From bc3db60911f3959ad221bfb240a4ee5f7619c8a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:38:33 +0200
Subject: [PATCH 01/16] ENH: Add option to run installation in non-interactive
 mode (no popups/prompting)

---
 .../InstallLogic.py                           | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/MultiverSeg/SegmentEditorMultiverSegLib/InstallLogic.py b/MultiverSeg/SegmentEditorMultiverSegLib/InstallLogic.py
index dfc71c6..1fb7715 100644
--- a/MultiverSeg/SegmentEditorMultiverSegLib/InstallLogic.py
+++ b/MultiverSeg/SegmentEditorMultiverSegLib/InstallLogic.py
@@ -14,6 +14,8 @@ class InstallLogic:
     SCRIBBLEPROMPT_FILE_NAME = "ScribblePrompt_unet_v1_nf192_res128.pt"
     SCRIBBLEPROMPT_DOWNLOAD_URL = "https://www.dropbox.com/scl/fi/pnw88n05irnv5z1snlklr/ScribblePrompt_unet_v1_nf192_res128.pt?rlkey=dr8xvkf0wj2r082h1zzpcmz5o&dl=1"
 
+    INTERACTIVE_MODE = True  # Can the user interact with the window
+
     @classmethod
     def downloadCheckpointsIfNeeded(cls):
         try:
@@ -32,7 +34,8 @@ def downloadMultiverSegCheckpointIfNeeded(cls):
         modelPath = cls.CKPT_DIR.joinpath("MultiverSeg_v0_nf256_res128.pt")
 
         if not modelPath.is_file():
-            if slicer.util.confirmOkCancelDisplay("The MultiverSeg model is required. Confirm to download (74MB)."):
+            if (not cls.INTERACTIVE_MODE) or slicer.util.confirmOkCancelDisplay(
+                    "The MultiverSeg model is required. Confirm to download (74MB)."):
 
                 cls._downloadModel(cls.MULTIVERSEG_FILE_NAME, cls.MULTIVERSEG_DOWNLOAD_URL)
                 return True  # Model downloaded correctly
@@ -45,7 +48,7 @@ def downloadScribblePromptCheckpointIfNeeded(cls):
         modelPath = cls.CKPT_DIR.joinpath(cls.SCRIBBLEPROMPT_FILE_NAME)
 
         if not modelPath.is_file():
-            if slicer.util.confirmOkCancelDisplay("The ScribblePrompt model is required. Confirm to download (16MB)."):
+            if (not cls.INTERACTIVE_MODE) or slicer.util.confirmOkCancelDisplay("The ScribblePrompt model is required. Confirm to download (16MB)."):
 
                 cls._downloadModel(cls.SCRIBBLEPROMPT_FILE_NAME, cls.SCRIBBLEPROMPT_DOWNLOAD_URL)
 
@@ -89,6 +92,7 @@ def reportProgress(logic, msg, level=None):
 
 
 class DependenciesLogic:
+    INTERACTIVE_MODE = True  # Can the user interact with the window
 
     # Install dependencies to torch and multiverseg if not already installed
     @classmethod
@@ -114,7 +118,7 @@ def installPyTorchExtensionIfNeeded(cls):
             import PyTorchUtils  # noqa
             return True
         except ModuleNotFoundError:
-            ret = slicer.util.confirmOkCancelDisplay("""This module requires PyTorch extension. Would you like to install it?
+            ret = (not cls.INTERACTIVE_MODE) or slicer.util.confirmOkCancelDisplay("""This module requires PyTorch extension. Would you like to install it?
                 
 Slicer will need to be restarted before continuing the install.""", "PyTorch extension not found.")
             if ret:
@@ -122,9 +126,10 @@ def installPyTorchExtensionIfNeeded(cls):
             return False  # Need restart or not installed
 
     # Install the PyTorch Utils extension
-    @staticmethod
-    def installPyTorchExtension():
+    @classmethod
+    def installPyTorchExtension(cls):
         extensionManager = slicer.app.extensionsManagerModel()
+        extensionManager.setInteractive(cls.INTERACTIVE_MODE)
         extName = "PyTorch"
         if extensionManager.isExtensionInstalled(extName):
             return
@@ -140,7 +145,7 @@ def installMultiverSegIfNeeded(cls):
             import multiverseg
             return True
         except ModuleNotFoundError:
-            ret = slicer.util.confirmOkCancelDisplay(
+            ret = (not cls.INTERACTIVE_MODE) or slicer.util.confirmOkCancelDisplay(
                 "This module requires the MultiverSeg python package. Would you like to install it?",
                 "MultiverSeg package not found.")
             if ret:
@@ -169,7 +174,7 @@ def installTorchIfNeeded(cls):
     def installTorch(cls):
         import PyTorchUtils
         torchLogic = PyTorchUtils.PyTorchUtilsLogic()
-        res = torchLogic.installTorch(askConfirmation=True)
+        res = torchLogic.installTorch(askConfirmation=cls.INTERACTIVE_MODE, torchvisionVersionRequirement=">=0.10")
 
         if res is None:
             raise RuntimeError("Failed to install torch and torchvision. "

From 5a310851d9b5dc29b0f0838b4e6251ce430df91c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:46:35 +0200
Subject: [PATCH 02/16] CI: Create action for slicer installation

---
 .github/actions/install-slicer/action.yml | 25 +++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 .github/actions/install-slicer/action.yml

diff --git a/.github/actions/install-slicer/action.yml b/.github/actions/install-slicer/action.yml
new file mode 100644
index 0000000..b9ebbf7
--- /dev/null
+++ b/.github/actions/install-slicer/action.yml
@@ -0,0 +1,25 @@
+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_folder:
+    description: Installation folder for Slicer
+    value: ${{ steps.slicer_folder.outputs.slicer_folder }}
+
+runs:
+  using: composite
+  steps:
+    - if: ${{runner.os == 'Windows'}}
+      run: choco install 3dslicer -y --version=${{ inputs.version }} --allowdowngrade
+      shell: bash
+    - if: ${{runner.os == 'Windows'}}
+      id: slicer_folder
+      shell: bash
+      run: |
+        folder=$(find "C:/ProgramData/slicer.org" -maxdepth 1 -type d -name Slicer* -exec stat --format "%Y %n" {} + |sort -nr | head -n1 | cut -d' ' -f2-)
+        echo "slicer_folder=$folder" >> $GITHUB_OUTPUT
+

From 3e2d8c3b38edd4c26d63e981d925d329495d9de7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:47:06 +0200
Subject: [PATCH 03/16] CI: Create action for running python script in slicer

---
 .../slicer-run-python-script/action.yml       | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 .github/actions/slicer-run-python-script/action.yml

diff --git a/.github/actions/slicer-run-python-script/action.yml b/.github/actions/slicer-run-python-script/action.yml
new file mode 100644
index 0000000..1b22455
--- /dev/null
+++ b/.github/actions/slicer-run-python-script/action.yml
@@ -0,0 +1,21 @@
+name: slicer-run-python-script
+author: Sebastien Goll (Kitware SAS)
+description: Run a python script through Slicer
+inputs:
+  slicer_dir:
+    description: Slicer directory
+    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: |
+        "$SLICER_EXE" --python-script "${{ inputs.script }}" ${{ inputs.additional_arguments }}
+      shell: bash
+      env:
+        SLICER_EXE: ${{inputs.slicer_dir}}/Slicer.exe
\ No newline at end of file

From 29770cb470626e56e8f4118b0e0ed7ae7c4ac1d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:47:52 +0200
Subject: [PATCH 04/16] CI: Add installation scripts for multiverseg

---
 .github/python_scripts/install_python_dependencies.py | 11 +++++++++++
 .github/python_scripts/install_pytorch_module.py      |  8 ++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 .github/python_scripts/install_python_dependencies.py
 create mode 100644 .github/python_scripts/install_pytorch_module.py

diff --git a/.github/python_scripts/install_python_dependencies.py b/.github/python_scripts/install_python_dependencies.py
new file mode 100644
index 0000000..436d3e9
--- /dev/null
+++ b/.github/python_scripts/install_python_dependencies.py
@@ -0,0 +1,11 @@
+import slicer.util
+from MultiverSeg.SegmentEditorMultiverSegLib import InstallLogic, DependenciesLogic
+
+if __name__ == '__main__':
+    DependenciesLogic.INTERACTIVE_MODE = False
+    InstallLogic.INTERACTIVE_MODE = False
+
+    DependenciesLogic.installTorchIfNeeded()
+    DependenciesLogic.installMultiverSegIfNeeded()
+    InstallLogic.downloadCheckpointsIfNeeded()
+    slicer.util.quit()
diff --git a/.github/python_scripts/install_pytorch_module.py b/.github/python_scripts/install_pytorch_module.py
new file mode 100644
index 0000000..02da728
--- /dev/null
+++ b/.github/python_scripts/install_pytorch_module.py
@@ -0,0 +1,8 @@
+import slicer.util
+
+from MultiverSeg.SegmentEditorMultiverSegLib import DependenciesLogic
+
+if __name__ == '__main__':
+    DependenciesLogic.INTERACTIVE_MODE = False
+    DependenciesLogic.installPyTorchExtensionIfNeeded()
+    slicer.util.quit()

From 214623265de85afd72172c9462977b33c310ff69 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:55:55 +0200
Subject: [PATCH 05/16] CI: Add action and script to run tests

---
 .../slicer-run-python-tests/action.yml        | 29 +++++++++++++++++++
 .github/python_scripts/run_tests.py           | 17 +++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 .github/actions/slicer-run-python-tests/action.yml
 create mode 100644 .github/python_scripts/run_tests.py

diff --git a/.github/actions/slicer-run-python-tests/action.yml b/.github/actions/slicer-run-python-tests/action.yml
new file mode 100644
index 0000000..e524408
--- /dev/null
+++ b/.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_dir:
+    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/python_scripts/run_tests.py
+        slicer_dir: ${{ inputs.slicer_dir }}
+        additional_arguments: --additional-module-paths ${{ inputs.module_paths }} ${{ inputs.additional_arguments }} ${{ inputs.tests_root_path }} ${{ inputs.tests_name_pattern }}
diff --git a/.github/python_scripts/run_tests.py b/.github/python_scripts/run_tests.py
new file mode 100644
index 0000000..0d84d88
--- /dev/null
+++ b/.github/python_scripts/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)

From 93024acfdb8c05e0646844ae8dc794034c99adb5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 13:58:13 +0200
Subject: [PATCH 06/16] CI: Update workflow to use actions

---
 .github/workflows/windows-testing.yml | 112 ++++++--------------------
 1 file changed, 26 insertions(+), 86 deletions(-)

diff --git a/.github/workflows/windows-testing.yml b/.github/workflows/windows-testing.yml
index 7f145a5..a5fb506 100644
--- a/.github/workflows/windows-testing.yml
+++ b/.github/workflows/windows-testing.yml
@@ -11,90 +11,30 @@ on:
 jobs:
   Tests-Windows:
     runs-on: windows-latest
-    outputs:
-      install_path: ${{ steps.slicerLocation.outputs.install_path }}
-      python_path: ${{ steps.pythonLocation.outputs.python_path }}
     steps:
-      - name: Install Slicer
-        run: choco install 3dslicer -y
-      - name: Get slicer executable
-        id: slicerLocation
-        run: |
-          $folder = Get-ChildItem -Path "C:\ProgramData\slicer.org" -Filter "Slicer.exe" -Recurse -ErrorAction SilentlyContinue -Force |
-          Select-Object -First 1 
-          
-          if ($folder) {
-            $installPath = $folder.FullName
-            Write-Host "Found Slicer at $installPath"
-            # Set the output
-            "install_path=$installPath" >> $env:GITHUB_OUTPUT
-          } else {
-            Write-Host "Slicer not found."
-            exit 1
-          }
-      - name: Get python env
-        id: pythonLocation
-        run: |
-          $pythonPath = Resolve-Path "${{ steps.slicerLocation.outputs.install_path }}/../bin/PythonSlicer.exe"
-          echo "$pythonPath"
-          "python_path=$pythonPath" >> $env:GITHUB_OUTPUT
-      - name: Install SlicerPytorch module
-        id: slicerpytorch
-        run: |
-          $path = "${{ steps.slicerLocation.outputs.install_path }}"
-          $process = Start-Process -FilePath "$path" -ArgumentList "--testing", "--no-splash", "--no-main-window", "--python-code `"slicer.app.extensionsManagerModel().installExtensionFromServer('PyTorch')`"" -Wait -RedirectStandardOutput "log_std.txt" -RedirectStandardError "log_err.txt" -PassThru
-          echo "Standard output:"
-          Get-Content log_std.txt
-          echo "Error output:"
-          Get-Content log_err.txt
-          $exitCode = $process.ExitCode
-          echo "Exit code: $exitCode"
-          $folder = Get-ChildItem -Path "${{ steps.slicerLocation.outputs.install_path }}/../slicer.org" -Include qt-*modules -Recurse | Select-Object -First 1
-          $folder = $folder.FullName
-          echo "PyTorch module installed at $folder"
-          "slicerPyTorch=$folder" >> $env:GITHUB_OUTPUT
-          exit $exitCode
-      - name: Install pytorch
-        run: |
-          $path = "${{ steps.slicerLocation.outputs.install_path }}"
-          $pytorchmodule = "${{ steps.slicerpytorch.outputs.slicerPyTorch }}"
-          $process = Start-Process -FilePath "$path" -ArgumentList "--testing", "--no-splash", "--no-main-window","--additional-module-paths `"$pytorchmodule`"" ,"--python-code `"import PyTorchUtils;PyTorchUtils.PyTorchUtilsLogic().installTorch(askConfirmation=False,torchvisionVersionRequirement='>=0.20')`"" -Wait -RedirectStandardOutput "log_std.txt" -RedirectStandardError "log_err.txt" -PassThru
-          echo "Standard output:"
-          Get-Content log_std.txt
-          echo "Error output:"
-          Get-Content log_err.txt
-          $exitCode = $process.ExitCode
-          echo "Exit code: $exitCode"
-          exit $exitCode
-      - name: Install multiverseg
-        run: |
-          $path = "${{ steps.pythonLocation.outputs.python_path }}"
-          & $path -m pip install "git+https://github.com/halleewong/MultiverSeg.git"
-      - name: Check out repository code
-        uses: actions/checkout@v4
-      - name: Download models
-        run: |
-          $path = "${{ steps.slicerLocation.outputs.install_path }}"
-          $modulepath= "${{ github.workspace }}/MultiverSeg"
-          $process = Start-Process -FilePath "$path" -ArgumentList "--testing", "--no-splash", "--no-main-window","--additional-module-paths `"$modulepath`"" ,"--python-code `"from SegmentEditorMultiverSegLib import InstallLogic as i;i._downloadModel(i.MULTIVERSEG_FILE_NAME, i.MULTIVERSEG_DOWNLOAD_URL);i._downloadModel(i.SCRIBBLEPROMPT_FILE_NAME, i.SCRIBBLEPROMPT_DOWNLOAD_URL)`"" -Wait -RedirectStandardOutput "log_std.txt" -RedirectStandardError "log_err.txt" -PassThru
-      - name: Test
-        run: |
-          $path = "${{ steps.slicerLocation.outputs.install_path }}"
-          $modulepath= "${{ github.workspace }}/MultiverSeg"
-          $pytorchmodule = "${{ steps.slicerpytorch.outputs.slicerPyTorch }}"
-          $testPath = "$modulepath/Testing/Python"
-          $testNames = Get-ChildItem ${{ github.workspace }} -Filter *TestCase.py -Recurse | ForEach-Object {$_.BaseName}
-          $exitCode = 0
-          echo "Found tests:"
-          echo $testNames
-          foreach($testCase in $testNames){
-            $process = Start-Process -FilePath "$path" -ArgumentList "--testing", "--no-splash", "--additional-module-paths `"$modulepath`" `"$pytorchmodule`"" ,"--python-code `"import slicer.testing; slicer.testing.runUnitTest(r'$testPath', '$testCase')`"" -Wait -RedirectStandardOutput "log_std.txt" -RedirectStandardError "log_err.txt" -PassThru
-            echo "Standard output:"
-            Get-Content log_std.txt
-            echo "Error output:"
-            Get-Content log_err.txt
-            $currentCode = $process.ExitCode
-            echo "Exit code: $currentCode"
-            $exitCode = ($currentCode , $exitCode | Measure-Object -Max).Maximum
-          }
-          exit $exitCode
\ No newline at end of file
+      - uses: actions/checkout@v4
+        name: Checkout
+      - uses: ./.github/actions/install-slicer
+        id: slicer_install
+        name: Install Slicer
+      - name: Install PyTorch module
+        uses: ./.github/actions/slicer-run-python-script
+        with:
+          script: './.github/python_scripts/install_pytorch_module.py'
+          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          additional_arguments: --no-main-window --no-splash
+      - name: Install Python dependencies
+        uses: ./.github/actions/slicer-run-python-script
+        with:
+          script: './.github/python_scripts/install_python_dependencies.py'
+          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          additional_arguments: --no-main-window --no-splash
+      - name: Run tests
+        uses: ./.github/actions/slicer-run-python-tests
+        with:
+          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          additional_arguments: --testing --no-splash
+          tests_root_path: './MultiverSeg/Testing/Python'
+          tests_name_pattern: '*TestCase.py'
+          module_paths: './MultiverSeg'
+

From 7a3fe8a5217d7630cb6f85e5584f82fac7068899 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 14:03:05 +0200
Subject: [PATCH 07/16] CI: Update run tests script location

(cherry picked from commit 92f6d429c89a151c46ce2dc2648f82bbdd83356f)
---
 .github/actions/slicer-run-python-tests/action.yml              | 2 +-
 .../slicer-run-python-tests}/run_tests.py                       | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename .github/{python_scripts => actions/slicer-run-python-tests}/run_tests.py (100%)

diff --git a/.github/actions/slicer-run-python-tests/action.yml b/.github/actions/slicer-run-python-tests/action.yml
index e524408..a664e3f 100644
--- a/.github/actions/slicer-run-python-tests/action.yml
+++ b/.github/actions/slicer-run-python-tests/action.yml
@@ -24,6 +24,6 @@ runs:
   steps:
     - uses: ./.github/actions/slicer-run-python-script
       with:
-        script: ./.github/python_scripts/run_tests.py
+        script: ${{ github.action_path }}/run_tests.py
         slicer_dir: ${{ inputs.slicer_dir }}
         additional_arguments: --additional-module-paths ${{ inputs.module_paths }} ${{ inputs.additional_arguments }} ${{ inputs.tests_root_path }} ${{ inputs.tests_name_pattern }}
diff --git a/.github/python_scripts/run_tests.py b/.github/actions/slicer-run-python-tests/run_tests.py
similarity index 100%
rename from .github/python_scripts/run_tests.py
rename to .github/actions/slicer-run-python-tests/run_tests.py

From d049cf189ea4d7b8d17c0892fa58e05177a85b53 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 14:41:55 +0200
Subject: [PATCH 08/16] CI: Allow to manually run the workflow

---
 .github/workflows/windows-testing.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/windows-testing.yml b/.github/workflows/windows-testing.yml
index a5fb506..4da4ffd 100644
--- a/.github/workflows/windows-testing.yml
+++ b/.github/workflows/windows-testing.yml
@@ -7,6 +7,8 @@ on:
   pull_request:
     branches:
       - main
+  workflow_dispatch:
+
 
 jobs:
   Tests-Windows:
@@ -38,3 +40,4 @@ jobs:
           tests_name_pattern: '*TestCase.py'
           module_paths: './MultiverSeg'
 
+

From 9caed097f7802c4445ec8a43041a9b16cf16269c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 15:32:53 +0200
Subject: [PATCH 09/16] CI: Add extension install action

(cherry picked from commit 8aee406421621ce2db4715e937bef93e2772a3cd)
---
 .../slicer-install-extensions/action.yml      | 23 +++++++++++++++++++
 .../install_extensions.py                     | 15 ++++++++++++
 2 files changed, 38 insertions(+)
 create mode 100644 .github/actions/slicer-install-extensions/action.yml
 create mode 100644 .github/actions/slicer-install-extensions/install_extensions.py

diff --git a/.github/actions/slicer-install-extensions/action.yml b/.github/actions/slicer-install-extensions/action.yml
new file mode 100644
index 0000000..ba00a36
--- /dev/null
+++ b/.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_dir:
+    description: Slicer directory
+    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_dir: ${{ inputs.slicer_dir }}
+        additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.extensions_name }}
diff --git a/.github/actions/slicer-install-extensions/install_extensions.py b/.github/actions/slicer-install-extensions/install_extensions.py
new file mode 100644
index 0000000..ff954b3
--- /dev/null
+++ b/.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()

From 0fd09f57b5bfc768aefe343599119a445f35c8de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Tue, 13 May 2025 15:54:32 +0200
Subject: [PATCH 10/16] CI: Add action to install python packages into slicer's
 python env

(cherry picked from commit 068ef8bc18c0b21d0a62732771601e11c20b8b77)
---
 .../slicer-install-python-packages/action.yml | 22 +++++++++++++++++++
 .../install_py_packages.py                    | 11 ++++++++++
 2 files changed, 33 insertions(+)
 create mode 100644 .github/actions/slicer-install-python-packages/action.yml
 create mode 100644 .github/actions/slicer-install-python-packages/install_py_packages.py

diff --git a/.github/actions/slicer-install-python-packages/action.yml b/.github/actions/slicer-install-python-packages/action.yml
new file mode 100644
index 0000000..813ece9
--- /dev/null
+++ b/.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_dir:
+    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_dir: ${{ inputs.slicer_dir }}
+        additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.package_names }}
diff --git a/.github/actions/slicer-install-python-packages/install_py_packages.py b/.github/actions/slicer-install-python-packages/install_py_packages.py
new file mode 100644
index 0000000..f6914b5
--- /dev/null
+++ b/.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()
\ No newline at end of file

From 41cb5e755c70d1b9f3e48e44c868d348a074be61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:23:40 +0200
Subject: [PATCH 11/16] CI: Add slicer download script

---
 .github/actions/install-slicer/downloader.sh | 30 ++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/actions/install-slicer/downloader.sh

diff --git a/.github/actions/install-slicer/downloader.sh b/.github/actions/install-slicer/downloader.sh
new file mode 100644
index 0000000..05a1d87
--- /dev/null
+++ b/.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"
+

From c8611aef42bb5977c0dfab24455de88d8d3343b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:24:05 +0200
Subject: [PATCH 12/16] CI: Add MacOS installation script

---
 .../actions/install-slicer/macos_installer.exp  | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100644 .github/actions/install-slicer/macos_installer.exp

diff --git a/.github/actions/install-slicer/macos_installer.exp b/.github/actions/install-slicer/macos_installer.exp
new file mode 100644
index 0000000..3e09c1c
--- /dev/null
+++ b/.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
\ No newline at end of file

From e78d03ee84e2919d3fbe3e916b67641b3c6fe2c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:24:16 +0200
Subject: [PATCH 13/16] CI: Update actions

---
 .github/actions/install-slicer/action.yml     | 71 ++++++++++++++++---
 .../slicer-install-extensions/action.yml      |  6 +-
 .../slicer-install-python-packages/action.yml |  4 +-
 .../slicer-run-python-script/action.yml       | 10 ++-
 .../slicer-run-python-tests/action.yml        |  4 +-
 5 files changed, 73 insertions(+), 22 deletions(-)

diff --git a/.github/actions/install-slicer/action.yml b/.github/actions/install-slicer/action.yml
index b9ebbf7..4515ebd 100644
--- a/.github/actions/install-slicer/action.yml
+++ b/.github/actions/install-slicer/action.yml
@@ -6,20 +6,73 @@ inputs:
     description: Version of Slicer available at https://community.chocolatey.org/packages/3dslicer#versionhistory
     default: ''
 outputs:
-  slicer_folder:
-    description: Installation folder for Slicer
-    value: ${{ steps.slicer_folder.outputs.slicer_folder }}
+  slicer_executable:
+    description: Slicer executable
+    value: ${{ steps.slicer_exe.outputs.executable }}
 
 runs:
   using: composite
   steps:
-    - if: ${{runner.os == 'Windows'}}
-      run: choco install 3dslicer -y --version=${{ inputs.version }} --allowdowngrade
+    - name: Setting the permission
+      run: chmod +x "${{ github.action_path }}/downloader.sh"
       shell: bash
-    - if: ${{runner.os == 'Windows'}}
-      id: slicer_folder
+    - name: Download installer
+      run: |
+        "${{ 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 "slicer_folder=$folder" >> $GITHUB_OUTPUT
-
+        echo "executable=$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
\ No newline at end of file
diff --git a/.github/actions/slicer-install-extensions/action.yml b/.github/actions/slicer-install-extensions/action.yml
index ba00a36..aebdc3d 100644
--- a/.github/actions/slicer-install-extensions/action.yml
+++ b/.github/actions/slicer-install-extensions/action.yml
@@ -3,8 +3,8 @@ author: Sebastien Goll (Kitware SAS)
 description: Install extensions for Slicer
 
 inputs:
-  slicer_dir:
-    description: Slicer directory
+  slicer_exe:
+    description: Slicer executable
     required: true
   additional_arguments:
     description: Additional arguments for Slicer executable
@@ -19,5 +19,5 @@ runs:
     - uses: ./.github/actions/slicer-run-python-script
       with:
         script: ${{ github.action_path }}/install_extensions.py
-        slicer_dir: ${{ inputs.slicer_dir }}
+        slicer_exe: ${{ inputs.slicer_exe }}
         additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.extensions_name }}
diff --git a/.github/actions/slicer-install-python-packages/action.yml b/.github/actions/slicer-install-python-packages/action.yml
index 813ece9..d3d1245 100644
--- a/.github/actions/slicer-install-python-packages/action.yml
+++ b/.github/actions/slicer-install-python-packages/action.yml
@@ -3,7 +3,7 @@ author: Sebastien Goll (Kitware SAS)
 description: Install python packages in Slicer's python environment
 
 inputs:
-  slicer_dir:
+  slicer_exe:
     description: Slicer directory
     required: true
   additional_arguments:
@@ -18,5 +18,5 @@ runs:
     - uses: ./.github/actions/slicer-run-python-script
       with:
         script: ${{ github.action_path }}/install_py_packages.py
-        slicer_dir: ${{ inputs.slicer_dir }}
+        slicer_exe: ${{ inputs.slicer_exe }}
         additional_arguments: ${{ inputs.additional_arguments }} ${{ inputs.package_names }}
diff --git a/.github/actions/slicer-run-python-script/action.yml b/.github/actions/slicer-run-python-script/action.yml
index 1b22455..5a26b71 100644
--- a/.github/actions/slicer-run-python-script/action.yml
+++ b/.github/actions/slicer-run-python-script/action.yml
@@ -2,8 +2,8 @@ name: slicer-run-python-script
 author: Sebastien Goll (Kitware SAS)
 description: Run a python script through Slicer
 inputs:
-  slicer_dir:
-    description: Slicer directory
+  slicer_exe:
+    description: Slicer executable
     required: true
   script:
     description: Path to python to run
@@ -15,7 +15,5 @@ runs:
   using: composite
   steps:
     - run: |
-        "$SLICER_EXE" --python-script "${{ inputs.script }}" ${{ inputs.additional_arguments }}
-      shell: bash
-      env:
-        SLICER_EXE: ${{inputs.slicer_dir}}/Slicer.exe
\ No newline at end of file
+        "${{inputs.slicer_exe}}" --python-script "${{ inputs.script }}" ${{ inputs.additional_arguments }}
+      shell: bash
\ No newline at end of file
diff --git a/.github/actions/slicer-run-python-tests/action.yml b/.github/actions/slicer-run-python-tests/action.yml
index a664e3f..bf42d5b 100644
--- a/.github/actions/slicer-run-python-tests/action.yml
+++ b/.github/actions/slicer-run-python-tests/action.yml
@@ -3,7 +3,7 @@ author: Sebastien Goll (Kitware SAS)
 description: Run python tests in Slicer
 
 inputs:
-  slicer_dir:
+  slicer_exe:
     description: Slicer directory
     required: true
   additional_arguments:
@@ -25,5 +25,5 @@ runs:
     - uses: ./.github/actions/slicer-run-python-script
       with:
         script: ${{ github.action_path }}/run_tests.py
-        slicer_dir: ${{ inputs.slicer_dir }}
+        slicer_exe: ${{ inputs.slicer_exe }}
         additional_arguments: --additional-module-paths ${{ inputs.module_paths }} ${{ inputs.additional_arguments }} ${{ inputs.tests_root_path }} ${{ inputs.tests_name_pattern }}

From dc56c5e3e09ed18e62237d463570aacff054b408 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:24:45 +0200
Subject: [PATCH 14/16] CI: Add matrix strategy to test runner

---
 .github/workflows/windows-testing.yml | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/windows-testing.yml b/.github/workflows/windows-testing.yml
index 4da4ffd..ce4df93 100644
--- a/.github/workflows/windows-testing.yml
+++ b/.github/workflows/windows-testing.yml
@@ -11,8 +11,13 @@ on:
 
 
 jobs:
-  Tests-Windows:
-    runs-on: windows-latest
+  Running-Tests:
+    timeout-minutes: 30
+    continue-on-error: true
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
         name: Checkout
@@ -23,18 +28,18 @@ jobs:
         uses: ./.github/actions/slicer-run-python-script
         with:
           script: './.github/python_scripts/install_pytorch_module.py'
-          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          slicer_exe: ${{ steps.slicer_install.outputs.slicer_executable }}
           additional_arguments: --no-main-window --no-splash
       - name: Install Python dependencies
         uses: ./.github/actions/slicer-run-python-script
         with:
           script: './.github/python_scripts/install_python_dependencies.py'
-          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          slicer_exe: ${{ steps.slicer_install.outputs.slicer_executable }}
           additional_arguments: --no-main-window --no-splash
       - name: Run tests
         uses: ./.github/actions/slicer-run-python-tests
         with:
-          slicer_dir: ${{ steps.slicer_install.outputs.slicer_folder }}
+          slicer_exe: ${{ steps.slicer_install.outputs.slicer_executable }}
           additional_arguments: --testing --no-splash
           tests_root_path: './MultiverSeg/Testing/Python'
           tests_name_pattern: '*TestCase.py'

From ab7af7b284fdfdbb3e024c27dad946d2bec84aee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:25:13 +0200
Subject: [PATCH 15/16] TEST: Update tests to pass CI on Linux and Mac

---
 MultiverSeg/Testing/Python/ContextLogicTestCase.py   | 12 +++++++++---
 .../Testing/Python/SegmentationLogicTestCase.py      |  5 +++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/MultiverSeg/Testing/Python/ContextLogicTestCase.py b/MultiverSeg/Testing/Python/ContextLogicTestCase.py
index 49fd8ab..b3c5601 100644
--- a/MultiverSeg/Testing/Python/ContextLogicTestCase.py
+++ b/MultiverSeg/Testing/Python/ContextLogicTestCase.py
@@ -1,5 +1,6 @@
 import unittest
 from pathlib import Path
+from shutil import rmtree
 from unittest import SkipTest
 
 import SampleData
@@ -15,6 +16,11 @@ def setUpClass(cls):
         emptyContextPath = Path(__file__).parent.joinpath("../TestData/Context/empty_context").resolve()
         emptyContextPath.mkdir(exist_ok=True)
 
+    @classmethod
+    def tearDownClass(cls):
+        emptyContextPath = Path(__file__).parent.joinpath("../TestData/Context/empty_context").resolve()
+        rmtree(emptyContextPath)
+
     def test_instantiation(self):
         logic = ContextLogic(None)
 
@@ -102,11 +108,11 @@ def test_saveNewExample(self):
         iTruth = logic.loadImage(ressourcePath.joinpath("image_0.png"))
         mTruth = logic.loadImage(ressourcePath.joinpath("mask_0.png"))
 
-        diff = torch.abs(i - iTruth)
-        self.assertEqual(torch.max(diff).item(), 0)
+        diff = torch.abs(i.to(torch.int16) - iTruth.to(torch.int16)).to(torch.uint8)
+        self.assertLessEqual(torch.max(diff).item(), 5) # Need tolerance to different compression methods
 
         diff = torch.abs(m - mTruth)
-        self.assertEqual(torch.max(diff).item(), 0)
+        self.assertLessEqual(torch.max(diff).item(), 5)
 
         import shutil
         shutil.rmtree(contextPath)
diff --git a/MultiverSeg/Testing/Python/SegmentationLogicTestCase.py b/MultiverSeg/Testing/Python/SegmentationLogicTestCase.py
index c54b358..79576db 100644
--- a/MultiverSeg/Testing/Python/SegmentationLogicTestCase.py
+++ b/MultiverSeg/Testing/Python/SegmentationLogicTestCase.py
@@ -9,6 +9,11 @@
 
 
 class SegmentationLogicTestCase(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        torch.backends.mps.is_available = lambda : False
+
     def test_instantiation(self):
         logic = SegmentationLogic(None)
 

From 5e8e785075724c2b0e154592bb340c72f5ae5668 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9bastien=20Goll?= <sebastien.goll@kitware.com>
Date: Thu, 15 May 2025 17:25:44 +0200
Subject: [PATCH 16/16] CI: Update script to add current dir to pythonpath

---
 .github/python_scripts/install_python_dependencies.py | 7 ++++++-
 .github/python_scripts/install_pytorch_module.py      | 8 +++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/python_scripts/install_python_dependencies.py b/.github/python_scripts/install_python_dependencies.py
index 436d3e9..2bb121f 100644
--- a/.github/python_scripts/install_python_dependencies.py
+++ b/.github/python_scripts/install_python_dependencies.py
@@ -1,7 +1,12 @@
+from pathlib import Path
+
 import slicer.util
-from MultiverSeg.SegmentEditorMultiverSegLib import InstallLogic, DependenciesLogic
+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
 
diff --git a/.github/python_scripts/install_pytorch_module.py b/.github/python_scripts/install_pytorch_module.py
index 02da728..63c6263 100644
--- a/.github/python_scripts/install_pytorch_module.py
+++ b/.github/python_scripts/install_pytorch_module.py
@@ -1,8 +1,14 @@
+import sys
+from pathlib import Path
+
 import slicer.util
 
-from MultiverSeg.SegmentEditorMultiverSegLib import DependenciesLogic
+
 
 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()