fix #1195
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| name: linux | |
| on: [pull_request, push] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| docs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: Install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: docs | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp | |
| cd docs | |
| make html | |
| flake: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: Install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: flake | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp | |
| flake8 --ignore=E501,E722,E402 --exclude tests,docs/conf.py,build/lib/snakePipes/shared/tools/three_prime_seq,snakePipes/shared/tools/three_prime_seq . | |
| CI: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: Install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: CI | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp | |
| ./.ci_stuff/test_dag.sh | |
| - name: pytest | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp | |
| pytest --verbosity=2 | |
| createEnvs: | |
| needs: CI | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| envs: [ | |
| 'CONDA_SHARED_ENV', | |
| 'CONDA_CREATE_INDEX_ENV', | |
| 'CONDA_RNASEQ_ENV', | |
| 'CONDA_RMATS_ENV', | |
| 'CONDA_scRNASEQ_ENV', | |
| 'CONDA_seurat3_ENV', | |
| 'CONDA_loompy_ENV', | |
| 'CONDA_alevinqc_ENV', | |
| 'CONDA_eisaR_ENV', | |
| 'CONDA_DNA_MAPPING_ENV', | |
| 'CONDA_CHIPSEQ_ENV', | |
| 'CONDA_ATAC_ENV', | |
| 'CONDA_HIC_ENV', | |
| 'CONDA_WGBS_ENV', | |
| 'CONDA_DSS_ENV', | |
| 'CONDA_RMD_ENV', | |
| 'CONDA_PREPROCESSING_ENV', | |
| 'CONDA_NONCODING_RNASEQ_ENV', | |
| 'CONDA_SAMBAMBA_ENV', | |
| 'CONDA_pysam_ENV' | |
| ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: mamba-org/setup-micromamba@main | |
| with: | |
| environment-file: .github/snakePipesEnvCI.yml | |
| condarc: | | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| channel_priority: 'strict' | |
| cache-downloads: true | |
| - name: install snakePipes | |
| run: | | |
| micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv | |
| - name: createEnvs | |
| run: | | |
| micromamba activate snakePipes_CI | |
| snakePipes config --tempDir /tmp | |
| snakePipes createEnvs --autodetectCondaEnvDir --only ${{matrix.envs}} |