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| # configuration derived from q2-katharoseq | |
| name: Python Package using Conda | |
| on: [push] | |
| jobs: | |
| build-linux: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install QIIME 2 ${{ matrix.os }} | |
| if: matrix.os == 'macos-latest' | |
| shell: bash -l {0} | |
| run: | | |
| wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-osx-conda.yml | |
| conda env create -q -n test-env --file qiime2-latest-py38-osx-conda.yml | |
| - name: Install QIIME 2 ${{ matrix.os }} | |
| if: matrix.os == 'ubuntu-latest' | |
| shell: bash -l {0} | |
| run: | | |
| wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml | |
| conda env create -q -n test-env --file qiime2-latest-py38-linux-conda.yml | |
| - name: Install q2-greengenes2 | |
| source activate test-env | |
| conda install flake8 pytest | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| source activate test-env | |
| flake8 q2_gg2 | |
| - name: Test with pytest | |
| run: | | |
| source activate test-env | |
| pytest | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: flake8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: lint | |
| run: | | |
| pip install -q flake8 | |
| flake8 q2_gg2 |