build: create independent environment files #96
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| name: tests | |
| on: | |
| pull_request: | |
| branches: | |
| - dev | |
| push: | |
| branches: | |
| - '*' | |
| jobs: | |
| static-code-analysis: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: Setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| activate-environment: mirflowz | |
| environment-file: install/environment.dev.yml | |
| auto-activate-base: false | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: flake8 | |
| working-directory: ./scripts | |
| run: flake8 ./*.py | |
| - name: mypy | |
| working-directory: ./scripts | |
| run: mypy ./*.py | |
| - name: pylint | |
| working-directory: ./scripts | |
| run: pylint --rcfile=../pylint.cfg ./*.py | |
| snakemake-format-graph-test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| activate-environment: mirflowz | |
| environment-file: install/environment.dev.root.yml | |
| auto-activate-base: false | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run test for snakemake format | |
| run: bash test/test_snakefmt.sh | |
| - name: run test for snakemate lint | |
| run: bash test/test_snakemake_lint.sh | |
| - name: run test for rule graph | |
| run: bash test/test_rule_graph.sh | |
| snakemake-singularity-integration-test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| activate-environment: mirflowz | |
| environment-file: install/environment.root.yml | |
| auto-activate-base: false | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run local test with Singularity | |
| run: bash test/test_workflow_local_with_singularity.sh | |
| snakemake-conda-integration-test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: check out repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| activate-environment: mirflowz | |
| environment-file: install/environment.yml | |
| auto-activate-base: false | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run local test with Conda | |
| run: bash test/test_workflow_local_with_conda.sh | |
| unit-testing: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v4 | |
| - name: setup Conda/Mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| channel-priority: true | |
| activate-environment: mirflowz | |
| environment-file: install/environment.dev.yml | |
| auto-activate-base: false | |
| - name: display environment info | |
| run: | | |
| conda info -a | |
| conda list | |
| - name: run unit tests | |
| working-directory: ./scripts/tests | |
| run: pytest --cov=scripts --cov-branch --cov-report=term-missing |