flake fixes #523
Workflow file for this run
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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 | |
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 | |
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 | |
./.ci_stuff/test_dag.sh | |
- name: pytest | |
run: | | |
micromamba activate snakePipes_CI | |
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 createEnvs --autodetectCondaEnvDir --force --only ${{matrix.envs}} |