Converting to mamba #36
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| name: Tests MacOS | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| branches: | |
| - dev | |
| - master | |
| - dev_graph | |
| push: | |
| branches: | |
| - dev | |
| - master | |
| - dev_graph | |
| jobs: | |
| build: | |
| name: Build (${{ matrix.os }}, Python ${{ matrix.python-version }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [macos-latest] | |
| python-version: ["3.8", "3.9", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install openslide | |
| shell: bash -l {0} | |
| run: brew install openslide | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| micromamba-version: '1.5.6-0' | |
| environment-name: pathml | |
| environment-file: requirements/environment_mac.yml | |
| init-shell: >- | |
| bash | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| - name: Install python-javabridge | |
| shell: bash -l {0} | |
| # run: pip install --use-pep517 numpy==1.23.5 python-javabridge==4.0.3 | |
| # run: pip install python-javabridge==4.0.3 | |
| run: pip install git+https://github.com/LeeKamentsky/python-javabridge | |
| - name: Install python-bioformats | |
| shell: bash -l {0} | |
| run: pip install python-bioformats==4.0.7 | |
| - name: Micromamba info | |
| shell: bash -l {0} | |
| run: | | |
| micromamba info | |
| micromamba config | |
| micromamba list | |
| - name: Set default Temurin JDK 17 | |
| run: | | |
| sudo update-java-alternatives --set temurin-17-jdk-amd64 || true | |
| java -version | |
| - name: Install PathML | |
| shell: bash -l {0} | |
| run: pip install -e . | |
| - name: Install torchvision | |
| shell: bash -l {0} | |
| run: pip install torchvision==0.14.1 | |
| - name: Test other modules with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude" | |
| - name: Test tile_stitcher with pytest and generate coverage | |
| shell: bash -l {0} | |
| run: | | |
| COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py |