tests.yml

name: Tests and Linting

on:
  workflow_dispatch:
  pull_request:
  push:
    branches: [master]

jobs:
  linting:
    name: Linting
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
        with:
          # requites to grab the history of the PR
          fetch-depth: 0
      - uses: actions/setup-python@v4
      - uses: pre-commit/action@v3.0.0
        with:
          extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}

  pytest:
    name: Pytest
    runs-on: ubuntu-latest
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.7", "3.8", "3.9"]
    steps:
      - uses: actions/checkout@v2

      - name: Cache downloaded resources
        uses: actions/cache@v3
        with:
          path: ~/.data/
          key: resources

      # - name: Cache pip
      #   uses: actions/cache@v3
      #   with:
      #     path: ~/.cache/pip
      #     key: ${{ runner.os }}-python-${{ matrix.python-version }}-pip

      - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
        shell: bash

      - uses: hynek/setup-cached-uv@v1
        with:
          cache-suffix: -tests-${{ matrix.python-version }}-${{ env.WEEK }}

      - name: Set up Java
        uses: actions/setup-java@v2
        with:
          distribution: "temurin" # See 'Supported distributions' for available options
          java-version: "8"

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install dependencies
        run: |
          uv venv
          pip install poetry
          source .venv/bin/activate
          uv pip install -e '.[dev,setup]' pytest-xdist pip

      - name: Test with Pytest on Python ${{ matrix.python-version }}
        env:
          UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
        run: |
          source .venv/bin/activate
          coverage run -m pytest --ignore tests/test_docs.py # -n auto
          # coverage combine
          # mv .coverage .coverage.${{ matrix.python-version }}
        if: matrix.python-version != '3.9'

      - name: Test with Pytest on Python ${{ matrix.python-version }}
        env:
          UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
        run: |
          source .venv/bin/activate
          coverage run -m pytest # -n auto
          # coverage combine
          # mv .coverage .coverage.${{ matrix.python-version }}
        if: matrix.python-version == '3.9'

      - name: Upload coverage data
        uses: actions/upload-artifact@v4
        with:
          name: coverage-data-${{ matrix.python-version }}
          path: .coverage.*
          if-no-files-found: ignore

  coverage:
    name: Coverage
    needs: pytest
    uses: aphp/foldedtensor/.github/workflows/coverage.yml@main
    with:
      base-branch: master
      coverage-data-pattern: coverage-data-*
      coverage-report: coverage.txt
      coverage-badge: coverage.svg
      coverage-branch: coverage

  documentation:
    name: Documentation
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2

    - uses: actions/setup-python@v4
      with:
        python-version: "3.9"
        # cache: 'pip'

    - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
      shell: bash

    - uses: hynek/setup-cached-uv@v1
      with:
        cache-suffix: -docs-${{ matrix.python-version }}-${{ env.WEEK }}

    - name: Install dependencies
      run: |
        uv venv
        uv pip install '.[dev]'

    - name: Build documentation
      run: |
        source .venv/bin/activate
        mkdocs build --clean

  simple-installation:
    name: Simple installation
    runs-on: ubuntu-latest
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.7", "3.8", "3.9"]
    steps:
      - uses: actions/checkout@v2

      - uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python-version }}

      - run: echo WEEK=$(date +%V) >>$GITHUB_ENV
        shell: bash

      - uses: hynek/setup-cached-uv@v1
        with:
          cache-suffix: -simple-install-${{ matrix.python-version }}-${{ env.WEEK }}

      - name: Install library
        run: |
          uv venv
          uv pip install .