Fix #531
Workflow file for this run
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| name: Test (PyPI) | |
| on: | |
| push: | |
| branches: | |
| - pypi | |
| schedule: | |
| - cron: "0 18 * * 1,3,5" | |
| jobs: | |
| test: | |
| name: Test PyPI (${{ matrix.os }}, py${{ matrix.python-version }}, tf${{ matrix.tensorflow }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # https://docs.github.com/en/actions/using-jobs/using-a-matrix-for-your-jobs | |
| os: [macos-latest] # macos-latest is arm64-based | |
| python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12'] | |
| tensorflow: [1, 2] | |
| include: | |
| # always set 'package-extras' conditional on tensorflow version | |
| - tensorflow: 1 | |
| package-extras: 'test,tf1' | |
| - tensorflow: 2 | |
| package-extras: 'test' | |
| # test bioimage.io export with python 3.7 and tensorflow 1 | |
| - python-version: '3.7' | |
| tensorflow: 1 | |
| package-extras: 'test,tf1,bioimageio' | |
| # install edt with numpy>=1.20 when testing with python 3.9 | |
| - python-version: '3.9' | |
| deps-extra: 'edt "numpy>=1.20"' | |
| # add extra run to test latest tensorflow with legacy keras | |
| - os: ubuntu-20.04 | |
| python-version: '>=3.12 <3.13' # intentionally be different than '3.12' to cause an additional combination | |
| tensorflow: 2 | |
| package-extras: 'test' | |
| deps-extra: 'tf_keras' | |
| exec-extra: 'echo "TF_USE_LEGACY_KERAS=1" >> $GITHUB_ENV' | |
| # cases for using x86_64-based runner (macos-13) | |
| - os: macos-13 | |
| python-version: '3.6' # no arm64 wheels | |
| tensorflow: 1 | |
| - os: macos-13 | |
| python-version: '3.6' # no arm64 wheels | |
| tensorflow: 2 | |
| - os: macos-13 | |
| python-version: '3.7' # no arm64 wheels | |
| tensorflow: 1 | |
| - os: macos-13 | |
| python-version: '3.7' # no arm64 wheels | |
| tensorflow: 2 | |
| - os: macos-13 | |
| python-version: '>=3.12 <3.13' # intentionally be different than '3.12' to cause an additional combination | |
| tensorflow: 2 | |
| package-extras: 'test' | |
| exclude: | |
| # https://www.tensorflow.org/install/source#tested_build_configurations | |
| - python-version: '3.8' | |
| tensorflow: 1 | |
| - python-version: '3.9' | |
| tensorflow: 1 | |
| - python-version: '3.10' | |
| tensorflow: 1 | |
| - python-version: '3.11' | |
| tensorflow: 1 | |
| - python-version: '3.12' | |
| tensorflow: 1 | |
| - os: windows-latest | |
| tensorflow: 1 | |
| steps: | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Upgrade pip, wheel, setuptools | |
| run: python -m pip install --upgrade pip wheel setuptools | |
| - name: Install TensorFlow | |
| run: pip install "tensorflow==${{ matrix.tensorflow }}.*" | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Install extra dependencies (if any) | |
| if: ${{ matrix.deps-extra }} | |
| run: pip install ${{ matrix.deps-extra }} | |
| - name: Install package from source (just to test wheel building) - Linux | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: pip install --no-binary stardist "stardist[${{ matrix.package-extras }}]" | |
| - name: Install package from source (just to test wheel building) - Windows | |
| if: startsWith(matrix.os, 'windows') | |
| run: pip install --no-binary stardist "stardist[${{ matrix.package-extras }}]" | |
| env: # cf. https://github.com/pypa/pip/issues/11231 | |
| TEMP: "/tmp" # notes: | |
| TMPDIR: "/tmp" # - /tmp should already exist on runner image | |
| TMP: "/tmp" # - set all temp-related env variables (had issues with when omitting some) | |
| # - name: Install package from source (just to test wheel building) - macOS | |
| # if: startsWith(matrix.os, 'macos') | |
| # run: ... | |
| - name: Install package from wheel | |
| shell: bash | |
| run: | | |
| [[ -z $(pip list | grep stardist) ]] && pip uninstall -y stardist | |
| pip install --no-cache-dir --only-binary stardist "stardist[${{ matrix.package-extras }}]>0" | |
| - name: Run extra commands (if any) | |
| if: ${{ matrix.exec-extra }} | |
| run: ${{ matrix.exec-extra }} | |
| shell: bash | |
| - name: Disable PytestReturnNotNoneWarning (Python 3.7+) | |
| if: matrix.python-version != 3.6 | |
| run: echo "PYTEST_ADDOPTS='-W ignore::pytest.PytestReturnNotNoneWarning'" >> $GITHUB_ENV | |
| shell: bash | |
| - name: Run tests | |
| run: pytest -m "not gpu" |