35 building documentation

.github/workflows/docs.yml

@@ -26,6 +26,7 @@ jobs:
         cd docs
         conda env create -f environment.yml
         source activate ipyniivue_docs
+        python -m ipykernel install --user --name=ipyniivue_docs
         make html
 
     - name: Deploy

dev-environment.yml

@@ -12,4 +12,4 @@ dependencies:
         - jupyter
         - jupyterlab>=0.34
         - notebook>=5.3
-        - jupyter_ui_poll
+        - jupyter-ui-poll

docs/environment.yml

@@ -8,4 +8,7 @@ dependencies:
   - sphinx
   - pydata-sphinx-theme
   - nbsphinx
-  - nbsphinx-link
+  - nbsphinx-link
+  - jupyter-ui-poll
+  - ipykernel
+

environment.yml

@@ -6,7 +6,7 @@ dependencies:
   - pip
   - ipyevents
   - ipywidgets
-  - jupyter_ui_poll
+  - jupyter-ui-poll
   - traitlets
   - pip:
     - ipyniivue==1.1.0

examples/tractography.ipynb

@@ -14,15 +14,31 @@
    "metadata": {},
    "source": [
     "### Installation\n",
-    "This notebook can be run on a local server or on a virtualized environement like Google Colab."
+    "This notebook can be run on a local server or on a virtualized environement like Google Colab.\n",
+    "\n",
+    "\n",
+    "##### Current limitations:\n",
+    "This notebook runs through `jupyter notebook` or `jupyter lab` but gets unresponsive when using JupyterLite (e.g., notebooks ran through VS Code or Google Colab)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "e8c48085-2e35-4d32-87dc-5d552482b994",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mDEPRECATION: pyodbc 4.0.0-unsupported has a non-standard version number. pip 23.3 will enforce this behaviour change. A possible replacement is to upgrade to a newer version of pyodbc or contact the author to suggest that they release a version with a conforming version number. Discussion can be found at https://github.com/pypa/pip/issues/12063\u001b[0m\u001b[33m\n",
+      "\u001b[0m\n",
+      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.2.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m23.3.1\u001b[0m\n",
+      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
+      "Note: you may need to restart the kernel to use updated packages.\n"
+     ]
+    }
+   ],
    "source": [
     "#run if using Google Colab or not building from source\n",
     "try:\n",
@@ -45,13 +61,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "14ca07b7-2838-45e8-a802-a0c96ac59ce9",
    "metadata": {},
    "outputs": [],
    "source": [
     "from ipyniivue import Niivue\n",
-    "import ipywidgets as widgets"
+    "import ipywidgets as widgets\n",
+    "from time import sleep, time\n",
+    "from jupyter_ui_poll import ui_events"
    ]
   },
   {
@@ -65,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "a2651106-3f99-4bb0-afd3-9e68a4be021d",
    "metadata": {
     "tags": []
@@ -135,10 +153,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "bd63fe41-444b-4ce7-a652-8d098a15eeff",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "d7cf5330ead0420d967e7138f82e13d6",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "VBox(children=(VBox(children=(IntSlider(value=3, description='Length', max=80, min=1), FloatSlider(value=1.0, …"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
    "source": [
     "# Creating a NiiVue object\n",
     "nv = Niivue(back_color=[0.8, 0.8, 1, 1], show_3D_crosshair=True)\n",
@@ -157,7 +190,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "ad7e5f38-9208-4845-b24a-84ffca1ff31c",
    "metadata": {
     "tags": []
@@ -178,7 +211,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "id": "34864ab3-a459-4e51-b27c-3c7df293aedf",
    "metadata": {
     "tags": []
@@ -198,16 +231,39 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
-   "id": "68574d16-54fc-4a81-9729-8df3f6045295",
-   "metadata": {
-    "tags": []
-   },
+   "execution_count": 7,
+   "id": "797e35b7",
+   "metadata": {},
    "outputs": [],
    "source": [
+    "################\n",
+    "# This block of code is currently necessary to avoid nv.meshes[0] being accessed before the\n",
+    "# mesh becomes accessible, in which case the notebook crashes with an IndexError.\n",
+    "# This error is triggered for example when the used hit \"cell -> Run all\"\n",
+    "################\n",
+    "timeout = 60\n",
+    "start = time()\n",
+    "i = 1\n",
+    "with ui_events() as poll:\n",
+    "    while True:\n",
+    "        poll(1)\n",
+    "        if len(nv.meshes):\n",
+    "            break\n",
+    "        if time() > start + timeout:\n",
+    "            raise TimeoutError\n",
+    "################\n",
+    "            \n",
     "nv.set_mesh_property(nv.meshes[0].id, \"colormap\", \"blue\")\n",
     "nv.set_clip_plane([-0.1, 270, 0])"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8eb0a3b0",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -226,7 +282,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.9.7"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {