tests.yml

name: Tests and Linting

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

env:
  # UV_INDEX_STRATEGY: "unsafe-first-match"
  # UV_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"
  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"

jobs:
  linting:
    name: Linting
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-22.04
    steps:
      - uses: actions/checkout@v3
        with:
          # requites to grab the history of the PR
          fetch-depth: 0

      - uses: actions/setup-python@v4
        with:
          cache: 'pip'

      - 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-22.04
    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 }}
          cache: 'pip'

      - name: Install dependencies
        run: |
          pip install poetry
          pip install -e '.[dev,setup]' pytest-xdist pip
#          uv venv
#          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: ${{ secrets.UMLS_API_KEY }}
        run: |
          coverage run -m pytest --ignore tests/test_docs.py # -n auto
          # coverage combine
          # mv .coverage .coverage.${{ matrix.python-version }}
#          source .venv/bin/activate
        if: matrix.python-version != '3.9'

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

  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-22.04
    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: |
        pip install '.[docs]'
#        uv venv
#        uv pip install '.[docs]'


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

  simple-installation:
    name: Simple installation
    runs-on: ubuntu-22.04
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
    steps:
      - uses: actions/checkout@v2

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

      - 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: |
          pip install ".[ml]" pytest
          pytest tests/pipelines/test_pipelines.py
#          uv venv
#          uv pip install .