Merge pull request #100 from bcalford/main

Added back pre commit
niivue · Dec 2, 2024 · 3b9247e · 3b9247e
2 parents 9d70d23 + dc9c08d
commit 3b9247e
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,8 @@
+repos:
+  - repo: https://github.com/srstevenson/nb-clean
+    rev: 4.0.1
+    hooks:
+      - id: nb-clean
+        args:
+          - --remove-empty-cells
+          - --
diff --git a/examples/additive_voxels.ipynb b/examples/additive_voxels.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "!mkdir -p ../images/\n",
-    "path=\"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
+    "path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
     "!wget {path}narps-4735_50GV-hypo1_unthresh.nii.gz -P ../images/\n",
     "!wget {path}narps-4965_9U7M-hypo1_unthresh.nii.gz -P ../images/\n",
     "!wget {path}mni152.nii.gz -P ../images/"
@@ -24,7 +24,7 @@
     "# based on https://niivue.github.io/niivue/features/additive.voxels.html\n",
     "\n",
     "volumes = [\n",
-    "    {   \"path\": \"../images/mni152.nii.gz\" },\n",
+    "    {\"path\": \"../images/mni152.nii.gz\"},\n",
     "    {\n",
     "        \"path\": \"../images/narps-4965_9U7M-hypo1_unthresh.nii.gz\",\n",
     "        \"colormap\": \"red\",\n",

diff --git a/examples/basic_multiplanar.ipynb b/examples/basic_multiplanar.ipynb
@@ -7,7 +7,7 @@
    "outputs": [],
    "source": [
     "!mkdir -p ../images/\n",
-    "path=\"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
+    "path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
     "!wget {path}mni152.nii.gz -P ../images/\n",
     "!wget {path}hippo.nii.gz -P ../images/"
    ]
@@ -23,11 +23,18 @@
     "# based on https://niivue.github.io/niivue/features/basic.multiplanar.html\n",
     "\n",
     "volumes = [\n",
-    "  { \"path\": \"../images/mni152.nii.gz\", \"colormap\": \"gray\",\n",
-    "    \"visible\": True, \"opacity\": 1.0 },\n",
-    "  { \"path\": \"../images/hippo.nii.gz\", \"colormap\": \"red\",\n",
-    "    \"visible\": True, \"opacity\": 1 },\n",
-    "\n",
+    "    {\n",
+    "        \"path\": \"../images/mni152.nii.gz\",\n",
+    "        \"colormap\": \"gray\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1.0,\n",
+    "    },\n",
+    "    {\n",
+    "        \"path\": \"../images/hippo.nii.gz\",\n",
+    "        \"colormap\": \"red\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1,\n",
+    "    },\n",
     "]\n",
     "nv = NiiVue(slice_type=SliceType.MULTIPLANAR)\n",
     "nv.load_volumes(volumes)\n",
@@ -51,9 +58,9 @@
    "outputs": [],
    "source": [
     "nv.show_3d_crosshair = True\n",
-    "nv.crosshair_color = [0,1,1,1]\n",
-    "nv.back_color = [1,1,1,1]\n",
-    "nv.clip_plane_color =  [0,1,1,1]\n",
+    "nv.crosshair_color = [0, 1, 1, 1]\n",
+    "nv.back_color = [1, 1, 1, 1]\n",
+    "nv.clip_plane_color = [0, 1, 1, 1]\n",
     "nv.is_colorbar = True\n",
     "nv.view_mode_hot_key = \"KeyN\""
    ]

diff --git a/examples/example_sideview.ipynb b/examples/example_sideview.ipynb
@@ -132,7 +132,7 @@
    ],
    "source": [
     "!mkdir -p ../images/\n",
-    "path=\"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
+    "path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
     "!wget {path}mni152.nii.gz -P ../images/\n",
     "!wget {path}hippo.nii.gz -P ../images/"
    ]
@@ -158,27 +158,33 @@
     "from ipyniivue import NiiVue, SliceType\n",
     "\n",
     "volumes = [\n",
-    "  { \"path\": \"../images/mni152.nii.gz\", \"colormap\": \"gray\",\n",
-    "   \"visible\": True, \"opacity\": 1.0 },\n",
-    "  { \"path\": \"../images/hippo.nii.gz\", \"colormap\": \"red\",\n",
-    "   \"visible\": True, \"opacity\": 1 },\n",
-    "\n",
+    "    {\n",
+    "        \"path\": \"../images/mni152.nii.gz\",\n",
+    "        \"colormap\": \"gray\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1.0,\n",
+    "    },\n",
+    "    {\n",
+    "        \"path\": \"../images/hippo.nii.gz\",\n",
+    "        \"colormap\": \"red\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1,\n",
+    "    },\n",
     "]\n",
     "nv = NiiVue(slice_type=SliceType.MULTIPLANAR)\n",
     "nv.load_volumes(volumes)\n",
     "\n",
     "\n",
-    "\n",
     "app = JupyterFrontEnd()\n",
     "split_panel = SplitPanel()\n",
     "\n",
     "# add the widgets to the split panel\n",
     "split_panel.children = [nv]\n",
     "\n",
-    "split_panel.title.label = 'NiiVue SplitPanel'\n",
-    "split_panel.title.icon_class = 'jp-PythonIcon'\n",
+    "split_panel.title.label = \"NiiVue SplitPanel\"\n",
+    "split_panel.title.icon_class = \"jp-PythonIcon\"\n",
     "split_panel.title.closable = True\n",
-    "app.shell.add(split_panel, 'main', { 'mode': 'split-right' })\n",
+    "app.shell.add(split_panel, \"main\", {\"mode\": \"split-right\"})\n",
     "print(\"Split panel created!\")"
    ]
   },

diff --git a/examples/mesh_layers.ipynb b/examples/mesh_layers.ipynb
@@ -8,7 +8,7 @@
    "outputs": [],
    "source": [
     "!mkdir -p ../images/\n",
-    "path=\"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
+    "path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
     "!wget {path}BrainMesh_ICBM152.lh.mz3 -P ../images/\n",
     "!wget {path}CIT168.mz3 -P ../images/\n",
     "!wget {path}BrainMesh_ICBM152.lh.motor.mz3 -P ../images/"
@@ -24,8 +24,7 @@
     "from ipyniivue import NiiVue\n",
     "\n",
     "nv = NiiVue(\n",
-    "    show_3d_crosshair=True, back_color=(1, 1, 1, 1),\n",
-    "    mesh_x_ray=0.3, is_colorbar=True\n",
+    "    show_3d_crosshair=True, back_color=(1, 1, 1, 1), mesh_x_ray=0.3, is_colorbar=True\n",
     ")\n",
     "\n",
     "mesh_layer = {\n",

diff --git a/examples/widgets.ipynb b/examples/widgets.ipynb
@@ -8,7 +8,7 @@
    "outputs": [],
    "source": [
     "!mkdir -p ../images/\n",
-    "path=\"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
+    "path = \"https://github.com/niivue/niivue/raw/main/demos/images/\"\n",
     "!wget {path}mni152.nii.gz -P ../images/\n",
     "!wget {path}hippo.nii.gz -P ../images/"
    ]
@@ -25,10 +25,18 @@
     "from ipyniivue import NiiVue, SliceType, WidgetObserver\n",
     "\n",
     "volumes = [\n",
-    "  { \"path\": \"../images/mni152.nii.gz\", \"colormap\": \"gray\",\n",
-    "    \"visible\": True, \"opacity\": 1.0 },\n",
-    "  { \"path\": \"../images/hippo.nii.gz\", \"colormap\": \"red\",\n",
-    "    \"visible\": True, \"opacity\": 1.0 },\n",
+    "    {\n",
+    "        \"path\": \"../images/mni152.nii.gz\",\n",
+    "        \"colormap\": \"gray\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1.0,\n",
+    "    },\n",
+    "    {\n",
+    "        \"path\": \"../images/hippo.nii.gz\",\n",
+    "        \"colormap\": \"red\",\n",
+    "        \"visible\": True,\n",
+    "        \"opacity\": 1.0,\n",
+    "    },\n",
     "]\n",
     "\n",
     "nv = NiiVue(slice_type=SliceType.MULTIPLANAR)\n",
@@ -37,74 +45,69 @@
     "widgetArray = []\n",
     "\n",
     "widget_slice_type = {\n",
-    "\n",
     "    \"widget\": ipywidgets.RadioButtons(\n",
-    "        options=[('Axial', 0), ('Coronal', 1), ('Sagittal', 2),\n",
-    "            ('Multiplanar', 3), ('Render', 4)],\n",
+    "        options=[\n",
+    "            (\"Axial\", 0),\n",
+    "            (\"Coronal\", 1),\n",
+    "            (\"Sagittal\", 2),\n",
+    "            (\"Multiplanar\", 3),\n",
+    "            (\"Render\", 4),\n",
+    "        ],\n",
     "        value=3,\n",
-    "        description='Slice Type:'),\n",
-    "\n",
+    "        description=\"Slice Type:\",\n",
+    "    ),\n",
     "    \"object\": nv,\n",
-    "\n",
-    "    \"attribute\": \"slice_type\"\n",
+    "    \"attribute\": \"slice_type\",\n",
     "}\n",
     "widgetArray.append(widget_slice_type)\n",
     "\n",
     "widget_scan_opacity = {\n",
-    "\n",
     "    \"widget\": ipywidgets.FloatSlider(\n",
     "        value=1.0,\n",
     "        min=0.0,\n",
     "        max=1.0,\n",
     "        step=0.1,\n",
-    "        description='Scan Opacity:',\n",
-    "        orientation='horizontal'),\n",
-    "\n",
+    "        description=\"Scan Opacity:\",\n",
+    "        orientation=\"horizontal\",\n",
+    "    ),\n",
     "    \"object\": nv.volumes[0],\n",
-    "\n",
-    "    \"attribute\": \"opacity\"\n",
+    "    \"attribute\": \"opacity\",\n",
     "}\n",
     "widgetArray.append(widget_scan_opacity)\n",
     "\n",
     "widget_hippo_opacity = {\n",
-    "\n",
     "    \"widget\": ipywidgets.FloatSlider(\n",
     "        value=1.0,\n",
     "        min=0.0,\n",
     "        max=1.0,\n",
     "        step=0.1,\n",
-    "        description='Hippocampus Opacity:',\n",
-    "        orientation='horizontal'),\n",
-    "\n",
+    "        description=\"Hippocampus Opacity:\",\n",
+    "        orientation=\"horizontal\",\n",
+    "    ),\n",
     "    \"object\": nv.volumes[1],\n",
-    "\n",
-    "    \"attribute\": \"opacity\"\n",
+    "    \"attribute\": \"opacity\",\n",
     "}\n",
     "widgetArray.append(widget_hippo_opacity)\n",
     "\n",
     "widget_scan_colormap = {\n",
-    "\n",
     "    \"widget\": ipywidgets.Select(\n",
-    "        options=['Gray', 'Red', 'Blue', 'Green'],\n",
-    "        value='Gray',\n",
-    "        description='Scan Colormap:'),\n",
-    "\n",
+    "        options=[\"Gray\", \"Red\", \"Blue\", \"Green\"],\n",
+    "        value=\"Gray\",\n",
+    "        description=\"Scan Colormap:\",\n",
+    "    ),\n",
     "    \"object\": nv.volumes[0],\n",
-    "\n",
-    "    \"attribute\": \"colormap\"\n",
+    "    \"attribute\": \"colormap\",\n",
     "}\n",
     "widgetArray.append(widget_scan_colormap)\n",
     "\n",
     "widget_hippo_colormap = {\n",
-    "\n",
     "    \"widget\": ipywidgets.Select(\n",
-    "        options=['Red', 'Blue', 'Green', 'Gray'],\n",
-    "        value='Red',\n",
-    "        description='Hippocampus Colormap:'),\n",
-    "\n",
+    "        options=[\"Red\", \"Blue\", \"Green\", \"Gray\"],\n",
+    "        value=\"Red\",\n",
+    "        description=\"Hippocampus Colormap:\",\n",
+    "    ),\n",
     "    \"object\": nv.volumes[1],\n",
-    "\n",
-    "    \"attribute\": \"colormap\"\n",
+    "    \"attribute\": \"colormap\",\n",
     "}\n",
     "widgetArray.append(widget_hippo_colormap)\n",
     "\n",

diff --git a/package-lock.json b/package-lock.json
diff --git a/scripts/generate_options_mixin.py b/scripts/generate_options_mixin.py
@@ -58,7 +58,7 @@ def get_value(value: typing.Any):
     return repr(value)
 
 
-def generate_mixin(options: typing.Dict[str, typing.Any]):
+def generate_mixin(options: typing.dict[str, typing.Any]):
     lines = [
         "# This file is automatically generated by scripts/generate_options_mixin.py",
         "# Do not edit this file directly",

diff --git a/src/ipyniivue/_constants.py b/src/ipyniivue/_constants.py
@@ -1,9 +1,9 @@
 import enum
 
 __all__ = [
-    "SliceType",
     "DragMode",
     "MuliplanarType",
+    "SliceType",
 ]
 
 

diff --git a/src/ipyniivue/_widget.py b/src/ipyniivue/_widget.py
@@ -111,6 +111,7 @@ def meshes(self):
         """Returns the list of meshes."""
         return list(self._meshes)
 
+
 class WidgetObserver:
     """Sets an observed for `widget` on the `attribute` of `object`."""