adding reader_options kwargs to open_virtual_dataset

virtualizarr/kerchunk.py

@@ -20,7 +20,10 @@
 
 
 def read_kerchunk_references_from_file(
-    filepath: str, filetype: Optional[str]
+    filepath: str, filetype: Optional[str],
+    reader_options: Optional[dict] = {'storage_options': {'anon': True}}
+
+
 ) -> KerchunkStoreRefs:
     """
     Read a single legacy file and return kerchunk references to its contents.
@@ -32,31 +35,33 @@ def read_kerchunk_references_from_file(
     filetype : str, default: None
         Type of file to be opened. Used to determine which kerchunk file format backend to use.
         If not provided will attempt to automatically infer the correct filetype from the the filepath's extension.
+    reader_options: dict, default {'storage_options': {'anon': True}}
+        Dict passed into Kerchunk file readers. Note: Each Kerchunk file reader has distinct arguments,
+        so ensure reader_options match selected Kerchunk reader arguments.
     """
 
     if filetype is None:
         filetype = _automatically_determine_filetype(filepath)
 
     if filetype.lower() == "netcdf3":
         from kerchunk.netCDF3 import NetCDF3ToZarr
-        refs = NetCDF3ToZarr(filepath).translate()
+        refs = NetCDF3ToZarr(filepath, **reader_options).translate()
 
     elif filetype.lower() == "netcdf4":
         from kerchunk.hdf import SingleHdf5ToZarr
-
-        refs = SingleHdf5ToZarr(filepath).translate()
+        refs = SingleHdf5ToZarr(filepath, **reader_options).translate()
     elif filetype == "grib":
         # TODO Grib files should be handled as a DataTree object
         # see https://github.com/TomNicholas/VirtualiZarr/issues/11
         raise NotImplementedError(f"Unsupported file type: {filetype}")
     elif filetype.lower() == "tiff":
         from kerchunk.tiff import tiff_to_zarr
 
-        refs = tiff_to_zarr(filepath)
+        refs = tiff_to_zarr(filepath, **reader_options)
     elif filetype.lower() == "fits":
         from kerchunk.fits import process_file
 
-        refs = process_file(filepath)
+        refs = process_file(filepath, **reader_options)
     else:
         raise NotImplementedError(f"Unsupported file type: {filetype}")
 

virtualizarr/tests/test_xarray.py

@@ -3,6 +3,7 @@
 import numpy as np
 import xarray as xr
 from xarray.core.indexes import Index
+import pytest
 
 from virtualizarr import open_virtual_dataset
 from virtualizarr.manifests import ChunkManifest, ManifestArray
@@ -268,3 +269,12 @@ def test_combine_by_coords(self, netcdf4_files):
         )
 
         assert combined_vds.xindexes["time"].to_pandas_index().is_monotonic_increasing
+
+
+pytest.importorskip("s3fs")
+@pytest.mark.xfail(reason="currently should xfail for None filetype and None indexes.",run=False)
+@pytest.mark.parametrize("filetype", ['netcdf4', None], ids=["netcdf4 filetype", "None filetype"])
+@pytest.mark.parametrize("indexes", [None, {}], ids=["None index", "empty dict index"])
+def test_anon_read_s3(filetype, indexes):
+    fpath = 's3://nex-gddp-cmip6/NEX-GDDP-CMIP6/CESM2/historical/r4i1p1f1/pr/pr_day_CESM2_historical_r4i1p1f1_gn_2010.nc'
+    assert open_virtual_dataset(fpath,filetype=filetype,indexes=indexes,reader_options={'storage_options': {'anon': True}})

virtualizarr/xarray.py

@@ -23,6 +23,7 @@ def open_virtual_dataset(
     drop_variables: Optional[List[str]] = None,
     indexes: Optional[Mapping[str, Index]] = None,
     virtual_array_class=ManifestArray,
+    reader_options: Optional[dict] = {'storage_options': {'anon': True}}
 ) -> xr.Dataset:
     """
     Open a file or store as an xarray Dataset wrapping virtualized zarr arrays.
@@ -48,12 +49,16 @@ def open_virtual_dataset(
     virtual_array_class
         Virtual array class to use to represent the references to the chunks in each on-disk array.
         Currently can only be ManifestArray, but once VirtualZarrArray is implemented the default should be changed to that.
+    reader_options: dict, default {'storage_options': {'anon': True}}
+        Dict passed into Kerchunk file readers. Note: Each Kerchunk file reader has distinct arguments,
+        so ensure reader_options match selected Kerchunk reader arguments.
     """
 
     # this is the only place we actually always need to use kerchunk directly
     vds_refs = kerchunk.read_kerchunk_references_from_file(
         filepath=filepath,
         filetype=filetype,
+        reader_options=reader_options,
     )
 
     if indexes is None: