update vole-app and demo uses bioio

.github/workflows/build.yml

@@ -15,78 +15,77 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout
-      uses: actions/checkout@v3
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Base Setup
-      uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
+      - name: Base Setup
+        uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
 
-    - name: Install dependencies
-      run: python -m pip install -U "jupyterlab>=4.0.0,<5"
+      - name: Install dependencies
+        run: python -m pip install -U "jupyterlab>=4.0.0,<5"
 
-    - name: Lint the extension
-      run: |
-        set -eux
-        jlpm
-        jlpm run lint:check
+      - name: Lint the extension
+        run: |
+          set -eux
+          jlpm
+          jlpm run lint:check
 
-    - name: Build the extension
-      run: |
-        set -eux
-        python -m pip install .[test]
+      - name: Build the extension
+        run: |
+          set -eux
+          python -m pip install .[test]
 
-        jupyter server extension list
-        jupyter server extension list 2>&1 | grep -ie "nbvv.*OK"
+          jupyter server extension list
+          jupyter server extension list 2>&1 | grep -ie "nbvv.*OK"
 
-        jupyter labextension list
-        jupyter labextension list 2>&1 | grep -ie "nbvv.*OK"
-        python -m jupyterlab.browser_check
+          jupyter labextension list
+          jupyter labextension list 2>&1 | grep -ie "nbvv.*OK"
+          python -m jupyterlab.browser_check
 
-    - name: Package the extension
-      run: |
-        set -eux
+      - name: Package the extension
+        run: |
+          set -eux
 
-        pip install build
-        python -m build
-        pip uninstall -y "nbvv" jupyterlab
+          pip install build
+          python -m build
+          pip uninstall -y "nbvv" jupyterlab
 
-    - name: Upload extension packages
-      uses: actions/upload-artifact@v3
-      with:
-        name: extension-artifacts
-        path: dist/nbvv*
-        if-no-files-found: error
+      - name: Upload extension packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: extension-artifacts
+          path: dist/nbvv*
+          if-no-files-found: error
 
   test_isolated:
     needs: build
     runs-on: ubuntu-latest
 
     steps:
-    - name: Install Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.9'
-        architecture: 'x64'
-    - uses: actions/download-artifact@v3
-      with:
-        name: extension-artifacts
-    - name: Install and Test
-      run: |
-        set -eux
-        # Remove NodeJS, twice to take care of system and locally installed node versions.
-        sudo rm -rf $(which node)
-        sudo rm -rf $(which node)
-
-        pip install "jupyterlab>=4.0.0,<5" nbvv*.whl
-
-
-        jupyter server extension list
-        jupyter server extension list 2>&1 | grep -ie "nbvv.*OK"
-
-        jupyter labextension list
-        jupyter labextension list 2>&1 | grep -ie "nbvv.*OK"
-        python -m jupyterlab.browser_check --no-browser-test
-
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+          architecture: 'x64'
+      - uses: actions/download-artifact@v4
+        with:
+          name: extension-artifacts
+      - name: Install and Test
+        run: |
+          set -eux
+          # Remove NodeJS, twice to take care of system and locally installed node versions.
+          sudo rm -rf $(which node)
+          sudo rm -rf $(which node)
+
+          pip install "jupyterlab>=4.0.0,<5" nbvv*.whl
+
+
+          jupyter server extension list
+          jupyter server extension list 2>&1 | grep -ie "nbvv.*OK"
+
+          jupyter labextension list
+          jupyter labextension list 2>&1 | grep -ie "nbvv.*OK"
+          python -m jupyterlab.browser_check --no-browser-test
 
   check_links:
     name: Check Links

.github/workflows/check-release.yml

@@ -24,7 +24,7 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload Distributions
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: nbvv-releaser-dist-${{ github.run_number }}
           path: .jupyter_releaser_checkout/dist

README.md

@@ -76,6 +76,15 @@ jupyter labextension develop . --overwrite
 jlpm build
 ```
 
+During development it may sometimes be useful to do some manual cleanup:
+
+```bash
+rm -rf node_modules
+rm -rf yarn.lock
+jlpm install
+jlpm build
+```
+
 You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.
 
 ```bash

RELEASE.md

@@ -82,7 +82,6 @@ Here is a summary of the steps to cut a new release:
 - If the repo generates PyPI release(s), create a scoped PyPI [token](https://packaging.python.org/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/#saving-credentials-on-github). We recommend using a scoped token for security reasons.
 
 - You can store the token as `PYPI_TOKEN` in your fork's `Secrets`.
-
   - Advanced usage: if you are releasing multiple repos, you can create a secret named `PYPI_TOKEN_MAP` instead of `PYPI_TOKEN` that is formatted as follows:
 
     ```text

examples/demo.ipynb

@@ -18,9 +18,9 @@
    ],
    "source": [
     "import numpy\n",
-    "from aicsimageio import AICSImage\n",
+    "from bioio import BioImage\n",
     "import nbvv\n",
-    "image = AICSImage(\"AICS-10_5_5.ome.tif\")\n",
+    "image = BioImage(\"AICS-10_5_5.ome.tif\")\n",
     "imgdata = image.get_image_data(\"CZYX\", T=0)\n",
     "imgdata.shape"
    ]
@@ -33,7 +33,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "14d9e3e11aed4e0cb6860a4c5797be66",
+       "model_id": "c0100108126a4cd98d505c060f15c644",
        "version_major": 2,
        "version_minor": 0
       },
@@ -74,7 +74,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

nbvv/img_prep.py

@@ -82,17 +82,19 @@ def atlas_dimensions(
         "sizeY": tile_height,
         "sizeZ": stack_height,
         "sizeC": aics_image.shape[0],
-        "physicalPixelSize": physical_pixel_size if physical_pixel_size is not None else [1, 1, 1],
+        "physicalPixelSize": (
+            physical_pixel_size if physical_pixel_size is not None else [1, 1, 1]
+        ),
         "spatialUnit": "µm",
-        "channelNames":  (
+        "channelNames": (
             channel_names
             if channel_names is not None
             else ["CH_" + str(i) for i in range(aics_image.shape[0])]
         ),
     }
-    
+
     # "originalSize": [aics_image.shape[3], aics_image.shape[2], aics_image.shape[1]],
- 
+
     return dims
 
 
@@ -118,7 +120,7 @@ def img_prep(img, shape=(128, 128)):
 
     # C Z Y X
     response = numpy.zeros(
-        (channels, img.shape[1], shape[1], shape[0]), dtype=numpy.uint8
+        (channels, img.shape[1], shape[1], shape[0]), dtype=img.dtype
     )
 
     for channel_index in range(channels):
@@ -127,11 +129,11 @@ def img_prep(img, shape=(128, 128)):
 
         resized_channel = resize(channel_data, (shape[0], shape[1]))
 
-        mn = min(0, resized_channel.min())
-        mx = resized_channel.max()
-        resized_channel = 255.0 * (resized_channel - mn) / (mx - mn)
-        # atlas = np.interp(atlas, (min(0, atlas.min()), atlas.max()), (0.0, 255.0))
-        resized_channel = resized_channel.astype(numpy.uint8)
+        # mn = min(0, resized_channel.min())
+        # mx = resized_channel.max()
+        # resized_channel = 255.0 * (resized_channel - mn) / (mx - mn)
+
+        # resized_channel = resized_channel.astype(numpy.uint8)
 
         response[channel_index] = resized_channel
 

nbvv/volume.py

@@ -3,7 +3,7 @@
 import nbvv.img_prep
 import numpy
 import traitlets
-from typing import List, Tuple
+from typing import List, Tuple, Optional
 
 # use this line if we are keeping package.json version up to date:
 semver_range_frontend = "~" + nbvv._version.__version__
@@ -39,7 +39,7 @@ def volshow(
     spacing: Tuple[float, float, float] = (1.0, 1.0, 1.0),
     density: float = 0.1,
     brightness: float = 1.0,
-    channel_names: List[str] = None,
+    channel_names: Optional[List[str]] = None,
     viewer_height: int = 500,
 ):
     """

package.json

@@ -21,6 +21,7 @@
         "style/**/*.{css,js,eot,gif,html,jpg,json,png,svg,woff2,ttf}",
         "src/**/*.{ts,tsx}"
     ],
+    "type": "module",
     "main": "lib/index.js",
     "types": "lib/index.d.ts",
     "repository": {
@@ -55,15 +56,15 @@
         "watch:labextension": "jupyter labextension watch ."
     },
     "dependencies": {
-        "@aics/web-3d-viewer": "^2.9.0",
+        "@aics/vole-app": "^2.13.5",
         "@babel/runtime": "7.24.1",
         "@jupyter-widgets/base": "^6.0.7",
         "@jupyterlab/application": "^4.0.0",
         "@jupyterlab/coreutils": "^6.0.0",
-        "@jupyterlab/services": "^7.0.0",
         "antd": "^5.16.2",
         "react": "^18.x",
-        "react-dom": "^18.x"
+        "react-dom": "^18.x",
+        "three": "^0.171.0"
     },
     "devDependencies": {
         "@jupyterlab/builder": "^4.0.0",
@@ -93,11 +94,12 @@
         "stylelint-config-standard": "^34.0.0",
         "stylelint-csstree-validator": "^3.0.0",
         "stylelint-prettier": "^4.0.0",
-        "typescript": "~5.0.2",
+        "typescript": "~5.8.3",
+        "webpack": "^5.101.0",
         "yjs": "^13.5.0"
     },
     "resolutions": {
-        "d3-selection": "1.3.0"
+        "d3-selection": "3"
     },
     "publishConfig": {
         "access": "public"
@@ -114,13 +116,15 @@
             }
         },
         "extension": true,
-        "outputDir": "nbvv/labextension"
+        "outputDir": "nbvv/labextension",
+        "webpackConfig": "./webpack.config.cjs"
     },
     "eslintIgnore": [
         "node_modules",
         "dist",
         "coverage",
-        "**/*.d.ts"
+        "**/*.d.ts",
+        "webpack.config.cjs"
     ],
     "eslintConfig": {
         "extends": [

src/index.ts

@@ -7,7 +7,7 @@ import * as base from '@jupyter-widgets/base';
 // eslint-disable-next-line @typescript-eslint/no-var-requires
 const semver_range = require('../package.json').version;
 
-import * as jupyter_volume from './view';
+import * as jupyter_volume from './view.js';
 
 /**
  * Initialization data for the nbvv extension.