linkml-schema
How to edit the LinkML schema in schema/*.yaml and why tvbo/datamodel/** is generated and must never be hand-edited.
Skill by virtual-twin
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What's inside
- Skill 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.
- License
- EUPL-1.2
- Metadata
- audience: maintainer
- Instructions
- 31 lines in SKILL.md · view on GitHub
Files (1)
- SKILL.md
SKILL.md (first lines)
# 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.
From virtual-twin/tvbo, EUPL-1.2.
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Signals
- Stars
- 5
- Forks
- 1
- Open issues
- 13
- Last commit (this folder)
- May 15, 2026 (5 months ago)
- Last release
- Jul 9, 2026 (3 months ago)
From GitHub (fetched Oct 24, 2026).
Details
- License
- EUPL-1.2
- Repository
- github.com/virtual-twin/tvbo
- Website
- tvbo.charite.de
- First seen
- Oct 24, 2026
- Last checked
- Oct 24, 2026
- Source
- GitHubgithub-graphql
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Cite this page
linkml-schema skill. Agent Mart. https://agentmart.dev/skills/virtual-twin-linkml-schema-122abf (last updated 2026-10-24)