Usage

This page describes the day-to-day command-line workflow for biosim-schema: generating schema outputs, rebuilding LinkML docs, and running verification checks that mirror CI.

Common generation workflow

Generate derived artefacts used by downstream tools:

biosim-schema-generate derived

Generate LinkML markdown documentation in docs/source/linkml:

biosim-schema-generate docs

Generate full project outputs (LinkML project artefacts, derived files, docs):

biosim-schema-generate all

Verify generated artefacts are up to date (used in CI):

biosim-schema-generate verify

If LinkML docs are committed and should also be checked:

biosim-schema-generate verify --include-docs

Command reference

Available subcommands:

  • project: generate full LinkML project artefacts

  • jsonld: generate JSON-LD output only

  • derived: generate webform fields, engine mappings, and summary files

  • docs: generate LinkML markdown docs

  • all: run project, derived, and docs generation

  • verify: regenerate and fail if tracked generated files differ

Validate example data

Schema validation is primarily exercised through tests. For ad hoc validation:

linkml-validate -s biosim_schema/schema/biosim_schema.yaml tests/test_validation/valid_data/test.json