WIP: support for zarr v3

Author: keller-mark

.python-version

@@ -1 +1 @@
-3.10
+3.12

docs/data_options.rst

@@ -129,15 +129,18 @@ This is currently supported for the ``AnnDataWrapper`` class using the ``adata_s
     vc.widget()
 
 
-Or, with a Zarr store instance (instead of a local string path to a DirectoryStore):
+Or, with a Zarr store instance (instead of a local string path to a LocalStore/DirectoryStore):
 
 .. code-block:: python
 
     import zarr
+    from obstore.store import HTTPStore
     from vitessce import VitessceConfig, AnnDataWrapper
 
-    # ...
-    store = zarr.storage.FSStore("s3://my_bucket/path/to/my_store.adata.zarr")
+    obs_store = HTTPStore.from_url("https://my_bucket.example.com/path/to/my_store.adata.zarr")
+    store = zarr.storage.ObjectStore(obs_store, read_only=True)
+    # or
+    store = zarr.storage.LocalStore("./path/to/my_store.adata.zarr")
 
     vc = VitessceConfig(name="My Vitessce Configuration")
     vc.add_dataset(name="My Dataset").add_object(AnnDataWrapper(

docs/notebooks/spatial_data_blobs.ipynb

@@ -115,7 +115,7 @@
     ")\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",
     "    obs_segmentations_path=\"labels/blobs_labels\",\n",
@@ -129,7 +129,7 @@
     "    }\n",
     ")\n",
     "points_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",
     "    obs_points_path=\"points/blobs_points\",\n",
     "    obs_feature_matrix_path=\"tables/table_points/X\", # TODO\n",
@@ -221,6 +221,27 @@
    "outputs": [],
    "source": []
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -245,7 +266,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.12.5"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 description = "Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce"
 readme = "README.md"
 license = {file = "LICENSE"}
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 keywords = ["ipython", "jupyter", "widgets"]
 classifiers = [
   'Development Status :: 4 - Beta',
@@ -30,7 +30,6 @@ dependencies = [
   'black>=21.11b1',
   'numpy>=1.21.2',
   'zarr>=3.0.0',
-  'numcodecs>=0.5.7,<0.16.0',
 ]
 
 [project.optional-dependencies]
@@ -61,7 +60,7 @@ docs = [
 all = [
   # For data_utils
   'negspy>=0.2.24',
-  'anndata>=0.7.8',
+  'anndata>=0.12.10',
   # 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',
@@ -70,13 +69,13 @@ all = [
 
   'jupyter-server-proxy>=1.5.2',
   'oxc-py>=0.1.1',
-  'anywidget>=0.9.10',
+  'anywidget>=0.11.0',
   'uvicorn>=0.17.0',
   'ujson>=4.0.1',
   'starlette>=0.14.0',
   'generate-tiff-offsets>=0.1.9',
   'kerchunk>=0.2.6',
-  'fsspec',
+  'obstore',
 
   # aiofiles is not explicitly referenced in our code,
   # but it is an implicit dependency of starlette==0.14.0.
@@ -88,8 +87,7 @@ building = []
 testing = []
 linting = []
 notebook = [
-  'spatialdata>=0.3.0',
-  'dask[dataframe]>=2025.2.0',
+  'spatialdata>=0.7.3',
   'marimo',
   'starlette>=0.42.0',
   'tqdm>=4.1.0',
@@ -121,8 +119,7 @@ dev = [
   'boto3>=1.16.30',
   'scikit-misc>=0.1.3',
   'autopep8>=2.0.2',
-  'spatialdata>=0.3.0',
-  'dask[dataframe]>=2025.2.0',
+  'spatialdata>=0.7.3',
 ]
 
 [tool.uv]