enh: improve speed of S3 file format by increasing chunk size #854
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| name: Checks | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.10', '3.11'] | |
| os: [macos-latest, ubuntu-latest, windows-latest] | |
| extras: ['all', 'dcor-s3', 'none'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Symlink gfortran (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| # make sure gfortran is available | |
| # https://github.com/actions/virtual-environments/issues/2524 | |
| # https://github.com/cbg-ethz/dce/blob/master/.github/workflows/pkgdown.yaml | |
| sudo ln -s /usr/local/bin/gfortran-11 /usr/local/bin/gfortran | |
| sudo mkdir /usr/local/gfortran | |
| sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib | |
| gfortran --version | |
| - name: Perform modifications (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| # make R lib location writable | |
| sudo chmod -R 777 /usr/local/lib/R/site-library | |
| - name: Install dependencies | |
| run: | | |
| # prerequisites | |
| python -m pip install --upgrade pip wheel | |
| python -m pip install coverage flake8 pytest | |
| - name: Downgrade rpy2 (Windows) | |
| if: runner.os == 'Windows' | |
| run: | | |
| # Force installation of rpy2 3.5.12 | |
| # https://github.com/rpy2/rpy2/issues/1044 | |
| python -m pip install rpy2==3.5.12 | |
| - name: Install dclab with all possible dependencies | |
| if: matrix.extras == 'all' | |
| run: | | |
| pip install -e .[all] | |
| # Install required R packages | |
| python -c "import dclab; dclab.lme4.install_lme4()" | |
| - name: Install dclab with DCOR dependencies | |
| if: matrix.extras == 'dcor-s3' | |
| run: | | |
| pip install -e .[dcor,s3] | |
| - name: Install dclab with minimal dependencies | |
| if: matrix.extras == 'none' | |
| run: | | |
| pip install -e . | |
| - name: List installed packages | |
| run: | | |
| pip freeze | |
| - name: Test with pytest | |
| run: | | |
| coverage run --source=dclab -m pytest tests | |
| - name: Lint with flake8 | |
| run: | | |
| flake8 --exclude _version.py . | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 |