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@haeussma haeussma released this 02 Nov 16:01
v2.3.0
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PyEnzyme 2.3.0

Highlights

  • New documents are now written as EnzymeML 2.1.
  • Moved to md-models 0.3.0 / mdmodels 0.4.0.
  • Python 3.14 added to the test matrix.

Fixes

  • UniProt: fixed TrEMBL entry parsing, fetcher error chaining and id_mapping.
  • Composer: real fetcher errors are surfaced instead of being swallowed.
  • PDB fetcher accepts integer PubMed IDs.
  • SBML: model.xml is flushed before it is added to the OMEX archive.

Packaging

  • __version__ is now read via importlib.metadata.
  • pydantic declared as an explicit dependency; fastobo updated to 0.14.1.

Dev / CI

  • pre-commit hooks for ruff and uv-lock; adopted ruff 0.16 (pinned in CI).
  • Network-dependent tests marked remote; remote-tests workflow removed.
  • GitHub Actions bumped (checkout v7, setup-python v7, setup-uv v9).

Full Changelog: v2.2.2...v2.3.0

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