fix simulate_samples #109
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| name: Python test on Mamba | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - 'releases/**' | |
| jobs: | |
| create-env: | |
| name: ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: checkout repository | |
| uses: actions/checkout@v3 | |
| - name: create environment with mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| channels: conda-forge,bioconda,defaults | |
| auto-activate-base: false | |
| activate-environment: fununifrac | |
| environment-file: environment.yml | |
| - name: check env | |
| run: | | |
| mamba env export | |
| - name: pytest | |
| run: | | |
| cd ./tests | |
| pytest . | |
| # I have tried below setup but failed with it because it basically does not activate any environment. | |
| # It is not a problem until we use subprocess.run in the test. Then subprocess try to use conda environment, which is not activated, | |
| # resulting in ModuleNotFoundError for any pip modules. | |
| # jobs: | |
| # build: | |
| # runs-on: [ubuntu-latest] | |
| # defaults: | |
| # run: | |
| # shell: bash -l {0} | |
| # strategy: | |
| # matrix: | |
| # python-version: ["3.9"] | |
| # steps: | |
| # - uses: actions/checkout@v3 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Install dependencies | |
| # run: | | |
| # python -m pip install --upgrade pip | |
| # $CONDA/bin/conda env update --file environment.yml --name base | |
| # - name: Lint with flake8 | |
| # run: | | |
| # $CONDA/bin/conda install flake8 | |
| # # stop the build if there are Python syntax errors or undefined names | |
| # $CONDA/bin/flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| # $CONDA/bin/flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| # - name: Test with pytest | |
| # run: | | |
| # cd ./tests | |
| # $CONDA/bin/pytest . |