Allow LindiH5pyFile.from_hdf5_file to accept remote URL for local file

lindi/LindiH5ZarrStore/LindiH5ZarrStore.py

@@ -443,7 +443,7 @@ def _get_external_array_link(self, parent_key: str, h5_item: h5py.Dataset):
                 if self._url is not None:
                     self._external_array_links[parent_key] = {
                         "link_type": "hdf5_dataset",
-                        "url": self._url,  # url is not going to be null based on the check in __init__
+                        "url": self._url,
                         "name": parent_key,
                     }
                 else:

lindi/LindiH5pyFile/LindiH5pyFile.py

@@ -58,7 +58,14 @@ def from_lindi_file(url_or_path: str, *, mode: LindiFileMode = "r", staging_area
         return LindiH5pyFile.from_reference_file_system(url_or_path, mode=mode, staging_area=staging_area, local_cache=local_cache, local_file_path=local_file_path)
 
     @staticmethod
-    def from_hdf5_file(url_or_path: str, *, mode: LindiFileMode = "r", local_cache: Union[LocalCache, None] = None, zarr_store_opts: Union[LindiH5ZarrStoreOpts, None] = None):
+    def from_hdf5_file(
+        url_or_path: str,
+        *,
+        mode: LindiFileMode = "r",
+        local_cache: Union[LocalCache, None] = None,
+        zarr_store_opts: Union[LindiH5ZarrStoreOpts, None] = None,
+        url: Union[str, None] = None
+    ):
         """
         Create a LindiH5pyFile from a URL or path to an HDF5 file.
 
@@ -73,11 +80,18 @@ def from_hdf5_file(url_or_path: str, *, mode: LindiFileMode = "r", local_cache:
             The local cache to use for caching data chunks, by default None.
         zarr_store_opts : Union[LindiH5ZarrStoreOpts, None], optional
             The options to use for the zarr store, by default None.
+        url : str or None
+            If url_or_path is a local file name, then this can
+            optionally be set to the URL of the remote file to be used when
+            creating references. If None, and the url_or_path is a
+            local file name, then you will need to set
+            zarr_store_opts.num_dataset_chunks_threshold to None, and you will not be able
+            to use the to_reference_file_system method.
         """
         from ..LindiH5ZarrStore.LindiH5ZarrStore import LindiH5ZarrStore  # avoid circular import
         if mode != "r":
             raise Exception("Opening hdf5 file in write mode is not supported")
-        zarr_store = LindiH5ZarrStore.from_file(url_or_path, local_cache=local_cache, opts=zarr_store_opts, url=url_or_path)
+        zarr_store = LindiH5ZarrStore.from_file(url_or_path, local_cache=local_cache, opts=zarr_store_opts, url=url)
         return LindiH5pyFile.from_zarr_store(
             zarr_store=zarr_store,
             mode=mode,