linkml-schema

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.
metadata	{"audience":"maintainer","applies_to":["schema/**/*.yaml","tvbo/datamodel/**"],"tags":["schema","codegen","linkml"]}

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

1. Edit the appropriate schema/*.yaml.
2. Regenerate the Python types via the LinkML pipeline (see Makefile / CI).
3. 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.