Use zero bytes when storing blank patches in TIFF #68
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| name: CI macOS 14 arm64 | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| release: | |
| types: [ published ] | |
| workflow_dispatch: | |
| env: | |
| BUILD_TYPE: Release | |
| MACOSX_DEPLOYMENT_TARGET: 11.0 | |
| jobs: | |
| build: | |
| runs-on: macos-14 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| brew reinstall zlib | |
| brew install openslide pcre libomp | |
| # Install a specific version of libomp (14.0.6) since newer versions fail with cmake | |
| #curl https://raw.githubusercontent.com/Homebrew/homebrew-core/c87d6a0c8360c4684e3375ce6c4576214acdd71b/Formula/libomp.rb > $(find $(brew --repository) -name libomp.rb) && brew reinstall libomp | |
| - name: Setup pyenv | |
| env: | |
| ACTIONS_ALLOW_UNSECURE_COMMANDS: true | |
| MACOSX_DEPLOYMENT_TARGET: 11.0 | |
| PYTHON_CONFIGURE_OPTS: "--enable-framework" | |
| CFLAGS: "-Wno-implicit-function-declaration" | |
| LDFLAGS: "-L/usr/local/opt/zlib/lib" | |
| CPPFLAGS: "-I/usr/local/opt/zlib/include" | |
| PKG_CONFIG_PATH: "/usr/local/opt/zlib/lib/pkgconfig" | |
| uses: "gabrielfalcao/pyenv-action@v18" | |
| with: | |
| default: 3.8.18 | |
| - name: Install pip dependencies | |
| run: | | |
| pip3 install --upgrade pip | |
| pip3 install numpy==1.21.6 twine wheel==0.37.1 | |
| - name: Debug | |
| run: | | |
| echo "$(dirname $(pyenv which python))" | |
| echo $(ls "$(dirname $(pyenv which python))/../include/") | |
| - name: Configure CMake | |
| run: | | |
| cmake -B ${{github.workspace}}/build \ | |
| -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}\ | |
| -DCMAKE_OSX_ARCHITECTURES:STRING="arm64" \ | |
| -DFAST_MODULE_OpenVINO=OFF \ | |
| -DFAST_MODULE_Dicom=ON \ | |
| -DFAST_MODULE_WholeSlideImaging=ON \ | |
| -DFAST_MODULE_OpenIGTLink=ON \ | |
| -DFAST_MODULE_Clarius=OFF \ | |
| -DFAST_MODULE_TensorFlow=OFF \ | |
| -DFAST_MODULE_HDF5=ON \ | |
| -DFAST_MODULE_Plotting=ON \ | |
| -DFAST_MODULE_Python=ON \ | |
| -DFAST_Python_Version="3.8" \ | |
| -DFAST_Python_Include="$(dirname $(pyenv which python))/../include/python3.8/" \ | |
| -DFAST_Python_Library="$(dirname $(pyenv which python))/../lib/libpython3.8.dylib" \ | |
| -DFAST_MODULE_RealSense=OFF \ | |
| -DFAST_BUILD_EXAMPLES=ON | |
| - name: Build | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} -j 4 | |
| - name: Build Python wheel | |
| env: | |
| MACOSX_DEPLOYMENT_TARGET: 11.0 | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --target python-wheel -j 4 | |
| - name: Package | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --target package -j 4 | |
| - name: Upload archive package | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Archive package (tar.xz) | |
| path: ${{github.workspace}}/build/fast_*.tar.xz | |
| if-no-files-found: error | |
| - name: Upload Python wheel | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Python wheel | |
| path: ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| if-no-files-found: error | |
| - name: Upload archive package to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_*.tar.xz | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload Python wheel to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload Python wheel to PyPi | |
| if: ${{ github.event_name == 'release' && !contains(github.ref, 'rc') }} | |
| run: | | |
| twine upload --username __token__ --password ${{ secrets.PYPI_API_TOKEN }} ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| # test-cpp: | |
| # name: Run C++ Tests | |
| # needs: [build] | |
| # runs-on: [self-hosted, macos] | |
| # steps: | |
| # - name: Download artifacts | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: 'Archive package (tar.xz)' | |
| # path: ${{github.workspace}}/download/ | |
| # - name: Extract artifact | |
| # run: | | |
| # mkdir -p ${{github.workspace}}/download/ | |
| # cd ${{github.workspace}}/download/ | |
| # tar -xf fast_*.tar.xz -C ${{github.workspace}} | |
| # - name: Download test data | |
| # run: | | |
| # cd ${{github.workspace}} | |
| # cd fast* | |
| # cd fast/bin/ | |
| # ./downloadTestData | |
| # - name: Run tests | |
| # run: | | |
| # cd ${{github.workspace}} | |
| # cd fast_* | |
| # cd fast/bin/ | |
| # ./testFAST ~[visual]~[unstablemac] | |
| # - name: Cleanup | |
| # if: always() | |
| # run: | | |
| # rm -Rf ${{github.workspace}} | |
| # rm -Rf $HOME/FAST/kernel_binaries/* | |
| # | |
| # test-python: | |
| # name: Run Python Tests | |
| # needs: [build] | |
| # runs-on: [self-hosted, macos] | |
| # steps: | |
| # - uses: actions/checkout@v2 | |
| # - name: Download artifacts | |
| # uses: actions/download-artifact@v3 | |
| # with: | |
| # name: 'Python wheel' | |
| # path: ${{github.workspace}}/download/ | |
| # - name: Create environment and install python packages | |
| # run: | | |
| # cd ${{github.workspace}} | |
| # mkdir tmp | |
| # cd tmp | |
| # virtualenv -p python3 venv | |
| # source venv/bin/activate | |
| # pip3 install pytest | |
| # pip3 install ${{github.workspace}}/download/pyFAST-*.whl | |
| # - name: Run tests | |
| # run: | | |
| # cd ${{github.workspace}}/tmp/ | |
| # source venv/bin/activate | |
| # pytest ../source/FAST/ | |
| # - name: Cleanup | |
| # if: always() | |
| # run: | | |
| # rm -Rf ${{github.workspace}}/download/ | |
| # rm -Rf ${{github.workspace}}/tmp/ | |
| # rm -Rf $HOME/FAST/kernel_binaries/* |