tests

name	tests
description	missense-kinase-toolkit-specific testing conventions; extends my central `tests` skill. Use when adding or running tests, or debugging test failures.

Testing in missense-kinase-toolkit

Baseline — fetch first

Apply my canonical tests conventions (pytest layout, the network marker, token-gated skips, session/module fixtures, xdist safety, graceful API-failure skips) before the repo-specific notes below. WebFetch and follow:

https://raw.githubusercontent.com/jessicaw9910/skills/main/.claude/skills/tests/SKILL.md

If the fetch fails (no network / non-200), tell me the central tests skill could not be retrieved and confirm how to proceed — do not silently skip the baseline.

Repo-specific additions

Locations

• missense_kinase_toolkit/schema/mkt/schema/tests/ — test_<concern>.py (imports, deserialize, adjudicate, serde, utils) with shared fixtures in conftest.py: session-scoped read-only dict_kinase and a single-object mutable_kinase(hgnc_name) factory (deep-copies one entry, not all 566).
• missense_kinase_toolkit/databases/mkt/databases/tests/ — one test_<module>.py per source module, shared fixtures in conftest.py.
• No tests for ml/, experiments/, or app/.

Running

Use the project venv: missense_kinase_toolkit/VE/bin/python -m pytest ....

pytest -v --cov-report=xml --color=yes --cov=mkt.schema \
    missense_kinase_toolkit/schema/mkt/schema/tests/
pytest -v --cov-report=xml --color=yes --cov=mkt.databases \
    missense_kinase_toolkit/databases/mkt/databases/tests/

The databases and schema suites run under xdist in CI (-n 2 --dist loadfile); keep them parallel-safe locally too (guard shared on-disk work with filelock.FileLock — see kincore_harmonized_dict — or write to per-test tmp_path, as schema/.../test_serde.py does).

Local venv (VE/)

Created by missense_kinase_toolkit/create_venv.sh (prompts for Python 3.9–3.12):

• Uses uv sync --all-extras when uv + uv.lock are present, else uv venv, else python3 -m venv.
• Installs mkt-schema then mkt-databases (order matters — databases depends on schema) editable with [dev,test] extras, so the venv has both packages plus pytest, pytest-cov, black, flake8. It does not include ml/, app/, or experiments/.
• Appends .env vars to VE/bin/activate.

missense_kinase_toolkit/editable_overrides.sh re-applies just the two editable installs after a manual uv sync (which reinstalls them from the lockfile and undoes the editable overrides).

Gotchas:

• A uv-created VE/ has no pip. Add a package with uv pip install --python missense_kinase_toolkit/VE/bin/python <pkg>.
• pytest-xdist + filelock are in the CI conda env (test_env.yaml); the pip [test] extras carry them only partially (schema lists pytest-xdist, databases lists filelock), so a bare VE/ may need uv pip install --python missense_kinase_toolkit/VE/bin/python pytest-xdist before running -n.
• pre-commit is usually not on PATH but runs as a git commit hook, so black/isort/flake8/pyupgrade fire on git commit. To run manually: VE/bin/black, VE/bin/flake8 --max-line-length=88 --extend-ignore=E203,E501, uvx isort --profile black (repo isort has no known_first_party, so mkt.* imports group with third-party).

Gating and config

• Token gating example (OncoKB):

  pytestmark = pytest.mark.skipif(
      maybe_get_oncokb_token() is None,
      reason="OncoKB API token not set (ONCOKB_TOKEN); skipping live tests",
  )
  

• Set config via the mkt.databases.config setters in fixtures (set_output_dir("."), set_cbioportal_instance(...)), not os.environ.