# Zarr Encoding Specification

In implementing support for the Zarr storage format, Xarray developers made some ad hoc choices about how to store NetCDF data in Zarr. Future versions of the Zarr spec will likely include a more formal convention for the storage of the NetCDF data model in Zarr; see Zarr spec repo for ongoing discussion.

First, Xarray can only read and write Zarr groups. There is currently no support for reading / writing individual Zarr arrays. Zarr groups are mapped to Xarray `Dataset` objects.

Second, from Xarray’s point of view, the key difference between NetCDF and Zarr is that all NetCDF arrays have dimension names while Zarr arrays do not. Therefore, in order to store NetCDF data in Zarr, Xarray must somehow encode and decode the name of each array’s dimensions.

To accomplish this, Xarray developers decided to define a special Zarr array attribute: `_ARRAY_DIMENSIONS`. The value of this attribute is a list of dimension names (strings), for example `["time", "lon", "lat"]`. When writing data to Zarr, Xarray sets this attribute on all variables based on the variable dimensions. When reading a Zarr group, Xarray looks for this attribute on all arrays, raising an error if it can’t be found. The attribute is used to define the variable dimension names and then removed from the attributes dictionary returned to the user.

Because of these choices, Xarray cannot read arbitrary array data, but only Zarr data with valid `_ARRAY_DIMENSIONS` or NCZarr attributes on each array (NCZarr dimension names are defined in the `.zarray` file).

After decoding the `_ARRAY_DIMENSIONS` or NCZarr attribute and assigning the variable dimensions, Xarray proceeds to [optionally] decode each variable using its standard CF decoding machinery used for NetCDF data (see `decode_cf()`).

Finally, it’s worth noting that Xarray writes (and attempts to read) “consolidated metadata” by default (the `.zmetadata` file), which is another non-standard Zarr extension, albeit one implemented upstream in Zarr-Python. You do not need to write consolidated metadata to make Zarr stores readable in Xarray, but because Xarray can open these stores much faster, users will see a warning about poor performance when reading non-consolidated stores unless they explicitly set `consolidated=False`. See Consolidated Metadata for more details.

As a concrete example, here we write a tutorial dataset to Zarr and then re-open it directly with Zarr:

    In [1]: import os

    In [2]: import xarray as xr

    In [3]: import zarr

    In [4]: ds = xr.tutorial.load_dataset("rasm")
    ---------------------------------------------------------------------------
    gaierror                                  Traceback (most recent call last)
    File /usr/lib/python3/dist-packages/urllib3/connection.py:198, in HTTPConnection._new_conn(self)
        197 try:
    --> 198     sock = connection.create_connection(
        199         (self._dns_host, self.port),
        200         self.timeout,
        201         source_address=self.source_address,
        202         socket_options=self.socket_options,
        203     )
        204 except socket.gaierror as e:

    File /usr/lib/python3/dist-packages/urllib3/util/connection.py:60, in create_connection(address, timeout, source_address, socket_options)
         58     raise LocationParseError(f"'{host}', label empty or too long") from None
    ---> 60 for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
         61     af, socktype, proto, canonname, sa = res

    File /usr/lib/python3.13/socket.py:977, in getaddrinfo(host, port, family, type, proto, flags)
        976 addrlist = []
    --> 977 for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
        978     af, socktype, proto, canonname, sa = res

    gaierror: [Errno -2] Name or service not known

    The above exception was the direct cause of the following exception:

    NameResolutionError                       Traceback (most recent call last)
    File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:787, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
        786 # Make the request on the HTTPConnection object
    --> 787 response = self._make_request(
        788     conn,
        789     method,
        790     url,
        791     timeout=timeout_obj,
        792     body=body,
        793     headers=headers,
        794     chunked=chunked,
        795     retries=retries,
        796     response_conn=response_conn,
        797     preload_content=preload_content,
        798     decode_content=decode_content,
        799     **response_kw,
        800 )
        802 # Everything went great!

    File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:488, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
        487         new_e = _wrap_proxy_error(new_e, conn.proxy.scheme)
    --> 488     raise new_e
        490 # conn.request() calls http.client.*.request, not the method in
        491 # urllib3.request. It also calls makefile (recv) on the socket.

    File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:464, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
        463 try:
    --> 464     self._validate_conn(conn)
        465 except (SocketTimeout, BaseSSLError) as e:

    File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:1093, in HTTPSConnectionPool._validate_conn(self, conn)
       1092 if conn.is_closed:
    -> 1093     conn.connect()
       1095 # TODO revise this, see https://github.com/urllib3/urllib3/issues/2791

    File /usr/lib/python3/dist-packages/urllib3/connection.py:704, in HTTPSConnection.connect(self)
        703 sock: socket.socket | ssl.SSLSocket
    --> 704 self.sock = sock = self._new_conn()
        705 server_hostname: str = self.host

    File /usr/lib/python3/dist-packages/urllib3/connection.py:205, in HTTPConnection._new_conn(self)
        204 except socket.gaierror as e:
    --> 205     raise NameResolutionError(self.host, self, e) from e
        206 except SocketTimeout as e:

    NameResolutionError: <urllib3.connection.HTTPSConnection object at 0x7ff7c2bfd1d0>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)

    The above exception was the direct cause of the following exception:

    MaxRetryError                             Traceback (most recent call last)
    File /usr/lib/python3/dist-packages/requests/adapters.py:667, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
        666 try:
    --> 667     resp = conn.urlopen(
        668         method=request.method,
        669         url=url,
        670         body=request.body,
        671         headers=request.headers,
        672         redirect=False,
        673         assert_same_host=False,
        674         preload_content=False,
        675         decode_content=False,
        676         retries=self.max_retries,
        677         timeout=timeout,
        678         chunked=chunked,
        679     )
        681 except (ProtocolError, OSError) as err:

    File /usr/lib/python3/dist-packages/urllib3/connectionpool.py:841, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
        839     new_e = ProtocolError("Connection aborted.", new_e)
    --> 841 retries = retries.increment(
        842     method, url, error=new_e, _pool=self, _stacktrace=sys.exc_info()[2]
        843 )
        844 retries.sleep()

    File /usr/lib/python3/dist-packages/urllib3/util/retry.py:519, in Retry.increment(self, method, url, response, error, _pool, _stacktrace)
        518     reason = error or ResponseError(cause)
    --> 519     raise MaxRetryError(_pool, url, reason) from reason  # type: ignore[arg-type]
        521 log.debug("Incremented Retry for (url='%s'): %r", url, new_retry)

    MaxRetryError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /pydata/xarray-data/raw/master/rasm.nc (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7ff7c2bfd1d0>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)"))

    During handling of the above exception, another exception occurred:

    ConnectionError                           Traceback (most recent call last)
    Cell In[4], line 1
    ----> 1 ds = xr.tutorial.load_dataset("rasm")

    File /build/python-xarray-HTRdgH/python-xarray-2025.03.1/xarray/tutorial.py:215, in load_dataset(*args, **kwargs)
        178 def load_dataset(*args, **kwargs) -> Dataset:
        179     """
        180     Open, load into memory, and close a dataset from the online repository
        181     (requires internet).
       (...)
        213     load_dataset
        214     """
    --> 215     with open_dataset(*args, **kwargs) as ds:
        216         return ds.load()

    File /build/python-xarray-HTRdgH/python-xarray-2025.03.1/xarray/tutorial.py:167, in open_dataset(name, cache, cache_dir, engine, **kws)
        164 downloader = pooch.HTTPDownloader(headers=headers)
        166 # retrieve the file
    --> 167 filepath = pooch.retrieve(
        168     url=url, known_hash=None, path=cache_dir, downloader=downloader
        169 )
        170 ds = _open_dataset(filepath, engine=engine, **kws)
        171 if not cache:

    File /usr/lib/python3/dist-packages/pooch/core.py:239, in retrieve(url, known_hash, fname, path, processor, downloader, progressbar)
        236 if downloader is None:
        237     downloader = choose_downloader(url, progressbar=progressbar)
    --> 239 stream_download(url, full_path, known_hash, downloader, pooch=None)
        241 if known_hash is None:
        242     get_logger().info(
        243         "SHA256 hash of downloaded file: %s\n"
        244         "Use this value as the 'known_hash' argument of 'pooch.retrieve'"
       (...)
        247         file_hash(str(full_path)),
        248     )

    File /usr/lib/python3/dist-packages/pooch/core.py:807, in stream_download(url, fname, known_hash, downloader, pooch, retry_if_failed)
        803 try:
        804     # Stream the file to a temporary so that we can safely check its
        805     # hash before overwriting the original.
        806     with temporary_file(path=str(fname.parent)) as tmp:
    --> 807         downloader(url, tmp, pooch)
        808         hash_matches(tmp, known_hash, strict=True, source=str(fname.name))
        809         shutil.move(tmp, str(fname))

    File /usr/lib/python3/dist-packages/pooch/downloaders.py:220, in HTTPDownloader.__call__(self, url, output_file, pooch, check_only)
        218     # pylint: enable=consider-using-with
        219 try:
    --> 220     response = requests.get(url, timeout=timeout, **kwargs)
        221     response.raise_for_status()
        222     content = response.iter_content(chunk_size=self.chunk_size)

    File /usr/lib/python3/dist-packages/requests/api.py:73, in get(url, params, **kwargs)
         62 def get(url, params=None, **kwargs):
         63     r"""Sends a GET request.
         64
         65     :param url: URL for the new :class:`Request` object.
       (...)
         70     :rtype: requests.Response
         71     """
    ---> 73     return request("get", url, params=params, **kwargs)

    File /usr/lib/python3/dist-packages/requests/api.py:59, in request(method, url, **kwargs)
         55 # By using the 'with' statement we are sure the session is closed, thus we
         56 # avoid leaving sockets open which can trigger a ResourceWarning in some
         57 # cases, and look like a memory leak in others.
         58 with sessions.Session() as session:
    ---> 59     return session.request(method=method, url=url, **kwargs)

    File /usr/lib/python3/dist-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
        584 send_kwargs = {
        585     "timeout": timeout,
        586     "allow_redirects": allow_redirects,
        587 }
        588 send_kwargs.update(settings)
    --> 589 resp = self.send(prep, **send_kwargs)
        591 return resp

    File /usr/lib/python3/dist-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
        700 start = preferred_clock()
        702 # Send the request
    --> 703 r = adapter.send(request, **kwargs)
        705 # Total elapsed time of the request (approximately)
        706 elapsed = preferred_clock() - start

    File /usr/lib/python3/dist-packages/requests/adapters.py:700, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
        696     if isinstance(e.reason, _SSLError):
        697         # This branch is for urllib3 v1.22 and later.
        698         raise SSLError(e, request=request)
    --> 700     raise ConnectionError(e, request=request)
        702 except ClosedPoolError as e:
        703     raise ConnectionError(e, request=request)

    ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /pydata/xarray-data/raw/master/rasm.nc (Caused by NameResolutionError("<urllib3.connection.HTTPSConnection object at 0x7ff7c2bfd1d0>: Failed to resolve 'github.com' ([Errno -2] Name or service not known)"))

    In [5]: ds.to_zarr("rasm.zarr", mode="w")
    Out[5]: <xarray.backends.zarr.ZarrStore at 0x7ff7c2ee5b40>

    In [6]: zgroup = zarr.open("rasm.zarr")

    In [7]: print(os.listdir("rasm.zarr"))
    ['time', 'zarr.json']

    In [8]: print(zgroup.tree())
    ---------------------------------------------------------------------------
    ModuleNotFoundError                       Traceback (most recent call last)
    File /usr/lib/python3/dist-packages/zarr/core/_tree.py:9
          8 try:
    ----> 9     import rich
         10     import rich.console

    ModuleNotFoundError: No module named 'rich'

    The above exception was the direct cause of the following exception:

    ImportError                               Traceback (most recent call last)
    Cell In[8], line 1
    ----> 1 print(zgroup.tree())

    File /usr/lib/python3/dist-packages/zarr/core/group.py:2300, in Group.tree(self, expand, level)
       2281 def tree(self, expand: bool | None = None, level: int | None = None) -> Any:
       2282     """
       2283     Return a tree-like representation of a hierarchy.
       2284
       (...)
       2298         A pretty-printable object displaying the hierarchy.
       2299     """
    -> 2300     return self._sync(self._async_group.tree(expand=expand, level=level))

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:208, in SyncMixin._sync(self, coroutine)
        205 def _sync(self, coroutine: Coroutine[Any, Any, T]) -> T:
        206     # TODO: refactor this to to take *args and **kwargs and pass those to the method
        207     # this should allow us to better type the sync wrapper
    --> 208     return sync(
        209         coroutine,
        210         timeout=config.get("async.timeout"),
        211     )

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:163, in sync(coro, loop, timeout)
        160 return_result = next(iter(finished)).result()
        162 if isinstance(return_result, BaseException):
    --> 163     raise return_result
        164 else:
        165     return return_result

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:119, in _runner(coro)
        114 """
        115 Await a coroutine and return the result of running it. If awaiting the coroutine raises an
        116 exception, the exception will be returned.
        117 """
        118 try:
    --> 119     return await coro
        120 except Exception as ex:
        121     return ex

    File /usr/lib/python3/dist-packages/zarr/core/group.py:1550, in AsyncGroup.tree(self, expand, level)
       1531 async def tree(self, expand: bool | None = None, level: int | None = None) -> Any:
       1532     """
       1533     Return a tree-like representation of a hierarchy.
       1534
       (...)
       1548         A pretty-printable object displaying the hierarchy.
       1549     """
    -> 1550     from zarr.core._tree import group_tree_async
       1552     if expand is not None:
       1553         raise NotImplementedError("'expand' is not yet implemented.")

    File /usr/lib/python3/dist-packages/zarr/core/_tree.py:13
         11     import rich.tree
         12 except ImportError as e:
    ---> 13     raise ImportError("'rich' is required for Group.tree") from e
         16 class TreeRepr:
         17     """
         18     A simple object with a tree-like repr for the Zarr Group.
         19
         20     Note that this object and it's implementation isn't considered part
         21     of Zarr's public API.
         22     """

    ImportError: 'rich' is required for Group.tree

    In [9]: dict(zgroup["Tair"].attrs)
    ---------------------------------------------------------------------------
    KeyError                                  Traceback (most recent call last)
    File /usr/lib/python3/dist-packages/zarr/core/group.py:727, in AsyncGroup._getitem_consolidated(self, store_path, key, prefix)
        726 try:
    --> 727     metadata = metadata.consolidated_metadata.metadata[indexer]
        728 except KeyError as e:
        729     # The Group Metadata has consolidated metadata, but the key
        730     # isn't present. We trust this to mean that the key isn't in
        731     # the hierarchy, and *don't* fall back to checking the store.

    KeyError: 'Tair'

    The above exception was the direct cause of the following exception:

    KeyError                                  Traceback (most recent call last)
    Cell In[9], line 1
    ----> 1 dict(zgroup["Tair"].attrs)

    File /usr/lib/python3/dist-packages/zarr/core/group.py:1842, in Group.__getitem__(self, path)
       1815 def __getitem__(self, path: str) -> Array | Group:
       1816     """Obtain a group member.
       1817
       1818     Parameters
       (...)
       1840
       1841     """
    -> 1842     obj = self._sync(self._async_group.getitem(path))
       1843     if isinstance(obj, AsyncArray):
       1844         return Array(obj)

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:208, in SyncMixin._sync(self, coroutine)
        205 def _sync(self, coroutine: Coroutine[Any, Any, T]) -> T:
        206     # TODO: refactor this to to take *args and **kwargs and pass those to the method
        207     # this should allow us to better type the sync wrapper
    --> 208     return sync(
        209         coroutine,
        210         timeout=config.get("async.timeout"),
        211     )

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:163, in sync(coro, loop, timeout)
        160 return_result = next(iter(finished)).result()
        162 if isinstance(return_result, BaseException):
    --> 163     raise return_result
        164 else:
        165     return return_result

    File /usr/lib/python3/dist-packages/zarr/core/sync.py:119, in _runner(coro)
        114 """
        115 Await a coroutine and return the result of running it. If awaiting the coroutine raises an
        116 exception, the exception will be returned.
        117 """
        118 try:
    --> 119     return await coro
        120 except Exception as ex:
        121     return ex

    File /usr/lib/python3/dist-packages/zarr/core/group.py:689, in AsyncGroup.getitem(self, key)
        687 # Consolidated metadata lets us avoid some I/O operations so try that first.
        688 if self.metadata.consolidated_metadata is not None:
    --> 689     return self._getitem_consolidated(store_path, key, prefix=self.name)
        690 try:
        691     return await get_node(
        692         store=store_path.store, path=store_path.path, zarr_format=self.metadata.zarr_format
        693     )

    File /usr/lib/python3/dist-packages/zarr/core/group.py:733, in AsyncGroup._getitem_consolidated(self, store_path, key, prefix)
        728     except KeyError as e:
        729         # The Group Metadata has consolidated metadata, but the key
        730         # isn't present. We trust this to mean that the key isn't in
        731         # the hierarchy, and *don't* fall back to checking the store.
        732         msg = f"'{key}' not found in consolidated metadata."
    --> 733         raise KeyError(msg) from e
        735 # update store_path to ensure that AsyncArray/Group.name is correct
        736 if prefix != "/":

    KeyError: "'Tair' not found in consolidated metadata."