba509a1f)
- Refactoring of ``pybel.struct.filters`` and ``pybel.struct.mutation`` - some imports might have to be updated

Added
~~~~~
- Importer from `Fraunhofer OrientDB <http://graphstore.scai.fraunhofer.de>`_ (https://github.com/pybel/pybel/pull/429)
- Exporter for `SPIA <https://bioconductor.org/packages/release/bioc/html/SPIA.html>`_ analytical tool (https://github.com/pybel/pybel/pull/430)