All in one file #1
Workflow file for this run
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| name: QATests | ||
| on: | ||
| push: | ||
| paths: | ||
| - '.github/workflows/QATests.yml' | ||
| - '.github/envs/test_env.yml' | ||
| jobs: | ||
| build: | ||
| runs-on: ubuntu-latest | ||
| matrix: | ||
| python-version: ["3.10"] | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
| env: | ||
| CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy | ||
| job1: | ||
| if: always() | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v3 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| pip install pylint | ||
| - name: Analysing the code with pylint | ||
| run: | | ||
| pylint --fail-under=6.2 $(git ls-files '*.py') --rcfile=/home/runner/work/CRISPResso2/CRISPResso2/.github/workflows/.pylintrc | ||
| job2: | ||
| if: always() | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Conda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| mamba-version: "*" | ||
| channels: conda-forge,bioconda,defaults | ||
| auto-activate-base: false | ||
| activate-environment: test_env | ||
| environment-file: .github/envs/test_env.yml | ||
| - name: Install apt dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl | ||
| - name: Install Pytest | ||
| run: | | ||
| pip install pytest pytest-cov | ||
| - name: Install CRISPResso | ||
| run: | | ||
| pip install -e . | ||
| - name: Run Pytest | ||
| run: | | ||
| pytest tests --cov CRISPResso2 | ||
| job3: | ||
| if: always() | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Conda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| mamba-version: "*" | ||
| channels: conda-forge,bioconda,defaults | ||
| auto-activate-base: false | ||
| activate-environment: test_env | ||
| environment-file: .github/envs/test_env.yml | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl | ||
| pip install ydiff | ||
| - name: Create directory for files | ||
| run: | | ||
| mkdir ../CRISPResso2_copy | ||
| cp -r * ../CRISPResso2_copy | ||
| - name: Copy C2_tests repo | ||
| uses: actions/checkout@master | ||
| with: | ||
| repository: edilytics/CRISPResso2_tests | ||
| token: ${{ secrets.ACCESS_CRISPRESSO2_TESTS }} | ||
| # ref: '<BRANCH_NAME>' // Use this to specify a branch other than master | ||
| - name: Run Basic | ||
| run: | | ||
| make basic test | ||
| - name: Run Params | ||
| if: success() || failure() | ||
| run: | | ||
| make params test | ||
| - name: Run Prime Editor | ||
| if: success() || failure() | ||
| run: | | ||
| make prime-editor test | ||
| - name: Run Batch | ||
| if: success() || failure() | ||
| run: | | ||
| make batch test | ||
| - name: Run Pooled | ||
| if: success() || failure() | ||
| run: | | ||
| make pooled test | ||
| - name: Run WGS | ||
| if: success() || failure() | ||
| run: | | ||
| make wgs test | ||
| - name: Run Compare | ||
| if: success() || failure() | ||
| run: | | ||
| make compare test | ||
