Fix endian bug and replace fileExtension with environmental variable omeconverter #228
Workflow file for this run
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| name: Package tests | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| - master | |
| - dev | |
| push: | |
| branches-ignore: | |
| - main | |
| - master | |
| - dev | |
| workflow_call: | |
| permissions: | |
| contents: read | |
| jobs: | |
| package-filter: | |
| name: Filter for updated package | |
| uses: ./.github/workflows/package-filter.yml | |
| with: | |
| num-commits: 0 | |
| ignore-missing-dev: false | |
| pre-commit: | |
| name: Pre-commit | ${{ matrix.package_name }} | |
| needs: package-filter | |
| if: ${{ needs.package-filter.outputs.num_packages > 0 }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Poetry | |
| uses: abatilo/actions-poetry@v2 | |
| - name: Install pre-commit | |
| run: | | |
| pip install pre-commit | |
| - name: Run pre-commit hooks and check for changes | |
| run: | | |
| cd "${{ matrix.package_dir }}" | |
| poetry run pre-commit run --files ./**/** | |
| if [[ $(git status --porcelain) ]] | |
| then | |
| echo "::error::pre-commit hooks failed for ${{ matrix.package_name }}" && exit 1 | |
| fi | |
| docker: | |
| name: Docker | Build ${{ matrix.package_name }} | |
| needs: package-filter | |
| if: ${{ needs.package-filter.outputs.num_packages > 0 }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Check if Dockerfile exists | |
| id: check_dockerfile | |
| run: | | |
| if [ -f "${{ matrix.package_dir }}/Dockerfile" ]; then | |
| echo "Dockerfile exists" | |
| echo "dockerfile_exists=true" >> $GITHUB_ENV | |
| else | |
| echo "Dockerfile does not exist" | |
| echo "dockerfile_exists=false" >> $GITHUB_ENV | |
| fi | |
| - name: Docker | Tag | |
| id: docker_tag | |
| if: env.dockerfile_exists == 'true' | |
| run: | | |
| version=$(cat ${{ matrix.package_dir }}/VERSION) | |
| tag=polusai/${{ matrix.package_name }}:${version} | |
| echo "tag will be ${tag}" | |
| echo "tag=${tag}" >> $GITHUB_OUTPUT | |
| - name: Docker | Setup Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Docker | Check if Image exists | |
| if: env.dockerfile_exists == 'true' | |
| run: | | |
| tag=${{ steps.docker_tag.outputs.tag }} | |
| docker pull ${tag} > /dev/null \ | |
| && $(echo "::error::${tag} already exists on DockerHub" && exit 1) \ | |
| || echo "success" | |
| - name: Docker | Build Image | |
| if: env.dockerfile_exists == 'true' | |
| run: | | |
| cp .gitignore ${{ matrix.package_dir }}/.dockerignore | |
| cd "${{ matrix.package_dir }}" | |
| if [ -f "build-docker.sh" ]; then | |
| bash build-docker.sh | |
| else | |
| docker build . -t ${{ steps.docker_tag.outputs.tag }} | |
| fi | |
| bash build-docker.sh | |
| # docker buildx build --platform linux/amd64,linux/arm64 -t ${tag} --push . | |
| tests: | |
| name: Test | ${{ matrix.package_name }} | |
| needs: package-filter | |
| if: ${{ needs.package-filter.outputs.num_packages > 0 }} | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| - name: Run tests with conda | |
| run: | | |
| package_dir=${{ matrix.package_dir }} | |
| cd $package_dir | |
| if [ -f "environment.yml" ]; then | |
| conda init bash | |
| source ~/.bashrc | |
| conda env create -f environment.yml | |
| conda activate project_env | |
| pip install -e ".[all]" | |
| conda install pytest | |
| python -X faulthandler -m pytest -v -p no:faulthandler | |
| echo "conda_installed=true" >> $GITHUB_ENV | |
| else | |
| echo "conda_installed=false" >> $GITHUB_ENV | |
| fi | |
| - name: Install Poetry | |
| uses: abatilo/actions-poetry@v2 | |
| - name: Run tests with poetry | |
| if: env.conda_installed == 'false' | |
| run: | | |
| poetry config virtualenvs.create false | |
| package_dir=${{ matrix.package_dir }} | |
| cd $package_dir | |
| poetry install | |
| python -X faulthandler -m pytest -v -p no:faulthandler |