Pin dependencies for zarr. Update spatialdata-blobs notebook

Author: keller-mark

docs/notebooks/spatial_data_blobs.ipynb

@@ -109,12 +109,12 @@
    "outputs": [],
    "source": [
     "vc = VitessceConfig(\n",
-    "    schema_version=\"1.0.16\",\n",
+    "    schema_version=\"1.0.17\",\n",
     "    name='Visium SpatialData Demo (blobs)',\n",
     ")\n",
     "# Add data to the configuration:\n",
     "wrapper = SpatialDataWrapper(\n",
-    "    sdata_path=spatialdata_filepath,\n",
+    "    sdata_store=spatialdata_filepath,\n",
     "    # The following paths are relative to the root of the SpatialData zarr store on-disk.\n",
     "    image_path=\"images/blobs_image\",\n",
     "    labels_path=\"labels/blobs_labels\",\n",
@@ -140,15 +140,26 @@
     "                \"spatialTargetC\": 0,\n",
     "                \"spatialChannelColor\": [255, 0, 0],\n",
     "                \"spatialChannelOpacity\": 1.0\n",
+    "            },\n",
+    "            {\n",
+    "                \"spatialTargetC\": 1,\n",
+    "                \"spatialChannelColor\": [0, 255, 0],\n",
+    "                \"spatialChannelOpacity\": 1.0\n",
+    "            },\n",
+    "            {\n",
+    "                \"spatialTargetC\": 2,\n",
+    "                \"spatialChannelColor\": [0, 0, 255],\n",
+    "                \"spatialChannelOpacity\": 1.0\n",
     "            }\n",
     "        ])\n",
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"image\"))\n",
     "\n",
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    'segmentationLayer': CL([{\n",
+    "        \"fileUid\": \"my_unique_id\",\n",
     "        'segmentationChannel': CL([{\n",
-    "            'spatialChannelVisible': False,\n",
+    "            'spatialChannelVisible': True,\n",
     "            'obsType': 'blob',\n",
     "        }]),\n",
     "    }]),\n",
@@ -206,7 +217,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.20"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -25,21 +25,21 @@ classifiers = [
   'Programming Language :: Python :: 3.12',
 ]
 dependencies = [
-  'zarr>=2.5.0',
-  'numcodecs>=0.5.7',
   'scipy>=1.2.1',
   'negspy>=0.2.24',
   'pandas>=1.1.2',
   'black>=21.11b1',
   'numpy>=1.21.2',
+  'zarr>=2.5.0,<3',
+  'numcodecs>=0.5.7',
   'anndata>=0.7.8',
-  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not 
+  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
   # Reference: https://github.com/scverse/scanpy/pull/3115/files
   'scanpy>=1.10.2',
-  'ome-zarr>=0.8.3',
+  'ome-zarr<9',
   'tifffile>=2020.10.1',
   'jsonschema>=3.2',
-  'tqdm>=4.1.0'
+  'tqdm>=4.1.0',
 ]
 
 [project.optional-dependencies]
@@ -74,9 +74,10 @@ all = [
   'uvicorn>=0.17.0',
   'ujson>=4.0.1',
   'starlette==0.14.0',
-  'generate-tiff-offsets>=0.1.8',
+  'generate-tiff-offsets>=0.1.9',
   'kerchunk>=0.2.6',
   'fsspec',
+  'spatialdata>=0.3.0',
 
   # aiofiles is not explicitly referenced in our code,
   # but it is an implicit dependency of starlette==0.14.0.