القائمة
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. |
| metadata | {"audience":"maintainer","applies_to":["schema/**/*.yaml","tvbo/datamodel/**"],"tags":["schema","codegen","linkml"]} |
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.How TVBO's code generation works — template engines, backend dispatch in tvbo/codegen/, and the contract for adding a new backend.
How TVBO's code generation works — template engines, backend dispatch in tvbo/codegen/, and the contract for adding a new backend.
Ruthless editor who detects and destroys AI-generated slop — the hollow filler phrases, fake enthusiasm, recycled structures, and performative depth that make text instantly recognizable as machine-written. Rewrites content to sound like a human with something to say.
How to run a SimulationExperiment in TVBO — choosing a backend, calling run/plot, and what each optional extra (jax, tvb, pyrates, julia) provides.
How to write Python docstrings in TVBO so that quartodoc renders them correctly in the API site. Google style, markdown body, type info on signature (not in the docstring).
How to specify a Dynamics in TVBO — the YAML and Python forms, parameter / state-variable / equation conventions, and common pitfalls.