main.yml

name: Python Test and Package

on:
  push:
    branches:
      - main
    tags:
      - "v*"
  pull_request:
    branches:
      - main

env:
  HEDWIG_ENV: dev

jobs:
  docs:
    runs-on: ubuntu-latest
    name: Docs
    needs: test
    steps:
      - uses: actions/checkout@v2
        with:
          fetch-depth: 0
      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      - name: Install dependencies
        run: |
          python -m pip install -r docs/requirements.txt
      - name: Build Sphinx Documentation
        run: |
          make -C docs html
      - name: Upload documentation
        if: github.event_name == 'push'
        uses: actions/upload-artifact@v1
        with:
          name: sphinx-docs
          path: docs/_build/html
      - name: Update gh-pages
        if: github.ref == 'refs/heads/main'
        run: |
          rm docs/_build/html/.buildinfo
          touch docs/_build/html/.nojekyll
          git update-ref refs/heads/${TARGET_BRANCH} origin/${TARGET_BRANCH}
          ./.github/workflows/update-gh-pages.sh docs/_build/html
          repo_uri="https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
          git push $repo_uri ${TARGET_BRANCH}
        env:
          GITHUB_TOKEN: ${{ secrets.github_token }}
          TARGET_BRANCH: "gh-pages"

  test:
    runs-on: ubuntu-latest
    name: Check coverage
    permissions:
      # Gives the action the necessary permissions for publishing new
      # comments in pull requests.
      pull-requests: write
      # Gives the action the necessary permissions for pushing data to the
      # python-coverage-comment-action branch, and for editing existing
      # comments (to avoid publishing multiple comments in the same PR)
      contents: write
    strategy:
      matrix:
        python-version: ["3.8"]
    steps:
      - uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - uses: actions/setup-java@v3
        with:
          distribution: 'zulu'
          java-version: '17'
      - uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - name: Create LFS file list
        run: |
          git lfs ls-files -l | cut -d' ' -f1 | sort > .lfs-assets-id
      - name: Restore LFS cache
        uses: actions/cache@v2
        id: lfs-cache
        with:
          path: .git/lfs
          key: lfs-v1-${{ hashFiles('.lfs-assets-id') }}
          restore-keys: lfs-v1-
      - name: Git LFS Pull
        run: |
          git lfs pull
      - name: Install dependencies
        run: |
          sudo apt -y update && sudo apt -y install libgl-dev graphicsmagick libblosc1
          IMOD=imod_4.11.24_RHEL7-64_CUDA10.1.sh
          export IMOD_DIR=/usr/local/IMOD
          export PATH=$IMOD_DIR/bin:$PATH
          wget https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD} &&  sudo sh ${IMOD} -yes &&  rm -f ${IMOD}
          BIO2R_V=0.7.0
          BIO2R_Z=bioformats2raw-${BIO2R_V}.zip
          export BIO2R_DIR=/usr/local/BIO2R
          export PATH=$BIO2R_DIR/bioformats2raw-${BIO2R_V}/bin:$PATH
          wget https://github.com/glencoesoftware/bioformats2raw/releases/download/v${BIO2R_V}/${BIO2R_Z} &&  sudo unzip ${BIO2R_Z} -d ${BIO2R_DIR} &&  rm -f ${BIO2R_Z}
          python -m pip install --upgrade pip
          pip install -e . -r requirements.txt

      - name: Directory setup
        run: |
          cp .env.sample .env

      - name: Test Coverage
        continue-on-error: true
        run: |
          BIO2R_V=0.7.0
          export BIO2R_DIR=/usr/local/BIO2R/bioformats2raw-${BIO2R_V}
          export IMOD_DIR=/usr/local/IMOD
          export PATH=$BIO2R_DIR/bin:$IMOD_DIR/bin:$PATH
          python -m pytest -v --log-cli-level=INFO -m "not (slow or localdata)" --cov-report term --cov=.

      - name: Coverage Badge
        uses: tj-actions/coverage-badge-py@v2

      - name: Coverage comment
        id: coverage_comment
        uses: py-cov-action/python-coverage-comment-action@v3
        with:
          GITHUB_TOKEN: ${{ github.token }}

      - name: Store Pull Request comment to be posted
        uses: actions/upload-artifact@v3
        if: steps.coverage_comment.outputs.COMMENT_FILE_WRITTEN == 'true'
        with:
          # If you use a different name, update COMMENT_ARTIFACT_NAME accordingly
          name: python-coverage-comment-action
          # If you use a different name, update COMMENT_FILENAME accordingly
          path: python-coverage-comment-action.txt