Merge branch 'Slicer:main' into main

MohammadRSalmanpour · web-flow · commit 4e7c77a5a2cb · 2025-12-18T14:36:07.000-08:00
diff --git a/.github/workflows/extension-ai-analysis.yml b/.github/workflows/extension-ai-analysis.yml
@@ -17,14 +17,14 @@ jobs:
     timeout-minutes: 30
     steps:
       - name: Checkout the fork PR code
-        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
           fetch-depth: 0 # Fetch full history for git diff
 
       - name: Setup Python
-        uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+        uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
           python-version: "3.12"
           cache: "pip"
@@ -70,7 +70,9 @@ jobs:
 
       - name: Run AI analysis
         env:
-          NEBULA_API_KEY: ${{ secrets.NEBULA_API_KEY }}
+          INFERENCE_URL: ${{ vars.INFERENCE_URL }}
+          INFERENCE_MODEL: ${{ vars.INFERENCE_MODEL }}
+          INFERENCE_API_KEY: ${{ secrets.INFERENCE_API_KEY }}
         id: ai-analysis
         run: |
           RESULT=$(python scripts/extension_ai_analysis.py \
diff --git a/.github/workflows/extension-validation.yml b/.github/workflows/extension-validation.yml
@@ -19,11 +19,11 @@ jobs:
       pull-requests: write
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
         with:
           fetch-depth: 0 # Fetch full history for git diff
 
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+      - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
           python-version: "3.12"
           cache: "pip"
@@ -103,7 +103,7 @@ jobs:
 
       - name: Upload validation reports
         if: always()
-        uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5.0.0
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
         with:
           name: validation-reports
           path: |
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -16,8 +16,8 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 5
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
-      - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
+      - uses: actions/setup-python@83679a892e2d95755f2dac6acb0bfd1e9ac5d548 # v6.1.0
         with:
           python-version: "3.12"
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
diff --git a/KonfAI.json b/KonfAI.json
@@ -0,0 +1,9 @@
+{
+  "$schema": "https://raw.githubusercontent.com/Slicer/Slicer/main/Schemas/slicer-extension-catalog-entry-schema-v1.0.1.json#",
+  "build_dependencies": [],
+  "build_subdirectory": ".",
+  "category": "Pipelines",
+  "scm_revision": "main",
+  "scm_url": "https://github.com/vboussot/SlicerKonfAI",
+  "tier": 3
+}
diff --git a/OpenLIFU.json b/OpenLIFU.json
@@ -3,7 +3,7 @@
   "build_dependencies": [],
   "build_subdirectory": ".",
   "category": "Utilities",
-  "scm_revision": "v1.5.0",
+  "scm_revision": "main",
   "scm_url": "https://github.com/OpenwaterHealth/SlicerOpenLIFU.git",
   "tier": 1
 }
diff --git a/QuantitativeReporting.json b/QuantitativeReporting.json
@@ -7,7 +7,7 @@
   ],
   "build_subdirectory": ".",
   "category": "Informatics",
-  "scm_revision": "2c0112785c9ba3af9be6a1f86d5ed7bb8b700705",
+  "scm_revision": "master",
   "scm_url": "https://github.com/QIICR/QuantitativeReporting.git",
   "tier": 5
 }
diff --git a/SegTemplateEditor.json b/SegTemplateEditor.json
@@ -0,0 +1,9 @@
+{
+  "$schema": "https://raw.githubusercontent.com/Slicer/Slicer/main/Schemas/slicer-extension-catalog-entry-schema-v1.0.1.json#",
+  "build_dependencies": [],
+  "build_subdirectory": ".",
+  "category": "Segmentation",
+  "scm_revision": "main",
+  "scm_url": "https://github.com/esheo-skia/Slicer-SegTemplateEditor.git",
+  "tier": 1
+}
diff --git a/SlicerMorph.json b/SlicerMorph.json
@@ -6,7 +6,7 @@
   ],
   "build_subdirectory": ".",
   "category": "SlicerMorph",
-  "scm_revision": "master",
+  "scm_revision": "geomorphTab",
   "scm_url": "https://github.com/SlicerMorph/SlicerMorph.git",
   "tier": 5
 }
diff --git a/TutorialMaker.json b/TutorialMaker.json
@@ -4,6 +4,6 @@
   "build_subdirectory": ".",
   "category": "Developer Tools",
   "scm_revision": "main",
-  "scm_url": "https://github.com/SlicerLatinAmerica/SlicerTutorialMaker.git",
+  "scm_url": "https://github.com/SoniaPujolLab/SlicerTutorialMaker.git",
   "tier": 1
 }
diff --git a/scripts/check_description_files.py b/scripts/check_description_files.py
@@ -105,9 +105,10 @@ def check_json_file_format(extension_name, metadata, extension_file_path):
             extension_name, check_name,
             f"Invalid JSON format: {str(e)}")
     # Force using LF-only line endings
-    with open(extension_file_path, 'r', encoding='utf-8') as f:
+    # Must open in binary mode to detect line endings
+    with open(extension_file_path, 'rb') as f:
         content = f.read()
-    if '\r\n' in content or '\r' in content:
+    if b'\r\n' in content or b'\r' in content:
         raise ExtensionCheckError(
             extension_name, check_name,
             "File contains non-LF line endings (CR or CRLF). Please convert to LF-only line endings.")
diff --git a/scripts/extension_ai_analysis.py b/scripts/extension_ai_analysis.py
@@ -15,13 +15,20 @@
 import subprocess
 import shutil
 
-# Use Nebula Block API endpoint for chat completions.
-# It offers capable models for free with an OpenAI-compatible API.
-INFERENCE_URL = "https://inference.nebulablock.com/v1/chat/completions"
-INFERENCE_MODEL = "mistralai/Mistral-Small-3.2-24B-Instruct-2506"
-INFERENCE_RESPONSE_PER_MINUTE_LIMIT = 4 #  slow down to not exceed token per minute (tpm) limit of 60k
-INFERENCE_API_KEY = os.getenv("NEBULA_API_KEY")
-INFERENCE_MAX_CHARACTERS = 100000  # max characters in all files provided to the model, approximately 25k tokens (limit is 32k)
+
+# Get inference server configuration from environment variables
+INFERENCE_URL = os.getenv("INFERENCE_URL")
+if not INFERENCE_URL:
+    raise ValueError("INFERENCE_URL environment variable is not set. Please set it before running the script.")
+INFERENCE_MODEL = os.getenv("INFERENCE_MODEL")
+if not INFERENCE_MODEL:
+    raise ValueError("INFERENCE_MODEL environment variable is not set. Please set it before running the script.")
+INFERENCE_API_KEY = os.getenv("INFERENCE_API_KEY")
+if not INFERENCE_API_KEY:
+    raise ValueError("INFERENCE_API_KEY environment variable is not set. Please set it before running the script.")
+
+INFERENCE_RESPONSE_PER_MINUTE_LIMIT = 10 #  slow down to not exceed token per minute (tpm) limit
+INFERENCE_MAX_CHARACTERS = 400000  # max characters in all files provided to the model, approximately 100k tokens
 
 QUESTIONS = [
     ["Is there a EXTENSION_DESCRIPTION variable in the CMakeLists.txt file that describes what the extension does in a few sentences that can be understood by a person knowledgeable in medical image computing?", ["cmake"]],
@@ -130,7 +137,9 @@ def collect_analyzed_files(folder):
 def ask_question(system_msg, question):
     headers = {
         "Content-Type": "application/json",
-        "Authorization": f"Bearer {INFERENCE_API_KEY}"
+        "Authorization": f"Bearer {INFERENCE_API_KEY}",
+        "HTTP-Referer": "slicer.org", # Optional. Site URL for rankings on openrouter.ai.
+        "X-Title": "3D Slicer", # Optional. Site title for rankings on openrouter.ai.
     }
 
     messages = [
@@ -157,6 +166,11 @@ def ask_question(system_msg, question):
     try:
         answer = response.json()["choices"][0]["message"]["content"]
     except Exception as e:
+        import traceback
+        traceback.print_exc()
+        print(f"Request data: {data}", file=sys.stderr)
+        print(f"Response status code: {response.status_code}", file=sys.stderr)
+        print(f"Response content: {response.text}", file=sys.stderr)
         raise RuntimeError(f"Error or unexpected response: {response.json()["error"]["message"]}")
 
     return answer
diff --git a/volbrain.json b/volbrain.json
@@ -0,0 +1,7 @@
+{
+  "$schema": "https://raw.githubusercontent.com/Slicer/Slicer/main/Schemas/slicer-extension-catalog-entry-schema-v1.0.1.json#",
+  "category": "Quantification",
+  "scm_url": "https://github.com/niyaziacer/SlicerVolBrain.git",
+  "scm_revision": "b4156f73b4ec0a0722778535ed353fce49cccd46",
+  "scm_type": "git"
+}

Original file line number	Diff line number	Diff line change
`@@ -3,7 +3,7 @@`
`3`	`3`	`"build_dependencies": [],`
`4`	`4`	`"build_subdirectory": ".",`
`5`	`5`	`"category": "Utilities",`
`6`		`- "scm_revision": "v1.5.0",`
	`6`	`+ "scm_revision": "main",`
`7`	`7`	`"scm_url": "https://github.com/OpenwaterHealth/SlicerOpenLIFU.git",`
`8`	`8`	`"tier": 1`
`9`	`9`	`}`
Original file line number	Diff line number	Diff line change
`@@ -7,7 +7,7 @@`
`7`	`7`	`],`
`8`	`8`	`"build_subdirectory": ".",`
`9`	`9`	`"category": "Informatics",`
`10`		`- "scm_revision": "2c0112785c9ba3af9be6a1f86d5ed7bb8b700705",`
	`10`	`+ "scm_revision": "master",`
`11`	`11`	`"scm_url": "https://github.com/QIICR/QuantitativeReporting.git",`
`12`	`12`	`"tier": 5`
`13`	`13`	`}`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`],`
`7`	`7`	`"build_subdirectory": ".",`
`8`	`8`	`"category": "SlicerMorph",`
`9`		`- "scm_revision": "master",`
	`9`	`+ "scm_revision": "geomorphTab",`
`10`	`10`	`"scm_url": "https://github.com/SlicerMorph/SlicerMorph.git",`
`11`	`11`	`"tier": 5`
`12`	`12`	`}`
Original file line number	Diff line number	Diff line change
`@@ -4,6 +4,6 @@`
`4`	`4`	`"build_subdirectory": ".",`
`5`	`5`	`"category": "Developer Tools",`
`6`	`6`	`"scm_revision": "main",`
`7`		`- "scm_url": "https://github.com/SlicerLatinAmerica/SlicerTutorialMaker.git",`
	`7`	`+ "scm_url": "https://github.com/SoniaPujolLab/SlicerTutorialMaker.git",`
`8`	`8`	`"tier": 1`
`9`	`9`	`}`