ci.yml

name: CI

on:
  push:
  pull_request:
  workflow_dispatch:
  schedule:
    - cron: "0 0 1 * *"

permissions:
  contents: read

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:
  lint:
    name: Ruff
    runs-on: ubuntu-latest
    timeout-minutes: 10
    steps:
      - name: Checkout
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.12.2"
          python-version: "3.14"
          enable-cache: true

      - name: Ruff
        run: uvx ruff@0.7.1 check

  documentation:
    name: Documentation
    runs-on: ubuntu-latest
    timeout-minutes: 15
    steps:
      - name: Checkout
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

      - name: Install uv and Python 3.14
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.12.2"
          python-version: "3.14"
          enable-cache: true
          cache-suffix: documentation

      - name: Install documentation dependencies
        run: uv sync --frozen --extra dev

      - name: Build documentation from clean sources
        run: uv run --frozen --no-sync sphinx-build -W --keep-going -E -a -d "${{ runner.temp }}/doctrees" -b html doc/source "${{ runner.temp }}/generated-docs"

      - name: Verify generated documentation is current
        run: diff -ru --exclude=.nojekyll "${{ runner.temp }}/generated-docs" docs

  test:
    name: Test (${{ matrix.os }}, Python ${{ matrix.python-version }})
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-2022, macos-15-intel, macos-15]
        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
    runs-on: ${{ matrix.os }}
    timeout-minutes: 30
    env:
      UV_PYTHON: ${{ matrix.python-version }}
    steps:
      - name: Checkout
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

      - name: Install uv and Python ${{ matrix.python-version }}
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.12.2"
          python-version: ${{ matrix.python-version }}
          enable-cache: true
          cache-suffix: ${{ matrix.os }}-${{ matrix.python-version }}

      - name: Install core test dependencies
        run: uv sync --frozen --extra dev

      - name: Run the canonical core suite
        run: uv run --frozen --no-sync python tests/test.py

      - name: Install optional dependencies
        run: uv sync --frozen --all-extras

      - name: Run the optional BGEN suite
        run: uv run --frozen --no-sync pytest pysnptools/distreader/test_bgen2.py

  build:
    name: Build distributions
    runs-on: ubuntu-latest
    timeout-minutes: 10
    steps:
      - name: Checkout
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

      - name: Install uv
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.12.2"
          python-version: "3.14"
          enable-cache: true

      - name: Build wheel and source distribution
        run: uv build --no-sources

      - name: Build wheel from the source distribution
        run: uv build --wheel --no-sources --out-dir sdist-dist dist/*.tar.gz

      - name: Compare direct and sdist-derived wheels
        shell: bash
        run: cmp dist/*.whl sdist-dist/*.whl

      - name: Upload distributions
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
        with:
          name: distributions
          path: |
            dist/*.whl
            dist/*.tar.gz
          if-no-files-found: error
          retention-days: 7

  artifact-test:
    name: Artifact test (${{ matrix.kind }}, Python ${{ matrix.python-version }})
    needs: build
    runs-on: ubuntu-latest
    timeout-minutes: 15
    strategy:
      fail-fast: false
      matrix:
        include:
          - kind: wheel
            python-version: "3.10"
            package: dist/*.whl
          - kind: sdist
            python-version: "3.10"
            package: dist/*.tar.gz
          - kind: wheel
            python-version: "3.14"
            package: dist/*.whl
          - kind: sdist
            python-version: "3.14"
            package: dist/*.tar.gz
    steps:
      - name: Install uv and Python ${{ matrix.python-version }}
        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
        with:
          version: "0.12.2"
          python-version: ${{ matrix.python-version }}
          no-project: true
          enable-cache: false

      - name: Download distributions
        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
        with:
          name: distributions
          path: dist

      - name: Create clean environment
        run: uv venv --python ${{ matrix.python-version }} .artifact-venv

      - name: Install exact ${{ matrix.kind }} artifact
        run: uv pip install --python .artifact-venv/bin/python ${{ matrix.package }}

      - name: Smoke-test installed package
        run: >-
          .artifact-venv/bin/python -c
          "from importlib.resources import files;
          import numpy as np;
          import pysnptools;
          from pysnptools.snpreader import SnpData;
          data = SnpData(iid=[['a','a'],['b','b']], sid=['s1','s2'], val=np.array([[0.0,1.0],[2.0,1.0]]));
          assert data.standardize().read().val.shape == (2,2);
          manifests = ['pysnptools.hashdown.json','bgen.hashdown.json','synth.hashdown.json'];
          assert all(files('pysnptools.util').joinpath(name).is_file() for name in manifests);
          assert '.artifact-venv' in pysnptools.__file__;
          print(pysnptools.__file__)"