diff --git a/README.md b/README.md index 2c4d27c..7019a55 100644 --- a/README.md +++ b/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 | diff --git a/docs/index.md b/docs/index.md index 130ba05..ae97c92 100644 --- a/docs/index.md +++ b/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 | diff --git a/docs/notebooks/image.ipynb b/docs/notebooks/image.ipynb index a299635..8d10805 100644 --- a/docs/notebooks/image.ipynb +++ b/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": { diff --git a/pyproject.toml b/pyproject.toml index 8ea280b..9e9a580 100644 --- a/pyproject.toml +++ b/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", diff --git a/src/ngio/tables/_ad_reader.py b/src/ngio/tables/_ad_reader.py index 1756987..e8a3c52 100644 --- a/src/ngio/tables/_ad_reader.py +++ b/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."):