switch to conda with libmamba #212
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Test and deploy | |
| on: | |
| push: | |
| branches: [ main ] | |
| tags: | |
| - 'v[0-9]+.[0-9]+.[0-9]+' | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - image: "ubuntu-latest" | |
| short: "linux" | |
| - image: "macos-13" | |
| short: "osx" | |
| qiime: | |
| - version: "2023.9" | |
| dist: "tiny" | |
| python: 38 | |
| - version: "2024.2" | |
| dist: "tiny" | |
| python: 38 | |
| runs-on: "${{matrix.os.image}}" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| - shell: bash -l {0} | |
| run: | | |
| conda info | |
| conda list | |
| - name: Download Qiime2 env file | |
| shell: bash -l {0} | |
| run: | | |
| wget https://data.qiime2.org/distro/${{matrix.qiime.dist}}/qiime2-${{matrix.qiime.dist}}-${{matrix.qiime.version}}-py${{matrix.qiime.python}}-${{matrix.os.short}}-conda.yml | |
| mv qiime2-${{matrix.qiime.dist}}-${{matrix.qiime.version}}-py${{matrix.qiime.python}}-${{matrix.os.short}}-conda.yml env.yml | |
| - name: Install Qiime 2 | |
| shell: bash -l {0} | |
| run: | | |
| conda env create -n qiime2-dev --file env.yml | |
| - name: Install CPLEX | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| conda install -v -c ibmdecisionoptimization cplex | |
| - name: Install q2-micom | |
| shell: bash -l {0} | |
| run: | | |
| conda activate qiime2-dev | |
| conda env update -n qiime2-dev -f q2-micom.yml | |
| pip install -e . | |
| - 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 --exit-zero --ignore=F203 --max-complexity=10 --max-line-length=88 --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 | |
| - name: Upload to codecov | |
| if: matrix.os.image == 'ubuntu-latest' | |
| uses: codecov/codecov-action@v4.6.0 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| release: | |
| needs: test | |
| if: startsWith(github.ref, 'refs/tags') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.11' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install setuptools wheel twine | |
| - name: Build and publish | |
| env: | |
| TWINE_USERNAME: "__token__" | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} | |
| run: | | |
| python setup.py sdist bdist_wheel | |
| twine upload dist/* | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: python-packages | |
| path: dist/* | |
| - name: Create Release | |
| uses: ncipollo/release-action@v1 | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| artifacts: 'dist/*' | |
| body: | | |
| Please see https://github.com/micom-dev/q2-micom/blob/main/NEWS.md for the full release notes. | |
| draft: false | |
| prerelease: false |