Pybel Versions Save

What's Changed

• Update citation enrichment functions by @cthoyt in https://github.com/pybel/pybel/pull/495
• Rearrange extra dependencies for grounding
• Use more modern project layout
• Add py310 by @cthoyt in https://github.com/pybel/pybel/pull/497

Full Changelog: https://github.com/pybel/pybel/compare/v0.15.4...v0.15.5

• Update dependencies on PyOBO and the Bioregistry
• Update README for Harvard funding!

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)

Added

• Add support for directly regulates relationships

Added

• Add support for named reactions (https://github.com/pybel/pybel/pull/485)

Changed

• Switch to GitHub Actions
• Use PyStow for file management
• Use Bioregistry for prefix normalization

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)

Added

• Importer from EMMAA (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).

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 (https://github.com/pybel/pybel/pull/429)
• Exporter for SPIA analytical tool (https://github.com/pybel/pybel/pull/430)

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)

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)