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C-AchardC-Achard
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Update Colab demo notebook (#128)
* Fix URL * Add uv install * Add force restart after install * Add better checks for install * Fix URL again * Fix commands syntax * Update Colab_inference_demo.ipynb * Update Colab_inference_demo.ipynb * Colab demo: ensure demo data; refine install flow Update Colab_inference_demo.ipynb to ensure demo data and improve setup flow. Add REPO_DIR/DEMO_FILE/REPO_URL constants, import time, and a run() print fix. Introduce ensure_demo_data() to clone the CellSeg3D repo and verify the expected example file, removing previous ad-hoc cloning logic. Track whether the package was installed with installed_package, improve user messages about runtime restart, add a short sleep before killing the process, and print a concise completion message when setup is already satisfied. * URL case fix * Update test_plugins.py
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2 files changed

Lines changed: 129 additions & 6 deletions

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‎napari_cellseg3d/_tests/test_plugins.py‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,10 +8,11 @@ def test_all_plugins_import(make_napari_viewer_proxy):
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plugins.napari_experimental_provide_dock_widget()
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def test_plugin_metrics(make_napari_viewer_proxy):
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def test_plugin_metrics(make_napari_viewer_proxy, qtbot):
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viewer = make_napari_viewer_proxy()
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w = m.MetricsUtils(viewer=viewer, parent=None)
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viewer.window.add_dock_widget(w)
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qtbot.addWidget(w)
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# viewer.window.add_dock_widget(w)
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im_path = str(Path(__file__).resolve().parent / "res/test.tif")
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labels_path = im_path

‎notebooks/Colab_inference_demo.ipynb‎

Lines changed: 126 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
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"id": "view-in-github"
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},
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"source": [
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"<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>"
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"<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>"
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]
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},
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{
@@ -53,9 +53,131 @@
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},
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"outputs": [],
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"source": [
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"# @markdown ##Install CellSeg3D and grab demo data\n",
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"!git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git --branch main --single-branch ./CellSeg3D\n",
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"!pip install napari-cellseg3d"
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"# @markdown ## Install CellSeg3D and ensure demo data\n",
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"\n",
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"import os\n",
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"import shutil\n",
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"import subprocess\n",
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"import sys\n",
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"import time\n",
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"from pathlib import Path\n",
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"\n",
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"REPO_DIR = Path(\"/content/CellSeg3D\")\n",
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"DEMO_FILE = REPO_DIR / \"examples\" / \"c5image.tif\"\n",
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"REPO_URL = \"https://github.com/AdaptiveMotorControlLab/CellSeg3D.git\"\n",
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"\n",
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"\n",
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"def run(cmd, **kwargs):\n",
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" print(\"+\", \" \".join(map(str, cmd)))\n",
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" subprocess.check_call(cmd, **kwargs)\n",
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"\n",
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"\n",
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"def cellseg3d_ok():\n",
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" try:\n",
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" import napari_cellseg3d\n",
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" from napari_cellseg3d.dev_scripts import remote_inference\n",
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"\n",
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" print(\"CellSeg3D import OK.\")\n",
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" return True\n",
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"\n",
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" except Exception as e:\n",
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" print(\"CellSeg3D import failed:\")\n",
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" print(type(e).__name__, e)\n",
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" return False\n",
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"\n",
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"\n",
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"def ensure_demo_data():\n",
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" if DEMO_FILE.is_file():\n",
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" print(f\"Demo data found: {DEMO_FILE}\")\n",
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" return\n",
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"\n",
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" print(\"Demo data not found. Cloning CellSeg3D repository...\")\n",
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"\n",
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" if REPO_DIR.exists():\n",
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" print(f\"Removing incomplete existing directory: {REPO_DIR}\")\n",
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" shutil.rmtree(REPO_DIR)\n",
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"\n",
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" run(\n",
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" [\n",
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" \"git\",\n",
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" \"clone\",\n",
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" REPO_URL,\n",
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" \"--branch\",\n",
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" \"main\",\n",
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" \"--single-branch\",\n",
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" str(REPO_DIR),\n",
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" ]\n",
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" )\n",
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"\n",
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" if not DEMO_FILE.is_file():\n",
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" raise FileNotFoundError(\n",
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" f\"Expected demo file was not found after cloning: {DEMO_FILE}\"\n",
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" )\n",
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"\n",
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" print(f\"Demo data ready: {DEMO_FILE}\")\n",
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"\n",
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"\n",
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"package_ok = cellseg3d_ok()\n",
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"installed_package = False\n",
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"\n",
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"if not package_ok:\n",
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" print(\"Installing CellSeg3D...\")\n",
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"\n",
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" if shutil.which(\"uv\") is None:\n",
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" run([sys.executable, \"-m\", \"pip\", \"install\", \"-q\", \"uv\"])\n",
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" else:\n",
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" print(\"uv already installed.\")\n",
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"\n",
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" run(\n",
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" [\n",
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" \"uv\",\n",
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" \"pip\",\n",
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" \"install\",\n",
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" \"--system\",\n",
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" \"napari-cellseg3d\",\n",
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" ]\n",
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" )\n",
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"\n",
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" installed_package = True\n",
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"\n",
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"else:\n",
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" print(\"CellSeg3D already available — skipping package install.\")\n",
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"\n",
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"\n",
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"ensure_demo_data()\n",
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"\n",
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"\n",
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"if installed_package:\n",
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" print(\"Restarting runtime to reload installed binary dependencies...\")\n",
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" print(\n",
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" \"Colab may show this as a crash, but it is expected. \"\n",
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" \"After the runtime reconnects, run the notebook again from the beginning. \"\n",
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" \"This cell should then skip installation and continue normally.\"\n",
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" )\n",
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"\n",
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" time.sleep(1)\n",
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" os.kill(os.getpid(), 9)\n",
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"\n",
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"else:\n",
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" print(\"Setup complete.\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"\n",
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"<div style=\"\n",
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" padding: 12px 16px;\n",
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" border-left: 5px solid #f59e0b;\n",
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" border-radius: 6px;\n",
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" margin: 12px 0;\n",
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"\">\n",
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" <b>⚠️ Runtime restart is required after installation</b><br>\n",
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"The runtime must be restarted after installing CellSeg3D to use the newly installed package. \n",
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"\n",
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"<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",
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"</div>"
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]
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},
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{

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