Regression: FsspecStore over ReferenceFileSystem fails with GroupNotFoundError (path '/' joined as '//key')

[TomNicholas]

Describe the bug

zarr.open_group on an FsspecStore wrapping fsspec.implementations.reference.ReferenceFileSystem raises GroupNotFoundError on current main, even though the reference set contains a valid zarr.json.

This appears to be a regression from #3679 (be0a7b8), which in FsspecStore._get replaced

path = _dereference_path(self.path, key)

with

path = _join_paths([self.path, key])

These differ when self.path == "/" (which is what FsspecStore(fs=ReferenceFileSystem(...)) ends up with):

• _dereference_path("/", "zarr.json") → "zarr.json" (root is rstrip("/")ed to "", so no prefix is added)
• _join_paths(["/", "zarr.json"]) → "//zarr.json" (only empty strings are filtered, so "/" is kept and joined with "/")

ReferenceFileSystem keys its refs by bare "zarr.json", so the lookup misses, _get raises FileNotFoundError, and open_group turns that into GroupNotFoundError.

Local-filesystem-backed FsspecStores aren't affected because their self.path is the full filesystem path (not "/"), so the extra slash never appears.

Steps to reproduce

Save as repro.py and run uv run repro.py:

# /// script
# requires-python = ">=3.11"
# dependencies = [
#     "fsspec",
#     "zarr",
# ]
# ///
import json

import fsspec
import zarr
from zarr.storage import FsspecStore
from zarr.storage._utils import _join_paths

group_json = json.dumps({"zarr_format": 3, "node_type": "group", "attributes": {}})
refs = {"version": 1, "refs": {"zarr.json": group_json}}

fs = fsspec.filesystem("reference", fo=refs, asynchronous=True)
store = FsspecStore(fs=fs, read_only=True)
print(f"zarr version: {zarr.__version__}")
print(f"store: {store!r}")
print(f"store.path: {store.path!r}")
print(f'_join_paths([store.path, "zarr.json"]) = {_join_paths([store.path, "zarr.json"])!r}')

zarr.open_group(store, mode="r")
print("SUCCESS — group opened")

Output on current main (3.1.7.dev45+g866aa8d67)

zarr version: 3.1.7.dev45+g866aa8d67
store: <FsspecStore(ReferenceFileSystem, /)>
store.path: '/'
_join_paths([store.path, "zarr.json"]) = '//zarr.json'
...
zarr.errors.GroupNotFoundError: No group found in store <FsspecStore(ReferenceFileSystem, /)> at path ''

Expected behavior

Same as on zarr 3.1.6: the group is opened successfully.

Environment

• zarr: 3.1.7.dev45+g866aa8d67 (broken), 3.1.6 (works)
• fsspec: 2026.3.0
• Python: 3.13
• OS: macOS / Linux (reproduced on both)

Bisect

Bisected v3.1.6..866aa8d6 to first bad commit be0a7b82 ("feat/memory store registry", #3679).

Downstream impact

Caught while reviewing zarr-developers/VirtualiZarr#957 — 18 kerchunk-roundtrip tests fail against upstream zarr for this reason.

[d-v-b]

Thanks for reporting this! We should get this fixed shortly

[d-v-b]

as a post-mortem: #3679 consolidated some internal path-handling routines, and also made more clear what those routines should do (combine path segments) and what they should not do (normalize path segments). This issue shows that those changes revealed a longstanding bug in fsspecstore, for which we did not have test coverage, wherein the user-provided input for the path attribute was taken as-is without any normalization.