tests.yml

name: Tests and Linting

on:
  pull_request:
  push:
    branches: [main]

jobs:
  Linting:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
      - name: Set PY variable
        run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
      - uses: actions/cache@v2
        with:
          path: ~/.cache/pre-commit
          key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
      - name: Install pre-commit
        run: |
          pip install pre-commit
          pre-commit install
      - name: Run pre-commit
        run: SKIP=no-commit-to-branch pre-commit run --all-files

  Pytest:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: true
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v2
      - name: Cache downloaded resources
        uses: actions/cache@v3
        with:
          path: ~/.data/
          key: resources
      - 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@v2
        with:
          python-version: ${{ matrix.python-version }}
          architecture: x64
      - name: Install dependencies
        run: |
          pip install --upgrade pip
          pip install -e '.[dev]'

      - name: Test with Pytest on Python ${{ matrix.python-version }}
        env:
          UMLS_API_KEY: ${{ secrets.UMLS_API_KEY }}
        run: python -m pytest --cov foldedtensor --cov-report xml --ignore tests/test_docs.py
        if: matrix.python-version != '3.9'

      - name: Test with Pytest on Python ${{ matrix.python-version }}
        run: coverage run -m pytest

      - 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: Combine & check coverage
    if: always()
    needs: Pytest
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          # Use latest Python, so it understands all syntax.
          python-version: "3.12"

      - uses: actions/download-artifact@v4
        with:
          pattern: coverage-data-*
          merge-multiple: true

      - name: Combine coverage & fail if it's <100%
        run: |
          python -Im pip install --upgrade coverage[toml]

          ls -lah

          python -Im coverage combine
          python -Im coverage html --skip-covered --skip-empty

          # Report and write to summary.
          python -Im coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
          cat $GITHUB_STEP_SUMMARY > step-summary.md

      - name: Upload HTML report if check failed
        uses: actions/upload-artifact@v4
        with:
          name: html-report
          path: htmlcov
        if: ${{ failure() }}

      - name: Post or Update Comment on PR
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        run: |
          COMMENT_BODY="$(cat step-summary.md)"
          HEADER="Authorization: token $GITHUB_TOKEN"
          PR_COMMENTS_URL="https://api.github.com/repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments"

          # Fetch existing comments to find if one from this workflow already exists
          COMMENTS=$(curl -s -H "$HEADER" "$PR_COMMENTS_URL")
          COMMENT_ID=$(echo "$COMMENTS" | jq -r '.[] | select(.user.login == "github-actions[bot]" and (.body | startswith("## Coverage Report"))) | .id')

          # Check if we have a comment ID, if so, update it, otherwise create a new one
          if [[ "$COMMENT_ID" ]]; then
            # Update existing comment
            curl -s -X PATCH -H "$HEADER" -H "Content-Type: application/json" -d "{\"body\":\"$COMMENT_BODY\"}" "https://api.github.com/repos/${{ github.repository }}/issues/comments/$COMMENT_ID"
          else
            # Post new comment
            curl -s -X POST -H "$HEADER" -H "Content-Type: application/json" -d "{\"body\":\"$COMMENT_BODY\"}" "$PR_COMMENTS_URL"


  Installation:
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"]
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install library
        run: |
          pip install .