Changelog

1.1.1-beta

Bug fix:

  • opy.obo._extract_synonym used by opy.Uberon.map_by_name wasn’t stripping whitespace, so missed some mapped names.

1.1.0-beta

  • New functionality:

    • Obo() class:

      • Added opy.Obo.merge(): merge one ontology into another.

      • Added opy.Obo.from_dict(): create Obo() from a dictionary.

      • Added opy.Obo.copy(): copies Obo() object.

      • Separated load_obo from Obo() class.

      • Added local functions that are used to extract synonyms and synonym types from synonym strings.

    • new opy.uberon module, containing:

      • Uberon() class that inherits from Obo(), including sample_map_by_ont method.

      • uberon_from_obo function

    • new Relations.format_all method.

  • Refactoring:

    • Made the static class variables for reading ontologies private variables.

    • Refactored opy.relations.Relations class to subclass Pandas DataFrame.

  • Testing:

    • Added test for obo.Obo.merge().

    • Updated tests to include new behaviour for synonyms

  • Documentation:

    • Improved docstrings for Obo() class.

    • Set up sphinx autodoc and used to document Obo() class.

1.0.2-beta

  • Fixed GitHub action for versioned docs [#9]

1.0.1-beta

  • Got documentation on gh-pages [#2]

  • Wrote sphinx extension to be able to access versioned docs (not yet easy to navigate)

  • Removed TravisCI for testing, and added GitHub Actions for testing, deploying docs, and packaging [#1].

Ontolopy 1.0.0-beta

  • Renamed module to Ontolopy [#4]

  • Refactored Obo() and Relations() class.

  • Obo() now extends dict.

  • Added unit tests for ontolopy.validate_term() and ontolopy.read_line_obo().

  • Added basic contents for Sphinx documentation [#2], with PyData Sphinx theme.

uberon-py 0.1.0

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