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althonos/pronto: 2.2.0

Martin Larralde; Alex Henrie; Spencer Mitchell; Tatsuya Sakaguchi

Added

  • threads parameter to Ontology constructor to control the number of threads used by parsers supporting multithreading (OBO and OBO JSON at the moment).
  • Deprecation warnings for suspected uses of the is_a pseudo-relationship since subclasses/superclasses is now to be handled by the owner Ontology.
  • Support for subclass/superclass edition directly from the objects returned by Term.subclasses() and Term.superclasses(). (#84) ### Changed
  • Updated fastobo to v0.8, which reduce memory footprint of identifiers, and improves the parser speed.
  • Improved OBO parser performance using threading plus zero-copy validation of identifiers on Xref instantiation.
  • Improved performance in debug mode by having the typechecker only extract the wrapped function signature once. ### Fixed
  • OBO parser crashing on files containing idspace clauses in their headers.
  • Reference management issue with binary operations of TermSet. ### Removed
  • nanoset depency, which was not useful anymore in Python 3.8 and caused issues with multithreading when processing OBO frames in parallel.

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