v0.15.5

What's Changed

• Update citation enrichment functions by @cthoyt in #495
• Rearrange extra dependencies for grounding
• Use more modern project layout
• Add py310 by @cthoyt in #497

Full Changelog: v0.15.4...v0.15.5

v0.15.4

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

v0.15.3

Added

• Exposed transitivities parsed via nested statements through pybel.BELGraph.transitivities (#490).

Fixed

• Some dependencies updated their interfaces (#491)

v0.15.2

Added

• Add support for directly regulates relationships

v0.15.1

Added

• Add support for named reactions (#485)

Changed

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

v0.15.0

Added

• Support for homomultimers in ML triples export
• Graph dispatches allow quick access to PyBEL functionality (#449)
• Add "Streamable" BEL I/O (#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 (#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 (d90578cb)
  and on bytes (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 (#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
  (#453).
• Remove the BEL default namespace. All usages get normalized to controlled vocabularies (mostly GO) automatically
  (#455).
• Improve namespace/annotation database insertion with Pandas (#454)
• Pickling now uses protocol 5 by default assisted by the pickle5 backport on Python 3.6 (679dcab7)
• Database now stores graphs in gzipped pickles (9ee9bf21)
• Unspecified molecular activities now use the top-level GO term (d56993e6)
• New annotation storage format using lists of annotations instead of dictionaries (#461)
• Citations now wrapped in dedicated data structure (#468)

Fixed

• Parser now correctly supports dashes and dots in namespaces as well as in names without quoting (#460)
• Bug in creating list abundances with name and list definition (#465)

v0.14.10

Added

• Importer from EMMAA (#432)
• I/O for Amazon S3 (#431)
• Improve TSV exporter (d7d1287, 74d51c1, e108252, 6ffc1df)
• Add identifier-based entity remapper (ba8aa93)
• Add annotation grounding (#435, #443)
• Add HiPathia export examples (#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 (9f74122 and
  #435; thanks @djinnome)
• Make Jupyter notebook export accessible from top level at pybel.to_jupyter (4d76faa)

Fixed

• Fix bug in display of nice labels in Jupyter notebook (775bdc3)

Removed

• Remove default service URL for BEL Commons exporter. The Fraunhofer instance was taken
  down (a9a540f).

v0.14.9

Changed

• Updated GraphDati and BioDati exports (c9f9534)
• Refactoring of pybel.struct.filters and pybel.struct.mutation - some imports might have to be updated

Added

• Importer from Fraunhofer OrientDB (#429)
• Exporter for SPIA analytical tool (#430)

v0.14.8

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() (#425)
• Content importer from BioDati with pybel.from_biodati() (#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. (#426)

v0.14.7

Added

• Support for transcription factor relationships in TSV (machine learning) output

Fixed

• Fixed incorrect parsing of OBO-style identifiers (#421)
• Make sure pop() works in translocations (#421)
• None and non-empty string checks in DSL (3156d51)
• Fixed Jupyter export (the interface changed in Jinja2; d6e7e61)