Allow numpy array passed into autothresholding function #756
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| name: Tests | |
| on: | |
| pull_request: | |
| branches: [main, "release/*"] | |
| workflow_dispatch: | |
| # Cancel actions when new commits are pushed to PR | |
| concurrency: | |
| group: ${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 70 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| #os: [ubuntu-latest, macOS-latest, windows-latest] | |
| os: [ubuntu-latest, windows-latest] | |
| python-version: [3.9, "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| use-mamba: true | |
| - name: Install dependencies | |
| shell: bash -el {0} | |
| run: | | |
| case "${{ matrix.os }}" in | |
| "ubuntu-latest") | |
| export PLATFORM="linux" | |
| ;; | |
| "macOS-latest") | |
| export PLATFORM="macos" | |
| ;; | |
| "windows-latest") | |
| export PLATFORM="windows" | |
| ;; | |
| esac | |
| conda activate test | |
| conda install -c conda-forge -n test fortran-compiler blas-devel | |
| pip install greenlet | |
| # need numpy for some builds. make sure to install a compatible version | |
| grep -E '^numpy==' requirements/$PLATFORM/test-requirements.txt | xargs -n 1 pip install | |
| pip install -r requirements/$PLATFORM/test-requirements.txt | |
| pip install . | |
| - name: List dependencies | |
| shell: bash -el {0} | |
| run: | | |
| python -m pip list | |
| - name: Run pytest | |
| shell: bash -el {0} | |
| run: | | |
| python -m pytest -v | |
| # upload code coverage report | |
| code-coverage: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| shell: bash -el {0} | |
| run: | | |
| conda activate test | |
| conda install -c conda-forge -n test pip fftw gfortran blas-devel | |
| # need numpy for some builds. make sure to install a compatible version | |
| grep -E '^numpy==' requirements/linux/test-requirements.txt | xargs -n 1 pip install | |
| pip install -r requirements/linux/test-requirements.txt | |
| pip install . | |
| - name: Run tests and collect coverage | |
| shell: bash -el {0} | |
| run: pytest --cov cyto_dl | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 |