| 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. |
LinkML Schema
The TVBO datamodel is defined in LinkML YAML in schema/ and generated into Python types under tvbo/datamodel/.
What is canonical
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.
Editing the schema
- Edit the appropriate
schema/*.yaml.
- Regenerate the Python types via the LinkML pipeline (see
Makefile / CI).
- Commit both the schema change and the regenerated
tvbo/datamodel/** in the same commit.
Never patch the generated file directly — the next regeneration will silently revert it.
When in doubt
- LinkML 1.11+ is required. See
dependencies in pyproject.toml.
- The LinkML schema is the source of truth for what fields a
SimulationExperiment, Dynamics, Network, etc. accept. Class implementations in tvbo/classes/ should match.
