Fix yml errors #2
Workflow file for this run
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| name: QATests | |
| on: | |
| push: | |
| paths: | |
| - '.github/workflows/QATests.yml' | |
| - '.github/envs/test_env.yml' | |
| jobs: | |
| job1: | |
| if: always() | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.10"] | |
| 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() | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| 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() | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| CRISPRESSO2_DIR: ${GITHUB_WORKSPACE}/../CRISPResso2_copy | |
| 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 |