ci

name	ci
description	missense-kinase-toolkit-specific CI/CD layout; extends my central `ci` skill. Use when editing .github/workflows, adding a sub-package, changing the test env, or debugging CI failures.

missense-kinase-toolkit CI/CD

Baseline — fetch first

Apply my canonical ci conventions (path-filtered per-package workflows, micromamba env, OS/Python matrix, Codecov flags, pre-commit hook set) before the repo-specific notes below. WebFetch and follow:

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

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

Repo-specific additions

Workflows (.github/workflows/)

One workflow per setuptools sub-package, path-filtered (plus a weekly cron: "0 0 * * 0"):

• schema-ci.yaml — paths missense_kinase_toolkit/schema/**, coverage flag schema, installs only the schema package.
• databases-ci.yaml — paths missense_kinase_toolkit/databases/**, coverage flag databases, installs schema then databases (--no-deps, because databases depends on schema). Runs pytest with -n 2 --dist loadfile.

Both: matrix os: [macOS, ubuntu, windows] × python: ["3.10", "3.11"], mamba-org/setup-micromamba@v1 with environment-file: devtools/conda-envs/test_env.yaml, then Codecov upload with the per-package flags. There is no workflow for ml/, experiments/, or app/.

Adding / changing

• New runtime/test dependency → add it to devtools/conda-envs/test_env.yaml (CI installs the package with --no-deps, so deps must be in the env file).

Pre-commit

.pre-commit-config.yaml is scoped to ^missense_kinase_toolkit (excluding KinaseInfo/): black, isort (profile black), flake8 (max-line-length 88, ignore E203/E501), pyupgrade --py39-plus, plus whitespace/yaml hooks.