P0: project setup (packaging, CI, licences, data/oracle scripts)

- pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE,
  THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf)
- CI workflow for Gitea/GitHub Actions: lint, type check, unit tests
- fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36"
  bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug
- make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs
- plan §17: corrected P0 dataset table
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kemal committed 2026-09-27 16:56:39 +01:00
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# Runs on Gitea Actions (reads .github/workflows) and GitHub Actions.
name: ci
on:
push:
pull_request:
jobs:
test:
runs-on: ubuntu-latest
strategy:
matrix:
python: ["3.12", "3.13"]
steps:
- uses: actions/checkout@v4
- uses: astral-sh/setup-uv@v5
with:
python-version: ${{ matrix.python }}
- name: Install
run: uv venv && uv pip install -e ".[dev]"
- name: Lint
run: uv run ruff check src tests && uv run ruff format --check src tests
- name: Type check
run: uv run mypy
- name: Unit tests (no downloaded data needed)
run: uv run pytest tests/unit -q