Update Colab demo notebook

napari_cellseg3d/_tests/test_plugins.py

@@ -8,10 +8,11 @@ def test_all_plugins_import(make_napari_viewer_proxy):
     plugins.napari_experimental_provide_dock_widget()
 
 
-def test_plugin_metrics(make_napari_viewer_proxy):
+def test_plugin_metrics(make_napari_viewer_proxy, qtbot):
     viewer = make_napari_viewer_proxy()
     w = m.MetricsUtils(viewer=viewer, parent=None)
-    viewer.window.add_dock_widget(w)
+    qtbot.addWidget(w)
+    # viewer.window.add_dock_widget(w)
 
     im_path = str(Path(__file__).resolve().parent / "res/test.tif")
     labels_path = im_path

notebooks/Colab_inference_demo.ipynb

@@ -7,7 +7,7 @@
     "id": "view-in-github"
    },
    "source": [
-    "<a href=\"https://colab.research.google.com/github/MMathisLab/CellSeg3d/blob/main/Notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+    "<a href=\"https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3D/blob/main/notebooks/Colab_inference_demo.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
    ]
   },
   {
@@ -53,9 +53,131 @@
    },
    "outputs": [],
    "source": [
-    "# @markdown ##Install CellSeg3D and grab demo data\n",
-    "!git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git --branch main --single-branch ./CellSeg3D\n",
-    "!pip install napari-cellseg3d"
+    "# @markdown ## Install CellSeg3D and ensure demo data\n",
+    "\n",
+    "import os\n",
+    "import shutil\n",
+    "import subprocess\n",
+    "import sys\n",
+    "import time\n",
+    "from pathlib import Path\n",
+    "\n",
+    "REPO_DIR = Path(\"/content/CellSeg3D\")\n",
+    "DEMO_FILE = REPO_DIR / \"examples\" / \"c5image.tif\"\n",
+    "REPO_URL = \"https://github.com/AdaptiveMotorControlLab/CellSeg3D.git\"\n",
+    "\n",
+    "\n",
+    "def run(cmd, **kwargs):\n",
+    "    print(\"+\", \" \".join(map(str, cmd)))\n",
+    "    subprocess.check_call(cmd, **kwargs)\n",
+    "\n",
+    "\n",
+    "def cellseg3d_ok():\n",
+    "    try:\n",
+    "        import napari_cellseg3d\n",
+    "        from napari_cellseg3d.dev_scripts import remote_inference\n",
+    "\n",
+    "        print(\"CellSeg3D import OK.\")\n",
+    "        return True\n",
+    "\n",
+    "    except Exception as e:\n",
+    "        print(\"CellSeg3D import failed:\")\n",
+    "        print(type(e).__name__, e)\n",
+    "        return False\n",
+    "\n",
+    "\n",
+    "def ensure_demo_data():\n",
+    "    if DEMO_FILE.is_file():\n",
+    "        print(f\"Demo data found: {DEMO_FILE}\")\n",
+    "        return\n",
+    "\n",
+    "    print(\"Demo data not found. Cloning CellSeg3D repository...\")\n",
+    "\n",
+    "    if REPO_DIR.exists():\n",
+    "        print(f\"Removing incomplete existing directory: {REPO_DIR}\")\n",
+    "        shutil.rmtree(REPO_DIR)\n",
+    "\n",
+    "    run(\n",
+    "        [\n",
+    "            \"git\",\n",
+    "            \"clone\",\n",
+    "            REPO_URL,\n",
+    "            \"--branch\",\n",
+    "            \"main\",\n",
+    "            \"--single-branch\",\n",
+    "            str(REPO_DIR),\n",
+    "        ]\n",
+    "    )\n",
+    "\n",
+    "    if not DEMO_FILE.is_file():\n",
+    "        raise FileNotFoundError(\n",
+    "            f\"Expected demo file was not found after cloning: {DEMO_FILE}\"\n",
+    "        )\n",
+    "\n",
+    "    print(f\"Demo data ready: {DEMO_FILE}\")\n",
+    "\n",
+    "\n",
+    "package_ok = cellseg3d_ok()\n",
+    "installed_package = False\n",
+    "\n",
+    "if not package_ok:\n",
+    "    print(\"Installing CellSeg3D...\")\n",
+    "\n",
+    "    if shutil.which(\"uv\") is None:\n",
+    "        run([sys.executable, \"-m\", \"pip\", \"install\", \"-q\", \"uv\"])\n",
+    "    else:\n",
+    "        print(\"uv already installed.\")\n",
+    "\n",
+    "    run(\n",
+    "        [\n",
+    "            \"uv\",\n",
+    "            \"pip\",\n",
+    "            \"install\",\n",
+    "            \"--system\",\n",
+    "            \"napari-cellseg3d\",\n",
+    "        ]\n",
+    "    )\n",
+    "\n",
+    "    installed_package = True\n",
+    "\n",
+    "else:\n",
+    "    print(\"CellSeg3D already available — skipping package install.\")\n",
+    "\n",
+    "\n",
+    "ensure_demo_data()\n",
+    "\n",
+    "\n",
+    "if installed_package:\n",
+    "    print(\"Restarting runtime to reload installed binary dependencies...\")\n",
+    "    print(\n",
+    "        \"Colab may show this as a crash, but it is expected. \"\n",
+    "        \"After the runtime reconnects, run the notebook again from the beginning. \"\n",
+    "        \"This cell should then skip installation and continue normally.\"\n",
+    "    )\n",
+    "\n",
+    "    time.sleep(1)\n",
+    "    os.kill(os.getpid(), 9)\n",
+    "\n",
+    "else:\n",
+    "    print(\"Setup complete.\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n",
+    "<div style=\"\n",
+    "  padding: 12px 16px;\n",
+    "  border-left: 5px solid #f59e0b;\n",
+    "  border-radius: 6px;\n",
+    "  margin: 12px 0;\n",
+    "\">\n",
+    "  <b>⚠️ Runtime restart is required after installation</b><br>\n",
+    "The runtime must be restarted after installing CellSeg3D to use the newly installed package. \n",
+    "\n",
+    "<b>The notebook will \"crash\" after installing, but this is expected, you may simply run the notebook again from the beginning after the runtime restarts.</b>\n",
+    "</div>"
    ]
   },
   {