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Move to md-models 0.3.0 and mdmodels 0.4.0 - #105
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- Require mdmodels >=0.4.0,<0.5 (mdmodels-core 0.3). - Point the specs submodule at enzymeml-specifications#34 (relaxed version pattern, vessel_id no longer mapped to schema:identifier). - Regenerate pyenzyme/versions/v2.py with `md-models convert -t python-pydantic -O astropy`. - New documents now say "version": "2.0" (the spec default); update the composer fixtures. Existing "2" documents still load. - SBML annotations now carry every mapped field, so the PEtab reference model is regenerated. rdflib gives the new blank nodes random IDs and order, so the test ignores both. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Follow enzymeml-specifications#34, which bumps the document version default to 2.1. Existing "2" and "2.0" documents still load unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Moves PyEnzyme to
mdmodels0.4.0 (mdmodels-core 0.3) and regenerates the v2 model with md-models 0.3.0.Depends on EnzymeML/enzymeml-specifications#34. The
specssubmodule points at that PR's commit (9775809). If EnzymeML/enzymeml-specifications#34 is squash- or rebase-merged, update the submodule to the merged commit before merging this.Changes
mdmodels>=0.4.0,<0.5, plusuv.lock.pyenzyme/versions/v2.pyregenerated withmd-models convert -t python-pydantic -O astropy."version": "2.1", the new spec default from EnzymeML 2.1: accept major-only versions, stop mapping vessel_id to schema:identifier enzymeml-specifications#34. Older md-models wrote"2". Existing"2"and"2.0"documents still load and keep their version, because EnzymeML 2.1: accept major-only versions, stop mapping vessel_id to schema:identifier enzymeml-specifications#34 relaxes the pattern md-models now enforces. The composer fixtures are updated to"2.1".constant, references), so the reference model is regenerated. rdflib gives the new blank nodes random IDs and writes them in random order, so the comparison ignores both.What changes for users (from md-models 0.3.0)
Patternconstraints, so values that never matched the spec are rejected on load.@lists;Identifierfields are literals;@id,@typeand@contextare read back from documents.Tested
uv run pytest: 121 passed, including the network tests; three runs in a row are stable."version": "2"files intests/andexamples/load.pyenzyme/andtests/passes.Not included: the fetcher changes from #104.
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