fix conda cache #960
Workflow file for this run
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| name: Python package | |
| on: [push, pull_request] | |
| jobs: | |
| setup_test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| test: ["test_config_generation"] | |
| test-case: ["atac", "chip-rx", "chip", "rna-rx", "rna", "snp"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Cache conda environment | |
| id: cache-conda | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/miniforge3/envs/test | |
| ~/.cache/pip | |
| key: ${{ runner.os }}-conda-${{ matrix.python-version }}-${{ hashFiles('**/testing.yml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-conda-${{ matrix.python-version }}- | |
| - name: Setup environment | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: test | |
| auto-activate-base: true | |
| channel-priority: strict | |
| channels: conda-forge, bioconda, defaults | |
| conda-solver: mamba | |
| environment-file: testing.yml | |
| environment-name: test | |
| mamba-version: latest | |
| miniforge-variant: Mambaforge | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| use-only-tar-bz2: true | |
| - name: Update environment | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| run: mamba env update -n test -f testing.yml | |
| - name: list conda envs | |
| run: | | |
| conda env list | |
| env_path="/home/runner/miniconda3/envs/test" | |
| if [ -d "$env_path" ]; then | |
| echo "Environment exists" | |
| else | |
| echo "Environment does not exist" | |
| fi | |
| shell: bash -l {0} | |
| - name: Install package | |
| if: steps.cache-conda.outputs.cache-hit != 'true' | |
| run: | | |
| source /home/runner/miniforge3/bin/activate test | |
| pip install . | |
| shell: bash -l {0} | |
| # - name: Verify and activate environment | |
| # run: | | |
| # source ~/miniforge3/bin/activate test | |
| # which seqnado | |
| # shell: bash -l {0} | |
| # - name: Run test | |
| # run: | | |
| # source ~/miniforge3/bin/activate test | |
| # pytest "tests/test_pipelines.py::${{ matrix.test }}[${{ matrix.test-case }}]" -vv -s --cores 4 -k | |
| # shell: bash -l {0} |