fix problem created by merge conflict when mergin develop #577
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| name: Python CI | |
| on: [push, pull_request] | |
| jobs: | |
| Changelog: | |
| name: CHANGELOG.md updated | |
| runs-on: ubuntu-latest | |
| if: github.event_name == 'pull_request' | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Checkout the whole history, in case the target is way far behind | |
| - name: Check if target branch has been merged | |
| run: | | |
| if git merge-base --is-ancestor ${{ github.event.pull_request.base.sha }} ${{ github.sha }}; then | |
| echo "Target branch has been merged into the source branch." | |
| else | |
| echo "Target branch has not been merged into the source branch. Please merge in target first." | |
| exit 1 | |
| fi | |
| - name: Check that CHANGELOG has been updated | |
| run: | | |
| # If this step fails, this means you haven't updated the CHANGELOG.md file with notes on your contribution. | |
| if git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep -q '^CHANGELOG.md$'; then | |
| echo "Thanks for helping keep our CHANGELOG up-to-date!" | |
| else | |
| echo "Please update the CHANGELOG.md file with notes on your contribution." | |
| exit 1 | |
| fi | |
| Lint: | |
| runs-on: ubuntu-latest | |
| env: | |
| MAX_LINE_LENGTH: 127 | |
| MAX_COMPLEXITY: 15 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Check cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }} | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install --upgrade -r requirements.txt; fi | |
| pip3 install --upgrade -r requirements/dev.txt | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --max-complexity=$MAX_COMPLEXITY --statistics --max-line-length=$MAX_LINE_LENGTH | |
| - name: Lint with isort | |
| run: | | |
| python3 -m isort --check --line-length $MAX_LINE_LENGTH merlin | |
| python3 -m isort --check --line-length $MAX_LINE_LENGTH tests | |
| python3 -m isort --check --line-length $MAX_LINE_LENGTH *.py | |
| - name: Lint with Black | |
| run: | | |
| python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 merlin | |
| python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 tests | |
| python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 *.py | |
| - name: Lint with PyLint | |
| run: | | |
| python3 -m pylint merlin --rcfile=setup.cfg --exit-zero | |
| python3 -m pylint tests --rcfile=setup.cfg --exit-zero | |
| Local-test-suite: | |
| runs-on: ubuntu-latest | |
| env: | |
| GO_VERSION: 1.18.1 | |
| SINGULARITY_VERSION: 3.9.9 | |
| OS: linux | |
| ARCH: amd64 | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }} | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip3 install -r requirements/dev.txt | |
| - name: Install singularity | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config | |
| wget https://go.dev/dl/go$GO_VERSION.$OS-$ARCH.tar.gz | |
| sudo tar -C /usr/local -xzf go$GO_VERSION.$OS-$ARCH.tar.gz | |
| rm go$GO_VERSION.$OS-$ARCH.tar.gz | |
| export PATH=$PATH:/usr/local/go/bin | |
| wget https://github.com/sylabs/singularity/releases/download/v$SINGULARITY_VERSION/singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| tar -xzf singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| cd singularity-ce-$SINGULARITY_VERSION | |
| ./mconfig && \ | |
| make -C ./builddir && \ | |
| sudo make -C ./builddir install | |
| - name: Install merlin to run unit tests | |
| run: | | |
| pip3 install -e . | |
| merlin config | |
| - name: Install CLI task dependencies generated from the 'feature demo' workflow | |
| run: | | |
| merlin example feature_demo | |
| pip3 install -r feature_demo/requirements.txt | |
| - name: Run integration test suite for local tests | |
| run: | | |
| python3 tests/integration/run_tests.py --verbose --local | |
| Unit-tests: | |
| runs-on: ubuntu-latest | |
| env: | |
| GO_VERSION: 1.18.1 | |
| SINGULARITY_VERSION: 3.9.9 | |
| OS: linux | |
| ARCH: amd64 | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }} | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip3 install -r requirements/dev.txt | |
| - name: Install singularity | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config | |
| wget https://go.dev/dl/go$GO_VERSION.$OS-$ARCH.tar.gz | |
| sudo tar -C /usr/local -xzf go$GO_VERSION.$OS-$ARCH.tar.gz | |
| rm go$GO_VERSION.$OS-$ARCH.tar.gz | |
| export PATH=$PATH:/usr/local/go/bin | |
| wget https://github.com/sylabs/singularity/releases/download/v$SINGULARITY_VERSION/singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| tar -xzf singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| cd singularity-ce-$SINGULARITY_VERSION | |
| ./mconfig && \ | |
| make -C ./builddir && \ | |
| sudo make -C ./builddir install | |
| - name: Install merlin to run unit tests | |
| run: | | |
| pip3 install -e . | |
| merlin config | |
| - name: Install CLI task dependencies generated from the 'feature demo' workflow | |
| run: | | |
| merlin example feature_demo | |
| pip3 install -r feature_demo/requirements.txt | |
| - name: Run pytest over unit test suite | |
| run: | | |
| python3 -m pytest -v --order-scope=module tests/unit/ | |
| Integration-tests: | |
| runs-on: ubuntu-latest | |
| env: | |
| GO_VERSION: 1.18.1 | |
| SINGULARITY_VERSION: 3.9.9 | |
| OS: linux | |
| ARCH: amd64 | |
| strategy: | |
| matrix: | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.pythonLocation }} | |
| key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }} | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip3 install -r requirements/dev.txt | |
| - name: Install merlin | |
| run: | | |
| pip3 install -e . | |
| merlin config | |
| - name: Install singularity | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config | |
| wget https://go.dev/dl/go$GO_VERSION.$OS-$ARCH.tar.gz | |
| sudo tar -C /usr/local -xzf go$GO_VERSION.$OS-$ARCH.tar.gz | |
| rm go$GO_VERSION.$OS-$ARCH.tar.gz | |
| export PATH=$PATH:/usr/local/go/bin | |
| wget https://github.com/sylabs/singularity/releases/download/v$SINGULARITY_VERSION/singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| tar -xzf singularity-ce-$SINGULARITY_VERSION.tar.gz | |
| cd singularity-ce-$SINGULARITY_VERSION | |
| ./mconfig && \ | |
| make -C ./builddir && \ | |
| sudo make -C ./builddir install | |
| - name: Install CLI task dependencies generated from the 'feature demo' workflow | |
| run: | | |
| merlin example feature_demo | |
| pip3 install -r feature_demo/requirements.txt | |
| # TODO remove the --ignore statement once those tests are fixed | |
| - name: Run integration test suite for distributed tests | |
| run: | | |
| python3 -m pytest -v --ignore tests/integration/test_celeryadapter.py tests/integration/ |