Testing and CI

make test    # api (99 Python tests), ml, pipeline loader, web (49)
make lint    # ruff + mypy for the API, svelte-check for the front end

What is tested, and why there

Tests are concentrated where a mistake would be silent rather than loud.

api/tests/test_triage.py — the ranking arithmetic, as pure logic. This is the scientific claim the app makes, so it is tested without a database in the way. Includes the regression for components scoring evidence nobody looked up.
ml/tests/test_hpo.py — ontology propagation and information content, including a property test against a reference transitive closure. That test exists because a subtly wrong graph walk silently deleted 399 terms; see Gotchas.
pipeline/tests/test_load_db.py — the loader, against a real PostgreSQL. Idempotency is asserted directly: loading twice must not duplicate variants.
api/tests/test_security.py — the vcf_uri boundary.
api/tests/test_migrations.py — Alembic upgrade and downgrade against a live database.

Database tests use an embedded PostgreSQL (pgserver) locally and a service container in CI, because the schema is part of the behaviour and SQLite would not exercise it.

CI

Runs on pull requests and pushes to main:

Job	Does
api	ruff, mypy, pytest against a Postgres service
ml	pytest
web	`npm run check`, vitest, production build
pipeline	loader tests against Postgres, then `nextflow run main.nf -stub-run`
terraform	`fmt -check` and `validate`
images	builds and pushes to Artifact Registry, `main` only

CI authenticates to Google Cloud with Workload Identity Federation. There is no service account key in the repository or in repository secrets.

A caution

CI does not run on branch pushes, only on pull requests and main. Work on a long-lived branch is therefore unverified by CI until the PR is opened — run make test && make lint locally.

rarelens

Understanding it

Working on it

Running it

When it goes wrong