Pass fsspec instance to ome-zarr

bioio_ome_zarr/reader.py

@@ -5,9 +5,10 @@
 from typing import Any, Dict, List, Optional, Tuple
 
 import xarray as xr
+import zarr.storage
 from bioio_base import constants, dimensions, exceptions, io, reader, types
 from fsspec.spec import AbstractFileSystem
-from ome_zarr.io import parse_url
+from ome_zarr.io import parse_url, ZarrLocation
 from ome_zarr.reader import Reader as ZarrReader
 
 from . import utils as metadata_utils
@@ -25,7 +26,7 @@ class Reader(reader.Reader):
     image: types.PathLike
         String or Path to the ZARR root
     fs_kwargs: Dict[str, Any]
-        Ignored
+        Passed to fsspec. For public S3 buckets, use {"anon": True}.
     """
 
     _xarray_dask_data: Optional["xr.DataArray"] = None
@@ -263,5 +264,5 @@ def _get_coords(
 
 def get_zarr_reader(fs: AbstractFileSystem, path: str) -> ZarrReader:
     if fs is not None:
-        path = fs.unstrip_protocol(path)
+        return ZarrReader(ZarrLocation(zarr.storage.FSStore(url=path, fs=fs)))
     return ZarrReader(parse_url(path, mode="r"))

pyproject.toml

@@ -4,10 +4,6 @@
 requires = ["setuptools>=65", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
-
-# package basics
-# https://peps.python.org/pep-0621/
 [project]
 name = "bioio-ome-zarr"
 description = "A BioIO reader plugin for reading Zarr files in the OME format."
@@ -27,10 +23,11 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-  "bioio-base>=1.0.0",
-  "fsspec>=2022.8.0",
-  "ome-zarr>=0.8.0",
-  "xarray>=0.16.1",
+    "bioio-base>=1.0.0",
+    "fsspec>=2022.8.0",
+    "ome-zarr>=0.9.0",
+    "xarray>=0.16.1",
+    "zarr>=2.18.2",
 ]
 
 [project.urls]