Update to 4.2.8 & migrate internal bio-formats #106
Workflow file for this run
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| jobs: | |
| build: | |
| name: build | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ macos-13, windows-2019 ] | |
| python-version: [ "3.8" ] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Checkout Repo | |
| - uses: actions/setup-python@v4 | |
| name: Install Python | |
| with: | |
| architecture: x64 | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: setup.py | |
| - uses: actions/setup-java@v3 | |
| name: Install Java | |
| with: | |
| distribution: "temurin" | |
| java-version: "11.0.20+8" # The JDK version to make available on the path. | |
| java-package: jdk | |
| architecture: x64 | |
| - name: Install build-time dependencies | |
| run: | | |
| pip install --upgrade wheel pip | |
| pip install setuptools==49 | |
| pip install numpy==1.23.1 | |
| pip install pyinstaller-hooks-contrib==2024.2 | |
| pip install pyinstaller==5.13.2 | |
| pip install imageio==2.34.0 | |
| pip install cython | |
| pip install lxml | |
| - env: | |
| LDFLAGS: -L/usr/local/opt/openssl/lib | |
| CERTIFICATE_OSX_APPLICATION: ${{ secrets.CERTIFICATE_OSX_APPLICATION }} | |
| CERTIFICATE_PASSWORD: ${{ secrets.CERTIFICATE_PASSWORD }} | |
| if: startsWith(matrix.os, 'macos') | |
| name: MacOS dependency install | |
| run: | | |
| brew install graphicsmagick imagemagick | |
| npm install --global create-dmg | |
| brew install [email protected] | |
| brew link [email protected] | |
| pip install mysqlclient==2.0.3 | |
| git clone https://github.com/glencoesoftware/core.git | |
| cd core | |
| git checkout compat-4-2 | |
| pip install --editable . --upgrade | |
| cd .. | |
| pip install --editable . | |
| pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation | |
| pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl | |
| - env: | |
| JDK_HOME: ${{ env.JAVA_HOME }} | |
| CPPFLAGS: -I/usr/local/opt/[email protected]/include | |
| LDFLAGS: "-L/usr/local/opt/[email protected]/lib -L/usr/local/opt/openssl/lib" | |
| if: startsWith(matrix.os, 'windows') | |
| name: Windows dependency install | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install mysqlclient==2.0.3 | |
| git clone https://github.com/glencoesoftware/core.git | |
| cd core | |
| git checkout compat-4-2 | |
| pip install --editable . --upgrade | |
| cd .. | |
| pip install --editable . | |
| pip install wxpython==4.1.1 | |
| pip install https://github.com/DavidStirling/prokaryote/releases/download/v2.4.5/prokaryote-2.4.5.tar.gz --no-cache-dir --no-build-isolation | |
| pip install https://github.com/DavidStirling/python-bioformats/releases/download/v4.1.10001/python_bioformats-4.1.10001-py3-none-any.whl | |
| - name: Install plugins | |
| run: | | |
| pip install torch==2.2.1 | |
| pip install cellpose==3.0.5 | |
| pip install csbdeep==0.7.4 | |
| pip install stardist==0.8.1 | |
| pip install tensorflow==2.12.1 | |
| pip install markupsafe==2.0.1 | |
| pip install h5py==3.6.0 | |
| - name: Display installed packages | |
| run: pip list | |
| - if: startsWith(matrix.os, 'windows') | |
| name: Windows pyinstaller build and package | |
| run: | | |
| pyinstaller distribution/windows/cellprofiler.spec | |
| rm ./dist/CellProfiler/jvm.dll | |
| iscc /dMyAppVersion="4.2.80001-ai" "distribution/windows/cellprofiler.iss" | |
| - if: startsWith(matrix.os, 'macos') | |
| name: MacOS pyinstaller build and package | |
| run: | | |
| pyinstaller -y ./distribution/macos/CellProfiler.spec | |
| - if: startsWith(matrix.os, 'macos') | |
| name: MacOS dmg package | |
| continue-on-error: true | |
| run: | | |
| cd dist | |
| echo Creating DMG | |
| create-dmg 'CellProfiler+AI.app' --dmg-title "CellProfiler+AI.dmg" | |
| - if: startsWith(matrix.os, 'macos') | |
| uses: actions/upload-artifact@v4 | |
| name: MacOS dmg upload | |
| with: | |
| name: CellProfiler-macOS-4.2.80001-ai.dmg | |
| path: ./dist/*.dmg | |
| - if: startsWith(matrix.os, 'windows') | |
| uses: actions/upload-artifact@v4 | |
| name: Windows artifact upload | |
| with: | |
| name: CellProfiler-Windows-4.2.80001-ai.exe | |
| path: ./distribution/windows/Output/*.exe | |
| upload: | |
| name: upload | |
| needs: build | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.ref, 'refs/tags/') | |
| steps: | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ./ | |
| merge-multiple: true | |
| - name: Create release | |
| uses: softprops/action-gh-release@v2 | |
| with: | |
| draft: true | |
| files: | | |
| ./*.exe | |
| ./*.dmg | |
| name: create-release | |
| on: | |
| push: | |
| branches: | |
| - compat-4-2-ai | |
| tags: | |
| - "v*" | |
| pull_request: | |
| branches: | |
| - compat-4-2-ai |