update tutorial #95
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| name: Test with qiime2-dev | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - image: "ubuntu-latest" | |
| short: "linux" | |
| - image: "macos-latest" | |
| short: "osx" | |
| runs-on: "${{matrix.os.image}}" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| use-mamba: true | |
| - shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Install Qiime 2 | |
| shell: bash -l {0} | |
| run: | | |
| wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-${{matrix.os.short}}-conda.yml | |
| mamba env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml | |
| rm qiime2-latest-py38-${{matrix.os.short}}-conda.yml | |
| - name: Install q2-micom | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| mamba env update -n qiime2-dev -f q2-micom-${{matrix.os.short}}.yml | |
| - name: Install CPLEX | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| mamba install -y -c ibmdecisionoptimization cplex | |
| - name: Lint with flake8 | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| pip install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --ignore=F203 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --ignore=F203 --exit-zero --statistics | |
| - name: Test with pytest | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| pip install pytest pytest-benchmark pytest-cov | |
| pytest --benchmark-skip --cov=q2_micom --cov-report=xml |