Merge pull request #16 from fractal-analytics-platform/fix_streaming

minor fix for streaming correcly streaming anndata

README.md

@@ -33,7 +33,7 @@ To get started, check out the [Getting Started](https://fractal-analytics-platfo
 | Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
 | Base Documentation | ✅ | End-September | API Documentation and Examples |
 | Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | ONGOING | December | Ngio can stream ome-zarr from fractal |
+| Streaming from Fractal | Ongoing | December | Ngio can stream ome-zarr from fractal |
 | Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
 | Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |

docs/index.md

@@ -27,7 +27,7 @@ To get started, check out the [Getting Started](getting-started.md) guide.
 | Basic Iterators | Ongoing | End-September | Read and Write Iterators for common access patterns |
 | Base Documentation | ✅ | End-September | API Documentation and Examples |
 | Beta Ready Testing | ✅ | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
-| Streaming from Fractal | ONGOING | December | Ngio can stream ome-zarr from fractal |
+| Streaming from Fractal | Ongoing | December | Ngio can stream ome-zarr from fractal |
 | Mask Iterators | Ongoing | Early 2025 | Iterators over Masked Tables |
 | Advanced Iterators | Not started | mid-2025 | Iterators for advanced access patterns |
 | Parallel Iterators | Not started | mid-2025 | Concurrent Iterators for parallel read and write |

docs/notebooks/image.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Images/Labels/Tables\n",
     "\n",
-    "In this notebook we will show how to use the `Image`, `Label` and `Table` objects."
+    "In this notebook we will show how to use the `Image`, `Label` and `Table` objects to do image processing."
    ]
   },
   {
@@ -305,13 +305,6 @@
     "\n",
     "feat_table.table"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

pyproject.toml

@@ -34,7 +34,7 @@ classifiers = [
 # add your package dependencies here
 dependencies = [
     "numpy",
-    "anndata",
+    "anndata>=0.8.0,<0.11.0",
     "pydantic",
     "pandas>=1.2.0",
     "requests",
@@ -52,6 +52,7 @@ test = ["zarr<3", "pytest", "pytest-cov"]
 
 dev2 = [
     "zarr<3",
+    "plotly",
     "dask[distributed]",
     "dask-image",
     "napari",

src/ngio/tables/_ad_reader.py

@@ -34,20 +34,22 @@ def custom_read_zarr(store: StoreOrGroup) -> AnnData:
     def callback(func: Callable, elem_name: str, elem: Any, iospec: Any) -> Any:
         if iospec.encoding_type == "anndata" or elem_name.endswith("/"):
             ad_kwargs = {}
+            # Some of these elem fail on https
+            # So we only include the ones that are strictly necessary
+            # for fractal tables
             base_elem = [
                 "X",
-                "layers",
+                # "layers",
                 "obs",
-                "obsm",
-                "obsp",
-                "uns",
+                # "obsm",
+                # "obsp",
+                # "uns",
                 "var",
-                "varm",
-                "varp",
+                # "varm",
+                # "varp",
             ]
-            # This should make sure that the function behaves the same as the original
-            # implementation.
-            base_elem += list(elem.keys())
+            # This fails on some https
+            # base_elem += list(elem.keys())
             for k in set(base_elem):
                 v = elem.get(k)
                 if v is not None and not k.startswith("raw."):