build.yml

name: Build

on:
  push:
    branches: [ master ]
    tags: '*'
  pull_request:
    branches: [ master ]

env:
  tool-id: nionswift-tool
  tool-package: nionswift
  tool-exe: nionswift --app

jobs:
  build_linux:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04]
        python-version: ["3.11", "3.12", "3.13"]
        qt-version: ["6.8.1"]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Display Python version
      shell: bash
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
    - name: Install Qt
      uses: jurplel/install-qt-action@v3
      with:
        version: ${{ matrix.qt-version }}
        host: 'linux'
        target: 'desktop'
        arch: 'linux_gcc_64'
    - name: Build
      shell: bash
      run: |
        python -m pip install --upgrade pip
        python -m pip install setuptools --upgrade
        python -m pip install packaging build cibuildwheel
        pushd launcher
        PYTHON=`python -c "import sys; print(sys.executable, end='')"`
        cmake CMakeLists.txt -DGIT_REPO=${{ github.repository }} -DGIT_REF=${{ github.ref }} -DGIT_SHA=${{ github.sha }}
        cmake --build . --config Release
        mkdir -p linux
        mv build linux/x64
        popd
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6Core.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6DBus.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6Gui.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6OpenGL.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6Widgets.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libQt6XcbQpa.so.6 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libicui18n.so.73 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libicudata.so.73 launcher/linux/x64
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/lib/libicuuc.so.73 launcher/linux/x64
        mkdir -p launcher/linux/x64/plugins/platforms
        mkdir -p launcher/linux/x64/plugins/imageformats
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/plugins/platforms/libqxcb.so launcher/linux/x64/plugins/platforms
        cp ../Qt/${{ matrix.qt-version }}/gcc_64/plugins/imageformats/libq* launcher/linux/x64/plugins/imageformats
        rm launcher/linux/x64/plugins/imageformats/libqsvg.so
        chrpath -r "\$ORIGIN" launcher/linux/x64/libicu*.so.73
        chrpath -r "\$ORIGIN/../.." launcher/linux/x64/plugins/platforms/libqxcb.so
        chrpath -r "\$ORIGIN/../.." launcher/linux/x64/plugins/imageformats/*.so
        printf "[Paths]\nPrefix=.\nPlugins=plugins\n" > launcher/linux/x64/qt.conf
        python -m build .
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.11"
        miniconda-version: "latest"
    - name: Build Conda Package
      shell: bash -l {0}
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
        conda update --all -q -y
        conda install -q conda-build -y
        conda build -q --python ${{ matrix.python-version }} ./.github/workflows/recipe
        OUT_FILE=$(conda build --python ${{ matrix.python-version }} --output ./.github/workflows/recipe)
        mv $OUT_FILE dist
    - name: Upload Wheel
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-linux-whl-${{ matrix.python-version }}
        path: dist/*.whl
    - name: Upload Conda Package
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-linux-conda-${{ matrix.python-version }}
        path: dist/*.tar.bz2
  build_macos:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macos-13]
        python-version: ["3.11", "3.12", "3.13"]
        architecture: [x86_64]
        qt-version: ["6.8.1"]
        include:
            - os: macos-14
              python-version: "3.12"
              architecture: arm64
              qt-version: "6.8.1"
            - os: macos-14
              python-version: "3.13"
              architecture: arm64
              qt-version: "6.8.1"
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Display Python version
      shell: bash
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
    - name: Install Qt
      uses: jurplel/install-qt-action@v3
      with:
        version: ${{ matrix.qt-version }}
        host: 'mac'
        target: 'desktop'
    - name: Build
      shell: bash
      env:
        MACOS_CERTIFICATE: ${{ secrets.MACOS_CERTIFICATE }}
        MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
        MACOS_KEYCHAIN_PASSWORD: ${{ secrets.MACOS_KEYCHAIN_PASSWORD }}
        MACOS_DEVELOPER_TEAM_ID: ${{ secrets.MACOS_DEVELOPER_TEAM_ID }}
      run: |
        APPNAME="Nion Swift"
        python -m pip install --upgrade pip
        python -m pip install --upgrade setuptools
        python -m pip install packaging build cibuildwheel
        pushd launcher
        PYTHON=`python -c "import sys; print(sys.executable, end='')"`
        cmake CMakeLists.txt -DGIT_REPO=${{ github.repository }} -DGIT_REF=${{ github.ref }} -DGIT_SHA=${{ github.sha }}
        cmake --build . --config Release
        pushd build
        echo -n "$MACOS_CERTIFICATE" | base64 -d > certificate.p12
        echo "Create keychain"
        security create-keychain -p "$MACOS_KEYCHAIN_PASSWORD" build.keychain
        echo "Set default keychain"
        security default-keychain -s build.keychain
        echo "Unlock keychain"
        security unlock-keychain -p "$MACOS_KEYCHAIN_PASSWORD" build.keychain
        echo "Import certificate (disabled)"
        security import certificate.p12 -k build.keychain -P "$MACOS_CERTIFICATE_PWD" -T /usr/bin/codesign
        echo "Find identity"
        security find-identity -v
        echo "Set key partition list (avoids dialog)"
        security set-key-partition-list -S apple-tool:,apple:,codesign: -s -k "$MACOS_KEYCHAIN_PASSWORD" build.keychain
        echo "Code sign"
        # remove files that will not be signed and have can be regenerated
        find "$APPNAME.app" -name "__pycache__" -exec rm -rf {} \; -prune
        find "$APPNAME.app" -name "*.pyc" -exec rm -rf {} \; -prune
        # sign files from the inside out. first ensure that dylibs are executable. then find all executable files
        # and sign them. then sign apps within frameworks. then sign frameworks. then sign the app itself.
        codesign --remove-signature --deep --force "$APPNAME.app/Contents/MacOS/$APPNAME"
        find "$APPNAME.app" -name "*.dylib" -exec chmod +x {} \;
        find "$APPNAME.app" -type f -perm +111 -and -not -name "*.py" -exec /usr/bin/codesign -s "$MACOS_DEVELOPER_TEAM_ID" {} --options runtime --timestamp --deep --force --verbose \;
        find "$APPNAME.app/Contents/Frameworks" -name "*.app" -exec /usr/bin/codesign -s "$MACOS_DEVELOPER_TEAM_ID" {} --options runtime --timestamp --deep --force --verbose \;
        find "$APPNAME.app" -name "*.framework" -exec /usr/bin/codesign -s "$MACOS_DEVELOPER_TEAM_ID" {} --options runtime --timestamp --deep --force --verbose \;
        /usr/bin/codesign -s "$MACOS_DEVELOPER_TEAM_ID" "$APPNAME.app" --entitlements ../entitlements.xml --options runtime --timestamp --deep --force --verbose
        rm certificate.p12
        popd
        mkdir -p build/Release
        mv build/*.app build/Release
        tar -czf "build/Release/$APPNAME.app.tar.gz" "build/Release/$APPNAME.app"
        popd
        PYTHON_VERSION_COMPRESSED=$(echo "${{ matrix.python-version }}" | sed 's/\.//g')
        export CIBW_ARCHS_MACOS="${{ matrix.architecture }}"
        export CIBW_BUILD=cp$PYTHON_VERSION_COMPRESSED-macosx_${{ matrix.architecture }}
        export CIBW_REPAIR_WHEEL_COMMAND=""
        python -m cibuildwheel --output-dir dist
    - name: Upload Wheel
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-macos-whl-${{ matrix.architecture }}-${{ matrix.python-version }}
        path: dist/*.whl
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.11"
        miniconda-version: "latest"
        architecture: ${{ matrix.architecture }}
    - name: Build Conda Package
      shell: bash -l {0}
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
        conda update --all -q -y
        conda install -q conda-build -y
        conda build -q --python ${{ matrix.python-version }} ./.github/workflows/recipe
        OUT_FILE=$(conda build --python ${{ matrix.python-version }} --output ./.github/workflows/recipe)
        mv $OUT_FILE dist
    - name: Upload Conda Package
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-macos-conda-${{ matrix.architecture }}-${{ matrix.python-version }}
        path: dist/*.tar.bz2
  build_win:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-2019]
        python-version: ["3.11", "3.12", "3.13"]
        qt-version: ["6.8.1"]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Display Python version
      shell: pwsh
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
    - name: Install Qt
      uses: jurplel/install-qt-action@v3
      with:
        version: ${{ matrix.qt-version }}
        host: 'windows'
        target: 'desktop'
        arch: 'win64_msvc2022_64'
    - name: Build
      shell: pwsh
      run: |
        python -m pip install --upgrade pip
        python -m pip install --upgrade setuptools
        python -m pip install packaging build cibuildwheel
        pushd launcher
        $PYTHON_EXEC = python -c "import sys; print(sys.executable, end='')"
        cmake CMakeLists.txt -DGIT_REPO=${{ github.repository }} -DGIT_REF=${{ github.ref }} -DGIT_SHA=${{ github.sha }}
        cmake --build . --config Release
        Get-ChildItem -Include *.pdb -Recurse | foreach { $_.Delete() }
        Get-ChildItem build\Release\imageformats -Include *d.dll -Recurse | foreach { $_.Delete() }
        Rename-Item -Path build\Release\NionSwiftLauncher.exe -NewName NionSwift.exe
        Remove-Item -Recurse -Force x64\*
        Move-Item -Path build\Release -Destination x64
        popd
        python -m build .
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        python-version: "3.11"
        miniconda-version: "latest"
    - name: Build Conda Package
      shell: bash -l {0}
      run: |
        python -c "import sys; print(sys.version)"
        python -c "import sys; print(sys.executable)"
        conda update --all -q -y
        conda install -q conda-build -y
        conda build -q --python ${{ matrix.python-version }} ./.github/workflows/recipe
        OUT_FILE=$(conda build --python ${{ matrix.python-version }} --output ./.github/workflows/recipe)
        mv $OUT_FILE dist
    - name: Upload Wheel
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-win-whl-${{ matrix.python-version }}
        path: dist/*.whl
    - name: Upload Conda Package
      uses: actions/upload-artifact@v4
      with:
        name: ${{ env.tool-id }}-win-conda-${{ matrix.python-version }}
        path: dist/*.tar.bz2
  test_linux:
    needs: build_linux
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
        python-version: ["3.11", "3.12", "3.13"]
    steps:
    - uses: actions/checkout@v4
    - name: Download Wheel
      uses: actions/download-artifact@v4
      id: download_wheel
      with:
        name: ${{ env.tool-id }}-linux-whl-${{ matrix.python-version }}
        path: downloads
    - name: Download Conda
      uses: actions/download-artifact@v4
      id: download_conda
      with:
        name: ${{ env.tool-id }}-linux-conda-${{ matrix.python-version }}
        path: conda_downloads
    - name: Set up Python ${{ matrix.python-version }} with official build
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Virtual screen
      shell: bash
      run: |
        # update package list. see https://github.com/actions/runner-images/issues/10785#issuecomment-2420741561
        sudo apt-get update
        sudo apt-get install xvfb -y
        # libopengl0: see https://bugreports.qt.io/browse/QTBUG-89754
        sudo apt-get install libopengl0 -y
        # see https://doc.qt.io/qt-6/linux-requirements.html
        sudo apt-get install libegl1 libfontconfig1 libfreetype6 libxcb1 libxcb-glx0 libxcb-keysyms1 libxcb-image0 libxcb-shm0 libxcb-icccm4 libxcb-xfixes0 libxcb-shape0 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xkb1 libxkbcommon-x11-0 libxcb-sync1 libxcb-cursor0 -y
        # sudo apt-get install libx11 libx11-xcb libxext libxfixes libxi libxrender libxcb-sync libxcb-util libxkbcommon
    - name: Test system Python installed with official build with virtual environment
      shell: bash
      run: |
        sudo apt update
        python -m pip install --upgrade pip
        SYSTEM_PYTHON_EXE=python
        $SYSTEM_PYTHON_EXE -m venv test_venv
        source test_venv/bin/activate
        python -m pip install --upgrade pip
        python -m pip install setuptools
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # python -m pip install ${{ env.tool-package }}
        python -m pip install ${{steps.download_wheel.outputs.download-path}}/*.whl
        python -m pip install numpy scipy h5py
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test... ${{ env.tool-exe }}"
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack
        sleep 5
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        sleep 5
        deactivate
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        activate-environment: test-environment
        miniconda-version: "latest"
        python-version: ${{ matrix.python-version }}
        auto-activate-base: false
    - name: Test Conda
      # this test is disabled on ubuntu until default channel supports numpy 2
      if: False
      shell: bash -l {0}
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        conda create -q -n test-env-conda -c conda-forge python=${{ matrix.python-version }} numpy scipy h5py imageio setuptools pip -y
        conda activate test-env-conda
        # this does not work on ubuntu with Qt 6.8.
        # until numpy 2 is available, use pip
        # pip install numpy scipy h5py imageio setuptools
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion ${{ env.tool-package }}
        conda install -q -y ${{steps.download_conda.outputs.download-path}}/*.tar.bz2
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack
        sleep 5
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        sleep 5
        conda deactivate
    - name: Test Conda Forge
      shell: bash -l {0}
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        conda create -q -n test-env -c conda-forge python=${{ matrix.python-version }} numpy scipy h5py imageio setuptools -y
        conda activate test-env
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion -c conda-forge ${{ env.tool-package }}
        conda install -q -y -c conda-forge ${{steps.download_conda.outputs.download-path}}/*.tar.bz2
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack
        sleep 5
        xvfb-run -a ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        sleep 5
        conda deactivate
    - name: Build/publish anaconda package
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'ubuntu-20.04'
      shell: bash -l {0}
      run: |
        # make a directory to avoid name conflicts with the channel. argh.
        mkdir conda_build
        pushd conda_build
        echo "conda create anaconda-client env"
        conda create -n upload-env -q conda-build anaconda-client -y
        echo "activate"
        conda activate upload-env
        echo "conda info"
        conda info
        echo "conda list"
        conda list
        echo "directory list"
        ls -Rl ${{steps.download_conda.outputs.download-path}}
        echo "anaconda upload"
        anaconda --token ${{ secrets.anaconda_token }} upload --user nion --skip-existing ${{steps.download_conda.outputs.download-path}}/*.tar.bz2
        echo "deactivate"
        conda deactivate
        echo "popd"
        popd
  test_macos:
    needs: build_macos
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [macos-13]
        python-version: ["3.11", "3.12", "3.13"]
        architecture: [x86_64]
        qt-version: ["6.8.1"]
        include:
            - os: macos-14
              python-version: "3.12"
              architecture: arm64
              qt-version: "6.8.1"
            - os: macos-14
              python-version: "3.13"
              architecture: arm64
              qt-version: "6.8.1"
    steps:
    - uses: actions/checkout@v4
    - name: Download Wheel
      uses: actions/download-artifact@v4
      id: download_wheel
      with:
        name: ${{ env.tool-id }}-macos-whl-${{ matrix.architecture }}-${{ matrix.python-version }}
        path: downloads
    - name: Download Conda
      uses: actions/download-artifact@v4
      id: download_conda
      with:
        name: ${{ env.tool-id }}-macos-conda-${{ matrix.architecture }}-${{ matrix.python-version }}
        path: conda_downloads
    - name: Set up Python ${{ matrix.python-version }} with official build
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Test system Python installed with brew with virtual environment
      shell: bash
      run: |
        brew update
        brew install python@${{ matrix.python-version }} || true
        SYSTEM_PYTHON_EXE=/usr/local/bin/python${{ matrix.python-version }}
        $SYSTEM_PYTHON_EXE -m venv test_venv
        source test_venv/bin/activate
        python -m pip install --upgrade pip
        python -m pip install setuptools
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # python -m pip install ${{ env.tool-package }}
        python -m pip install ${{steps.download_wheel.outputs.download-path}}/*.whl
        python --version
        python -m pip install numpy scipy h5py
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
    - name: Test system Python installed with official build with virtual environment
      shell: bash
      run: |
        SYSTEM_PYTHON_EXE=python3
        $SYSTEM_PYTHON_EXE -m venv test_venv
        source test_venv/bin/activate
        python -m pip install --upgrade pip
        python -m pip install setuptools
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # python -m pip install ${{ env.tool-package }}
        python -m pip install ${{steps.download_wheel.outputs.download-path}}/*.whl
        python --version
        python -m pip install numpy scipy h5py
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        deactivate
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        activate-environment: test-environment
        miniconda-version: "latest"
        python-version: ${{ matrix.python-version }}
        architecture: ${{ matrix.architecture }}
        auto-activate-base: false
    - name: Test Conda
      shell: bash -l {0}
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        # until numpy 2 is available, use pip
        pip install numpy scipy h5py imageio setuptools
        ## use nomkl until anaconda gets its act together
        # conda install -q nomkl numpy scipy h5py imageio setuptools -y
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion ${{ env.tool-package }}
        FILENAME=$(find '${{steps.download_conda.outputs.download-path}}' -name "*.tar.bz2")
        echo "Installing '$FILENAME'"
        conda install -q -y -c conda-forge $FILENAME
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
    - name: Test Conda Forge
      shell: bash -l {0}
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        # use nomkl until anaconda gets its act together
        conda create -n test-env -c conda-forge -q python=${{ matrix.python-version }} numpy scipy h5py imageio setuptools -y
        conda activate test-env
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion -c conda-forge ${{ env.tool-package }}
        FILENAME=$(find '${{steps.download_conda.outputs.download-path}}' -name "*.tar.bz2")
        echo "Installing '$FILENAME'"
        conda install -q -y -c conda-forge $FILENAME
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        conda deactivate
    - name: Build/publish anaconda package
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
      shell: bash -l {0}
      run: |
        # make a directory to avoid name conflicts with the channel. argh.
        mkdir conda_build
        pushd conda_build
        conda create -n upload-env -q conda-build anaconda-client -y
        conda activate upload-env
        FILENAME=$(find '${{steps.download_conda.outputs.download-path}}' -name "*.tar.bz2")
        echo "Send to Anaconda '$FILENAME'"
        anaconda --token ${{ secrets.anaconda_token }} upload --user nion --skip-existing $FILENAME
        conda deactivate
        popd
  test_win:
    needs: build_win
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-2019]
        python-version: ["3.11", "3.12", "3.13"]
    steps:
    - uses: actions/checkout@v4
    - name: Download Wheel
      uses: actions/download-artifact@v4
      id: download_wheel
      with:
        name: ${{ env.tool-id }}-win-whl-${{ matrix.python-version }}
        path: downloads
    - name: Download Conda
      uses: actions/download-artifact@v4
      id: download_conda
      with:
        name: ${{ env.tool-id }}-win-conda-${{ matrix.python-version }}
        path: conda_downloads
    - name: Set up Python ${{ matrix.python-version }} with official build
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}
    - name: Test system Python installed with official build with virtual environment
      shell: pwsh
      run: |
        python -m pip install --upgrade pip
        python -m venv test_venv
        test_venv\Scripts\activate
        python -m pip install --upgrade pip
        python -m pip install setuptools
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # python -m pip install ${{ env.tool-package }}
        $filename = Get-ChildItem -name ${{steps.download_wheel.outputs.download-path}}\*.whl
        python -m pip install ${{steps.download_wheel.outputs.download-path}}\$filename
        python --version
        python -m pip install numpy scipy h5py
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        deactivate
    - name: Set up Miniconda ${{ matrix.python-version }}
      uses: conda-incubator/setup-miniconda@v3
      with:
        auto-update-conda: true
        activate-environment: test-environment
        miniconda-version: "latest"
        python-version: ${{ matrix.python-version }}
        auto-activate-base: false
    - name: Test Conda
      shell: pwsh
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        conda update -q --all -y
        # until numpy 2 is available, use pip
        pip install numpy scipy h5py imageio setuptools
        # conda install -q numpy scipy h5py imageio setuptools pip -y
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion ${{ env.tool-package }}
        $filename = Get-ChildItem -name ${{steps.download_conda.outputs.download-path}}\*.tar.bz2
        conda install -q -y ${{steps.download_conda.outputs.download-path}}\$filename
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
    - name: Test Conda Forge
      shell: pwsh
      run: |
        # use conda versions instead of pypi versions. install before anything else.
        conda create -n test-env -c conda-forge -q python=${{ matrix.python-version }} numpy scipy h5py imageio setuptools -y
        conda activate test-env
        # until numpy 2 compatible versions are on nion channel, use direct source
        pip install git+https://github.com/nion-software/nionutils.git#egg=nionutils
        pip install git+https://github.com/nion-software/nionui.git#egg=nionui
        pip install git+https://github.com/nion-software/niondata.git#egg=niondata
        pip install git+https://github.com/nion-software/nionswift-io.git#egg=nionswift-io
        pip install git+https://github.com/nion-software/nionswift.git#egg=nionswift
        # conda install -q -y -c nion -c conda-forge ${{ env.tool-package }}
        $filename = Get-ChildItem -name ${{steps.download_conda.outputs.download-path}}\*.tar.bz2
        conda install -q -y -c conda-forge ${{steps.download_conda.outputs.download-path}}\$filename
        pushd nionui_app_test
        python -m pip install .
        popd
        echo "Running test..."
        conda list
        ${{ env.tool-exe }} nionui_app.test_ack
        ${{ env.tool-exe }} nionui_app.test_ack | grep ACK
        conda deactivate
    - name: Build/publish anaconda package
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && matrix.os == 'windows-2019'
      shell: bash -l {0}
      run: |
        # make a directory to avoid name conflicts with the channel. argh.
        mkdir conda_build
        pushd conda_build
        conda create -n upload-env -q conda-build anaconda-client -y
        conda activate upload-env
        FILENAME=$(find '${{steps.download_conda.outputs.download-path}}' -name "*.tar.bz2")
        echo "Send to Anaconda '$FILENAME'"
        anaconda --token ${{ secrets.anaconda_token }} upload --user nion --skip-existing $FILENAME
        conda deactivate
        popd
  pypi-publish:
    name: Upload release to PyPI
    needs: [test_linux, test_macos, test_win]
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
    environment:
      name: release
      url: https://pypi.org/p/nionswift-tool
    permissions:
      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
    steps:
    - name: Download All Artifacts
      uses: actions/download-artifact@v4
    - name: Remove all the files except the ones to upload to PyPI.
      shell: bash
      run: |
        mkdir dist
        find . -name "*cp311*.whl" -exec cp {} dist \;
        ls -Rl .
    - name: Publish package distributions to PyPI
      uses: pypa/gh-action-pypi-publish@release/v1
      with:
        skip-existing: true
        print-hash: true