Precommit Checks

Run all quality checks on the mycelium codebase. Auto-fix issues where possible.

Steps

1. Lint + format — Fix lint and format issues automatically:

   cd fastapi-backend && uv run ruff check --fix . && uv run ruff format .
   cd mycelium-cli && uv run ruff check --fix . && uv run ruff format .
   

2. Type check (ty) — Both backend and CLI must come back clean. CI gates on this:

   cd fastapi-backend && uv run ty check .
   cd mycelium-cli && uv run ty check .
   

   Generated client (mycelium-cli/src/mycelium_backend_client/) is excluded via [tool.ty.src] since openapi-python-client templates produce diagnostics we can't fix without forking the generator. New diagnostics outside that path must be resolved before commit — don't paper over with # ty: ignore unless the underlying issue is a typeshed/library bug (CORSMiddleware add_middleware is the canonical example).

   Stale client signal: if ty reports unknown-argument or unresolved-attribute on a type imported from mycelium_backend_client, the generated client is out of date — skip to step 6 and regenerate before re-running ty.

3. Backend tests — Run pytest:

   cd fastapi-backend && uv run pytest tests/ -x -q
   

4. Frontend — Type-check, test, and build. All three: tsc and next build between them prove the app compiles, not that it behaves, and the component suite is where the interaction bugs actually get caught.

   cd mycelium-frontend && npx tsc --noEmit && npx vitest run && npx next build
   

   npm run lint is tsc --noEmit — there's no separate ESLint pass. The suite should come back fully green; a failure that looks environmental (missing DOM API, a global the runtime shapes differently) belongs in vitest.setup.ts as a guarded stub next to the others, not left failing for the next person to rediscover.

5. CLI docs — If any CLI command files were changed (mycelium-cli/src/mycelium/commands/):

   • Ensure new commands have @doc_ref decorators
   • Run /generate-cli-docs to regenerate the HTML CLI reference
   • If markdown source files changed (mycelium-cli/src/mycelium/docs/**/*.md), also run cd mycelium-cli && uv run python ../docs/generate_docs.py to regenerate the docs site (docs/index.html, docs/adapters.html, docs/reference.html, plus docs/search-index.js and docs/llms-full.txt). --page <start|adapters|reference> limits what gets written; every page is still assembled, because the persistent nav and the search index span the whole site. The script reads <!-- keep -->-marked hand-coded sections from the existing HTML — don't delete those files between edits.

6. Generated OpenAPI clients — Two clients are vendored from live OpenAPI specs. CI gates on the mycelium one being current; the CFN one is regenerated by hand when we bump the image.

   Mycelium backend → CLI client. If any backend schemas or routes changed (fastapi-backend/app/schemas.py, fastapi-backend/app/routes/), regenerate. If openapi.json is already current (i.e. you ran snapshot-openapi.sh or the spec wasn't updated), no backend is needed:

   SPEC_FILE=openapi.json ./scripts/gen-mycelium-client.sh
   

   If the spec itself needs refreshing from a live backend first:

   docker compose -f mycelium-cli/src/mycelium/docker/compose.yml up -d mycelium-backend
   ./scripts/gen-mycelium-client.sh
   

   Writes to mycelium-client/mycelium_backend_client/ and mycelium-cli/src/mycelium_backend_client/. CI fails if the committed copy drifts from live /openapi.json.

   CFN client. app/services/cfn_negotiation.py uses the generated typed ioc_cfn_svc_api_client (from fastapi-backend/cfn_swagger.json). If the CFN image was bumped in mycelium-cli/src/mycelium/docker/compose.yml, refresh + regenerate: CFN_URL=http://localhost:9002 ./scripts/gen-cfn-client.sh (or point at the ioc-cfn-svc repo's docs/swagger.json), then cd fastapi-backend && uv run ty check .. Type errors at call sites mean the CFN contract changed. The typecheck IS the contract test. (cfn_knowledge.py stays on httpx by design: json.RawMessage payload + graph endpoints absent from swagger.)

7. Docs consistency — If any user-facing behavior changed (commands renamed, new features, API changes), grep for stale references and fix them in:

   • docs/index.html (Guide), docs/adapters.html, docs/reference.html — main docs site (3 pages, generated), plus docs/search-index.js
   • docs/mycelium-dataflow.html — scrolly presentation deck
   • docs/demo-script.md — live demo script
   • README.md — quickstart and overview
   • mycelium-cli/src/mycelium/docs/ — built-in CLI docs
   • Adapter skills (mycelium-cli/src/mycelium/integrations/*/assets/skills/)

8. Doctor sanity check — If any file under mycelium-cli/src/mycelium/commands/doctor.py, mycelium-cli/src/mycelium/commands/adapter.py, or an adapter's shipped assets (mycelium-cli/src/mycelium/integrations/claude_code/assets/, .../cursor/assets/) was changed, run mycelium doctor to verify every check still passes against the current install:

   mycelium doctor
   

   All checks should be green (✓). If any come back as warnings (~) or errors (✗), act on them before committing — doctor is the fastest way to catch adapter-install regressions (stale manifests, drift between installed vs packaged plugin, channel config issues).

   If you added new failure modes that doctor should catch, add a new check function to doctor.py following the _check_*() -> CheckResult pattern and register it in _run_all_checks(). Doctor is the user's first debugging tool — new silent-failure classes should land here alongside their fix.

9. Report — Summarize what was fixed and any remaining issues.