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How to edit the LinkML schema in schema/*.yaml and why tvbo/datamodel/** is generated and must never be hand-edited.
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| name | linkml-schema |
| description | How to edit the LinkML schema in schema/*.yaml and why tvbo/datamodel/** is generated and must never be hand-edited. |
The TVBO datamodel is defined in LinkML YAML in schema/ and generated into Python types under tvbo/datamodel/.
schema/common.yaml, schema/SANDS.yaml, schema/openMINDS_tvbo/** — hand-written LinkML definitions.tvbo/datamodel/pydantic.py, tvbo/datamodel/schema.py — generated. Do not edit.pyproject.toml makes this explicit:
tool.ruff.extend-exclude includes tvbo/datamodel/**tool.ruff.lint.exclude includes tvbo/datamodel/**tool.mypy.exclude includes tvbo/datamodel/If your diff touches tvbo/datamodel/** and anything else, that is a bug — split the change.
schema/*.yaml.Makefile / CI).tvbo/datamodel/** in the same commit.Never patch the generated file directly — the next regeneration will silently revert it.
dependencies in pyproject.toml.SimulationExperiment, Dynamics, Network, etc. accept. Class implementations in tvbo/classes/ should match.