GitHub actions

.github/actions/install-slicer/action.yml

@@ -0,0 +1,78 @@
+name: install-slicer
+author: Sebastien Goll (Kitware SAS)
+description: Install 3D Slicer
+inputs:
+  version:
+    description: Version of Slicer available at https://community.chocolatey.org/packages/3dslicer#versionhistory
+    default: ''
+outputs:
+  slicer_executable:
+    description: Slicer executable
+    value: ${{ steps.slicer_exe.outputs.executable }}
+
+runs:
+  using: composite
+  steps:
+    - name: Setting the permission
+      run: chmod +x "${{ github.action_path }}/downloader.sh"
+      shell: bash
+    - name: Download installer
+      run: |
+        "${{ github.action_path }}/downloader.sh" ${{ runner.os }}
+      shell: bash
+    - name: Get installer file
+      id: installer
+      run: |
+        installer=$(find "./installer" -maxdepth 1 -name "Slicer*" | head -n1 | xargs realpath)
+        echo "slicer_installer=$installer" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: Windows Slicer install
+      id: win_install
+      if: ${{runner.os == 'Windows'}}
+      run: |
+        ${{ steps.installer.outputs.slicer_installer }} //S
+        folder=$(find "C:/ProgramData/slicer.org" -maxdepth 1 -type d -name Slicer* -exec stat --format "%Y %n" {} + |sort -nr | head -n1 | cut -d' ' -f2-)
+        echo "executable=$folder/Slicer.exe" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: Linux env setup
+      if: ${{ runner.os == 'Linux' }}
+      run: |
+        sudo apt-get install libglu1-mesa libpulse-mainloop-glib0 libnss3 libasound2t64 qt5dxcb-plugin libxcb-util1 xvfb
+        mkdir ./Slicer
+        export DISPLAY=:99
+        Xvfb :99 -screen 0 1920x1080x24 > /dev/null 2>&1 &
+        echo "DISPLAY=:99" >> $GITHUB_ENV
+      shell: bash
+    - name: Linux Slicer install
+      id: linux_install
+      if: ${{ runner.os == 'Linux' }}
+      run: |
+        tar xzf "${{ steps.installer.outputs.slicer_installer }}" -C "."
+        folder=$(find "." -maxdepth 1 -name "Slicer*" -type d | head -n1 | xargs realpath)
+        echo "executable=$folder/Slicer" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: Max env setup
+      if: ${{ runner.os == 'macOS' }}
+      run: |
+        brew install expect
+        chmod +x "${{ github.action_path }}/macos_installer.exp"
+      shell: bash
+    - name: Mac Slicer install
+      if: ${{ runner.os == 'macOS' }}
+      id: mac_install
+      run: |
+        MOUNT_POINT=$("${{ github.action_path }}/macos_installer.exp" ${{ steps.installer.outputs.slicer_installer }} | grep -o '/Volumes/[^ ]*'| tr -d '\r\n')
+        cp -R "$MOUNT_POINT/Slicer.app" /Applications/
+        hdiutil detach "$MOUNT_POINT"
+        echo "executable=/Applications/Slicer.app/Contents/MacOS/Slicer" >> $GITHUB_OUTPUT
+      shell: bash
+    - id: slicer_exe
+      run: |
+        if [ ${{ runner.os }} == "Windows" ]; then
+          echo "executable=${{ steps.win_install.outputs.executable }}" >> $GITHUB_OUTPUT
+        elif [ ${{ runner.os }} == "Linux" ]; then
+          echo "executable=${{ steps.linux_install.outputs.executable }}" >> $GITHUB_OUTPUT
+        elif [ ${{ runner.os }} == "macOS" ]; then
+          echo "executable=${{ steps.mac_install.outputs.executable }}" >> $GITHUB_OUTPUT
+        fi
+      shell: bash

.github/actions/install-slicer/downloader.sh

@@ -0,0 +1,30 @@
+if [ $1 == "Windows" ]; then
+    PACK_OS="win"
+elif [ $1 == "Linux" ]; then
+  PACK_OS="linux"
+elif [ $1 == "macOS" ]; then
+  PACK_OS="macosx"
+fi
+
+PACK_ARCH="amd64"
+BASE_URL="https://slicer-packages.kitware.com/api/v1"
+
+APP_ID=$(curl -s "$BASE_URL/app?name=Slicer&limit=1" | jq -r '.[0]._id')
+echo "Application id found for Slicer: $APP_ID"
+
+RELEASE_NAME=$(curl -s "$BASE_URL/app/$APP_ID/release?sort=meta.revision&sortdir=-1" | jq -r '.[0].lowerName')
+echo "Realease name found: $RELEASE_NAME"
+
+PACK=$(curl -s "$BASE_URL/app/$APP_ID/package?release_id_or_name=$RELEASE_NAME&os=$PACK_OS&arch=$PACK_ARCH&limit=1" | jq '.[0]')
+PACK_ID=$(jq -r '._id' <<< "$PACK")
+PACK_NAME=$(jq -r '.name' <<< "$PACK")
+echo "Name of the package found: $PACK_NAME ($PACK_ID)"
+
+mkdir -p installer
+
+HEADER_TMP=$(mktemp)
+curl -# -D "$HEADER_TMP" "$BASE_URL/item/$PACK_ID/download" -o file
+CONTENT_DISPOSITION=$(grep -i '^Content-Disposition:' "$HEADER_TMP")
+FILENAME=$(echo "$CONTENT_DISPOSITION" | sed -n 's/.*filename="\(.*\)".*/\1/p')
+mv file "installer/$FILENAME"
+

.github/actions/install-slicer/macos_installer.exp

@@ -0,0 +1,17 @@
+#!/usr/bin/expect -f
+
+set timeout 10
+set dmg_file [lindex $argv 0]
+
+spawn hdiutil attach "$dmg_file"
+
+sleep 2
+send "q\r"
+
+expect {
+    "Agree Y/N?" {
+        send "y\r"
+    }
+}
+
+expect eof

.github/actions/slicer-install-extensions/action.yml

@@ -0,0 +1,23 @@
+name: slicer-install-extensions
+author: Sebastien Goll (Kitware SAS)
+description: Install extensions for Slicer
+
+inputs:
+  slicer_exe:
+    description: Slicer executable
+    required: true
+  additional_arguments:
+    description: Additional arguments for Slicer executable
+    default: '--no-main-window --no-splash'
+  extensions_name:
+    description: Extensions names to install
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - uses: ./.github/actions/slicer-run-python-script
+      with:
+        script: ${{ github.action_path }}/install_extensions.py
+        slicer_exe: ${{ inputs.slicer_exe }}
+        additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.extensions_name }}

.github/actions/slicer-install-extensions/install_extensions.py

@@ -0,0 +1,15 @@
+import sys
+import slicer.util
+
+if __name__ == '__main__':
+
+    extension_names = sys.argv[1:]
+    print("Found extensions: ", extension_names)
+
+    em = slicer.app.extensionsManagerModel()
+    em.setInteractive(False)
+
+    for name in extension_names:
+        em.installExtensionFromServer(name, False)
+
+    slicer.util.quit()

.github/actions/slicer-install-python-packages/action.yml

@@ -0,0 +1,22 @@
+name: slicer-install-python-packages
+author: Sebastien Goll (Kitware SAS)
+description: Install python packages in Slicer's python environment
+
+inputs:
+  slicer_exe:
+    description: Slicer directory
+    required: true
+  additional_arguments:
+    description: Additional arguments for Slicer executable
+    default: '--no-main-window --no-splash'
+  package_names:
+    description: Packages to install
+    required: true
+runs:
+  using: composite
+  steps:
+    - uses: ./.github/actions/slicer-run-python-script
+      with:
+        script: ${{ github.action_path }}/install_py_packages.py
+        slicer_exe: ${{ inputs.slicer_exe }}
+        additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.package_names }}

.github/actions/slicer-install-python-packages/install_py_packages.py

@@ -0,0 +1,11 @@
+import sys
+
+import slicer.util
+
+if __name__ == "__main__":
+
+    print("Packages found:",sys.argv[1:])
+
+    for package in sys.argv[1:]:
+        slicer.util.pip_install(package)
+    slicer.util.quit()

.github/actions/slicer-run-python-script/action.yml

@@ -0,0 +1,19 @@
+name: slicer-run-python-script
+author: Sebastien Goll (Kitware SAS)
+description: Run a python script through Slicer
+inputs:
+  slicer_exe:
+    description: Slicer executable
+    required: true
+  script:
+    description: Path to python to run
+    required: true
+  additional_arguments:
+    description: Additional arguments for Slicer executable
+    default: ''
+runs:
+  using: composite
+  steps:
+    - run: |
+        "${{inputs.slicer_exe}}" --python-script "${{ inputs.script }}" ${{ inputs.additional_arguments }}
+      shell: bash

.github/actions/slicer-run-python-tests/action.yml

@@ -0,0 +1,29 @@
+name: slicer-run-python-tests
+author: Sebastien Goll (Kitware SAS)
+description: Run python tests in Slicer
+
+inputs:
+  slicer_exe:
+    description: Slicer directory
+    required: true
+  additional_arguments:
+    description: Additional arguments for Slicer executable
+    default: ''
+  tests_root_path:
+    description: Root path to search for tests
+    required: true
+  tests_name_pattern:
+    description: Pattern used to find test files
+    required: true
+  module_paths:
+    description: Paths to the tested modules
+    required: true
+
+runs:
+  using: composite
+  steps:
+    - uses: ./.github/actions/slicer-run-python-script
+      with:
+        script: ${{ github.action_path }}/run_tests.py
+        slicer_exe: ${{ inputs.slicer_exe }}
+        additional_arguments: --additional-module-paths ${{ inputs.module_paths }} ${{ inputs.additional_arguments }} ${{ inputs.tests_root_path }} ${{ inputs.tests_name_pattern }}

.github/actions/slicer-run-python-tests/run_tests.py

@@ -0,0 +1,17 @@
+import sys
+from pathlib import Path
+
+import slicer.testing
+
+if __name__ == "__main__":
+
+    if len(sys.argv) < 3:
+        raise AttributeError(f"run_tests.py requires 2 arguments, found {sys.argv[1:]}")
+
+    root = Path(sys.argv[1])
+    files = list(root.glob(sys.argv[2]))
+
+    print(f"Found {len(files)} test file(s).")
+
+    for file in files:
+        slicer.testing.runUnitTest(file.parent.as_posix(), file.stem)

.github/python_scripts/install_python_dependencies.py

@@ -0,0 +1,16 @@
+from pathlib import Path
+
+import slicer.util
+import sys
+
+if __name__ == '__main__':
+    sys.path.append(Path(__file__).parent.joinpath("../..").resolve().as_posix())
+
+    from MultiverSeg.SegmentEditorMultiverSegLib import InstallLogic, DependenciesLogic
+    DependenciesLogic.INTERACTIVE_MODE = False
+    InstallLogic.INTERACTIVE_MODE = False
+
+    DependenciesLogic.installTorchIfNeeded()
+    DependenciesLogic.installMultiverSegIfNeeded()
+    InstallLogic.downloadCheckpointsIfNeeded()
+    slicer.util.quit()

.github/python_scripts/install_pytorch_module.py

@@ -0,0 +1,14 @@
+import sys
+from pathlib import Path
+
+import slicer.util
+
+
+
+if __name__ == '__main__':
+    sys.path.append(Path(__file__).parent.joinpath("../..").resolve().as_posix())
+
+    from MultiverSeg.SegmentEditorMultiverSegLib import DependenciesLogic
+    DependenciesLogic.INTERACTIVE_MODE = False
+    DependenciesLogic.installPyTorchExtensionIfNeeded()
+    slicer.util.quit()