Ship the LinkML source with the package

[jdkent]

The LinkML YAML sat at the repo root, outside the package, so a consumer that depends on study_schema could reach it only through a git export. Neurostore's tests did exactly that, with a gitignored git archive of the pinned commit. This is the fourth of the PRs for neurostore's review app.

What changes

• The LinkML moves. The schemas, their module directories and extraction-evidence.yaml move to src/study_schema/linkml/, shipped as package data. Git shows them as renames.
  • extraction-deviations.yaml and extraction-to-storage.map.yaml move with them, because pondie checks the projection against them.
  • storage-parameter-priorities.yaml is triage data and stays at the root; the README says it isn't packaged.
• Path constants. study_schema.linkml.EXTRACTION, STORAGE and PAPER_PARSE are pathlib.Paths of the three schemas. Relative imports resolve inside the packaged tree.
• The generator. tools/generate_models.py reads the schemas through that module. Generated output is unchanged (--check).
• Docs. The README states the location once, and the docs' links are updated.

Needs a change in pondie: python3 -m pondie.schema.generate writes these files to the repo root. It must write into src/study_schema/linkml/ instead, or regenerating will leave stale copies at the root.

Tests

• tests/test_linkml.py checks that every constant points at a packaged schema, and that every relative import resolves inside the packaged tree.
• It also builds a wheel with setuptools.build_meta and checks every YAML file is in it, the two moved contract files by name. CI's pip install provides setuptools, so this test runs there.
• With linkml 1.12: pytest tests passes (125 passed, 2 skipped where setuptools or pyarrow is missing locally), and generate_models.py --check passes.

🤖 Generated with Claude Code