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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

IndexedEUPL-1.2★ 5
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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.

Use cases: writing

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What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

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  • codeload.github.com · found in install command

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  • ~/.claude/skills/linkml-schema

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
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.

More from virtual-twin/tvbo

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

Same skill elsewhere

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Cite this page

linkml-schema skill. Agent Mart. https://agentmart.dev/skills/virtual-twin-linkml-schema (last updated 2026-10-24)