Update pyproject.toml #96
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Test imc package | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| linux: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel pytest | |
| pip install .[deepcell,astir] | |
| - name: Test with pytest | |
| run: | | |
| # Test package | |
| python -m pytest imc/ | |
| # Run pipeline | |
| mkdir -p imctest | |
| cd imctest | |
| imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1 | |
| # List output files | |
| ls -l processed/ | |
| ls -l processed/${SAMPLE} | |
| ls -l results/phenotyping | |
| - name: Cache resources | |
| id: cache-resources | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/$USER/.imc | |
| key: imc-resources-linux | |
| osx: | |
| runs-on: macos-10.14 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel pytest | |
| pip install .[deepcell,astir] | |
| - name: Test with pytest | |
| run: | | |
| # Test package | |
| python -m pytest imc/ | |
| # Run example processing pipeline | |
| mkdir -p imctest | |
| cd imctest | |
| imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1 | |
| # List output files | |
| ls -l processed/ | |
| ls -l processed/${SAMPLE} | |
| ls -l results/phenotyping | |
| - name: Cache resources | |
| id: cache-resources | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/$USER/.imc | |
| key: imc-resources-osx |