Install dependencies the way Slicer expects, fix the failing self-test, add a real icon

CMakeLists.txt

@@ -8,7 +8,7 @@ set(EXTENSION_CONTRIBUTORS "Jona Richter, Mark Daniel Arndt")
 set(EXTENSION_DESCRIPTION "Zebrafish body length, curvature, and eye metrics from 2D microscopy images.")
 set(EXTENSION_ICONURL "https://raw.githubusercontent.com/MarkDanielArndt/SlicerZebrafishEmbryoAnalyzer/main/ZebrafishEmbryoAnalyzer/Resources/Icons/ZebrafishEmbryoAnalyzer.png")
 set(EXTENSION_SCREENSHOTURLS "https://raw.githubusercontent.com/MarkDanielArndt/SlicerZebrafishEmbryoAnalyzer/main/Documentation_images/gallery.png https://raw.githubusercontent.com/MarkDanielArndt/SlicerZebrafishEmbryoAnalyzer/main/Documentation_images/detail.png https://raw.githubusercontent.com/MarkDanielArndt/SlicerZebrafishEmbryoAnalyzer/main/Documentation_images/setup_dialog.png https://raw.githubusercontent.com/MarkDanielArndt/SlicerZebrafishEmbryoAnalyzer/main/Documentation_images/manual_correction.png")
-set(EXTENSION_DEPENDS "NA")
+set(EXTENSION_DEPENDS "PyTorch")
 
 find_package(Slicer REQUIRED)
 include(${Slicer_USE_FILE})

README.md

@@ -74,14 +74,35 @@ On first open you will be prompted to install:
 
 | Package | Purpose |
 |---------|---------|
-| `torch`, `torchvision`, `timm`, `segmentation-models-pytorch` | ML inference |
-| `opencv-python`, `scipy`, `scikit-image`, `pillow` | Image processing |
-| `openpyxl`, `matplotlib` | Export |
-| `numpy<2` | Pinned for torch compatibility |
-| `platformdirs` | Cache path lookup (soft dependency, falls back gracefully) |
+| `torch`, `torchvision` | ML inference — installed through the PyTorch extension, not by this one |
+| `segmentation-models-pytorch`, `timm` | Segmentation models |
+| `scikit-image`, `opencv-python-headless` | Image processing |
+| `huggingface_hub` | Model download |
+| `openpyxl` | Excel export |
+| `pytesseract` | Scale bar text recognition |
+
+Nothing else is installed. `numpy`, `scipy`, `pillow` and `matplotlib` are used but
+ship with Slicer's Python, so the extension never touches them.
+
+Torch comes from the PyTorch extension so that the build matching your hardware
+(CUDA, MPS or CPU) is selected, and so that any platform-specific constraints are
+applied by the extension that owns them rather than by us. If the PyTorch extension
+is not installed yet, it is installed first; Slicer then needs a restart before torch
+itself can follow, and the remaining packages are installed on that next run.
 
 Total download is several GB (PyTorch alone ~2 GB). Takes several minutes.
 
+### A note on NumPy for macOS users
+
+The newest PyTorch build available for macOS is 2.2, which is compiled against the NumPy 1
+C API. The PyTorch extension therefore holds NumPy below 2 on that platform, and the
+remaining packages are installed in the same step so that pip picks versions that fit.
+On Linux and Windows a current PyTorch is used and NumPy is left alone.
+
+During installation pip prints a warning that `pyjpegls` requires `numpy>=2.0`. This is a
+metadata-level conflict only — `pyjpegls`, which Slicer ships for JPEG-LS DICOM decoding,
+was verified to work with NumPy 1.26.
+
 <img src="Documentation_images/setup_dialog.png" width="500" alt="Setup dialog showing packages and optional model download">
 
 You can also pre-download models here to skip the prompt on first run.

ZebrafishEmbryoAnalyzer/Testing/CMakeLists.txt

@@ -4,9 +4,13 @@ set(KIT_PYTHON_SCRIPTS
 
 set(KIT_PYTHON_RESOURCES)
 
+# The script path must be absolute. slicer_add_python_unittest derives the directory it
+# puts on sys.path from SCRIPT, and only falls back to CMAKE_CURRENT_SOURCE_DIR when that
+# directory comes out empty. A relative "Python/..." yields the bare relative "Python",
+# which is not empty, so the fallback is skipped and the test module cannot be imported.
 foreach(script ${KIT_PYTHON_SCRIPTS})
   slicer_add_python_unittest(
-    SCRIPT ${script}
+    SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/${script}
     SLICER_ARGS --disable-cli-modules
   )
 endforeach()

ZebrafishEmbryoAnalyzer/ZebrafishEmbryoAnalyzer.py

@@ -42,7 +42,7 @@ class ZebrafishEmbryoAnalyzer(ScriptedLoadableModule):
     def __init__(self, parent):
         ScriptedLoadableModule.__init__(self, parent)
         self.parent.title = "Zebrafish Embryo Analyzer"
-        self.parent.categories = ["Quantification"]
+        self.parent.categories = ["Analysis"]
         self.parent.dependencies = []
         self.parent.contributors = ["Jona Richter", "Mark Daniel Arndt"]
         self.parent.helpText = (
@@ -107,7 +107,12 @@ def enter(self):
             self.initializeParameterNode()
         if self._main is not None:
             self._main.apply_shell_layout()
-            self._main.prompt_install_if_missing()
+            # Refreshes the in-panel notice about missing packages. Deliberately not a
+            # dialog: opening the module must not interrupt, and browsing results of an
+            # existing scene needs none of the packages. But the user has to learn about a
+            # pending install before loading images and setting parameters, so the notice
+            # is updated here. Each action that needs packages still checks for itself.
+            self._main.refresh_dependency_status()
 
     def exit(self):
         if self._main is not None: