From 3a0fa4cf7f3e785464be2124e38d2802f8d34778 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 7 May 2024 11:38:06 -0600
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate (#101)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.4.3)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2bf64990..49e28b73 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,14 +3,14 @@ ci:
   autoupdate_schedule: monthly
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.3.5"
+    rev: "v0.4.3"
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -20,7 +20,7 @@ repos:
   #     - id: velin
   #       args: ["--write", "--compact"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         # Copied from setup.cfg

From a3dab6c970c062a756f664abe373b3b3b53ba487 Mon Sep 17 00:00:00 2001
From: Julius Busecke <julius@ldeo.columbia.edu>
Date: Tue, 7 May 2024 13:54:00 -0400
Subject: [PATCH 2/2] Bump Ruff version and add formatting (#98)

* Bump Ruff version and add formatting

- [ ] Closes #96

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add config options to conform closer to black for linting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update pyproject.toml

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Tom Nicholas <tom@cworthy.org>
---
 .pre-commit-config.yaml                       | 12 ++--
 pyproject.toml                                | 17 +++---
 virtualizarr/kerchunk.py                      |  6 +-
 virtualizarr/manifests/manifest.py            |  4 +-
 virtualizarr/tests/conftest.py                |  1 +
 virtualizarr/tests/test_kerchunk.py           | 47 +++++++++-------
 .../tests/test_manifests/test_array.py        |  3 +-
 .../tests/test_manifests/test_manifest.py     |  6 +-
 virtualizarr/tests/test_xarray.py             |  5 +-
 virtualizarr/tests/test_zarr.py               | 33 ++++++-----
 virtualizarr/vendor/zarr/utils.py             |  8 ++-
 virtualizarr/xarray.py                        | 49 +++++++++++------
 virtualizarr/zarr.py                          | 55 +++++++++++--------
 13 files changed, 145 insertions(+), 101 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 49e28b73..a1af21fa 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -10,15 +10,15 @@ repos:
       - id: check-yaml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
     rev: "v0.4.3"
     hooks:
+      # Run the linter.
       - id: ruff
-        args: ["--fix"]
-  # - repo: https://github.com/Carreau/velin
-  #   rev: 0.0.8
-  #   hooks:
-  #     - id: velin
-  #       args: ["--write", "--compact"]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.10.0
     hooks:
diff --git a/pyproject.toml b/pyproject.toml
index 7bde54f5..afdde7a7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -75,24 +75,21 @@ datatree = ["py.typed"]
 files = "virtualizarr/**/*.py"
 show_error_codes = true
 
-
-
-
-
 [tool.ruff]
-line-length = 100
+# Same as Black.
+line-length = 88
+indent-width = 4
 target-version = "py39"
 
 exclude = [
     "docs",
     ".eggs"]
 
-
 [tool.ruff.lint]
 # Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
-select = ["E4", "E7", "E9", "F"]
+select = ["E4", "E7", "E9", "F", "I"]
 per-file-ignores = {}
 
 # E402: module level import not at top of file
@@ -101,7 +98,13 @@ per-file-ignores = {}
 
 ignore = ["E402", "E731"]
 
+# Allow fix for all enabled rules (when `--fix`) is provided.
+fixable = ["ALL"]
+unfixable = []
+
 [tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
 # Indent with spaces, rather than tabs.
 indent-style = "space"
 # Respect magic trailing commas.
diff --git a/virtualizarr/kerchunk.py b/virtualizarr/kerchunk.py
index 0d5c507a..f826502e 100644
--- a/virtualizarr/kerchunk.py
+++ b/virtualizarr/kerchunk.py
@@ -20,12 +20,14 @@
 
 from enum import Enum, auto
 
+
 class AutoName(Enum):
     # Recommended by official Python docs for auto naming:
     # https://docs.python.org/3/library/enum.html#using-automatic-values
     def _generate_next_value_(name, start, count, last_values):
         return name
 
+
 class FileType(AutoName):
     netcdf3 = auto()
     netcdf4 = auto()
@@ -34,6 +36,7 @@ class FileType(AutoName):
     fits = auto()
     zarr = auto()
 
+
 def read_kerchunk_references_from_file(
     filepath: str, filetype: Optional[FileType]
 ) -> KerchunkStoreRefs:
@@ -57,6 +60,7 @@ def read_kerchunk_references_from_file(
 
     if filetype.name.lower() == "netcdf3":
         from kerchunk.netCDF3 import NetCDF3ToZarr
+
         refs = NetCDF3ToZarr(filepath, inline_threshold=0).translate()
 
     elif filetype.name.lower() == "netcdf4":
@@ -87,7 +91,7 @@ def _automatically_determine_filetype(filepath: str) -> FileType:
 
     if file_extension == ".nc":
         # based off of: https://github.com/TomNicholas/VirtualiZarr/pull/43#discussion_r1543415167
-        with open(filepath, 'rb') as f:
+        with open(filepath, "rb") as f:
             magic = f.read()
         if magic[0:3] == b"CDF":
             filetype = FileType.netcdf3
diff --git a/virtualizarr/manifests/manifest.py b/virtualizarr/manifests/manifest.py
index b12813eb..a0c6922d 100644
--- a/virtualizarr/manifests/manifest.py
+++ b/virtualizarr/manifests/manifest.py
@@ -117,7 +117,9 @@ def from_zarr_json(cls, filepath: str) -> "ChunkManifest":
         with open(filepath, "r") as manifest_file:
             entries_dict = json.load(manifest_file)
 
-        entries = {cast(ChunkKey, k): ChunkEntry(**entry) for k, entry in entries_dict.items()}
+        entries = {
+            cast(ChunkKey, k): ChunkEntry(**entry) for k, entry in entries_dict.items()
+        }
         return cls(entries=entries)
 
     def to_zarr_json(self, filepath: str) -> None:
diff --git a/virtualizarr/tests/conftest.py b/virtualizarr/tests/conftest.py
index 1ffa50e1..51d672d7 100644
--- a/virtualizarr/tests/conftest.py
+++ b/virtualizarr/tests/conftest.py
@@ -1,6 +1,7 @@
 import pytest
 import xarray as xr
 
+
 @pytest.fixture
 def netcdf4_file(tmpdir):
     # Set up example xarray dataset
diff --git a/virtualizarr/tests/test_kerchunk.py b/virtualizarr/tests/test_kerchunk.py
index 7a2ffb88..7a10f465 100644
--- a/virtualizarr/tests/test_kerchunk.py
+++ b/virtualizarr/tests/test_kerchunk.py
@@ -1,19 +1,19 @@
 import numpy as np
+import pytest
 import ujson  # type: ignore
 import xarray as xr
 import xarray.testing as xrt
-import pytest
-
 
-from virtualizarr.kerchunk import _automatically_determine_filetype, FileType
+from virtualizarr.kerchunk import FileType, _automatically_determine_filetype
 from virtualizarr.manifests import ChunkEntry, ChunkManifest, ManifestArray
 from virtualizarr.xarray import dataset_from_kerchunk_refs
 
+
 def gen_ds_refs(
-        zgroup: str = '{"zarr_format":2}',
-        zarray: str = '{"chunks":[2,3],"compressor":null,"dtype":"<i8","fill_value":null,"filters":null,"order":"C","shape":[2,3],"zarr_format":2}',
-        zattrs: str = '{"_ARRAY_DIMENSIONS":["x","y"]}',
-        chunk: list = ["test1.nc", 6144, 48],
+    zgroup: str = '{"zarr_format":2}',
+    zarray: str = '{"chunks":[2,3],"compressor":null,"dtype":"<i8","fill_value":null,"filters":null,"order":"C","shape":[2,3],"zarr_format":2}',
+    zattrs: str = '{"_ARRAY_DIMENSIONS":["x","y"]}',
+    chunk: list = ["test1.nc", 6144, 48],
 ):
     return {
         "version": 1,
@@ -25,9 +25,10 @@ def gen_ds_refs(
         },
     }
 
+
 def test_dataset_from_df_refs():
     ds_refs = gen_ds_refs()
-    ds =  dataset_from_kerchunk_refs(ds_refs)
+    ds = dataset_from_kerchunk_refs(ds_refs)
     assert "a" in ds
     da = ds["a"]
     assert isinstance(da.data, ManifestArray)
@@ -45,11 +46,21 @@ def test_dataset_from_df_refs():
         "0.0": {"path": "test1.nc", "offset": 6144, "length": 48}
     }
 
+
 def test_dataset_from_df_refs_with_filters():
-    filters = [{"elementsize":4,"id":"shuffle"},{"id":"zlib","level":4}]
-    zarray = {"chunks":[2,3],"compressor":None,"dtype":"<i8","fill_value":None,"filters":filters,"order":"C","shape":[2,3],"zarr_format":2}
+    filters = [{"elementsize": 4, "id": "shuffle"}, {"id": "zlib", "level": 4}]
+    zarray = {
+        "chunks": [2, 3],
+        "compressor": None,
+        "dtype": "<i8",
+        "fill_value": None,
+        "filters": filters,
+        "order": "C",
+        "shape": [2, 3],
+        "zarr_format": 2,
+    }
     ds_refs = gen_ds_refs(zarray=ujson.dumps(zarray))
-    ds =  dataset_from_kerchunk_refs(ds_refs)
+    ds = dataset_from_kerchunk_refs(ds_refs)
     da = ds["a"]
     assert da.data.zarray.filters == filters
 
@@ -163,15 +174,13 @@ def test_automatically_determine_filetype_netcdf3_netcdf4():
     assert FileType("netcdf4") == _automatically_determine_filetype(netcdf4_file_path)
 
 
-
-
 def test_FileType():
     # tests if FileType converts user supplied strings to correct filetype
-    assert 'netcdf3' == FileType("netcdf3").name
-    assert 'netcdf4' == FileType("netcdf4").name
-    assert 'grib' == FileType("grib").name
-    assert 'tiff' == FileType("tiff").name
-    assert 'fits' == FileType("fits").name
-    assert 'zarr' == FileType("zarr").name
+    assert "netcdf3" == FileType("netcdf3").name
+    assert "netcdf4" == FileType("netcdf4").name
+    assert "grib" == FileType("grib").name
+    assert "tiff" == FileType("tiff").name
+    assert "fits" == FileType("fits").name
+    assert "zarr" == FileType("zarr").name
     with pytest.raises(ValueError):
         FileType(None)
diff --git a/virtualizarr/tests/test_manifests/test_array.py b/virtualizarr/tests/test_manifests/test_array.py
index f6c01dcf..d4824cf5 100644
--- a/virtualizarr/tests/test_manifests/test_array.py
+++ b/virtualizarr/tests/test_manifests/test_array.py
@@ -130,8 +130,7 @@ def test_not_equal_chunk_entries(self):
         assert not (marr1 == marr2).all()
 
     @pytest.mark.skip(reason="Not Implemented")
-    def test_partly_equals(self):
-        ...
+    def test_partly_equals(self): ...
 
 
 # TODO we really need some kind of fixtures to generate useful example data
diff --git a/virtualizarr/tests/test_manifests/test_manifest.py b/virtualizarr/tests/test_manifests/test_manifest.py
index 4a977837..7e364d78 100644
--- a/virtualizarr/tests/test_manifests/test_manifest.py
+++ b/virtualizarr/tests/test_manifests/test_manifest.py
@@ -156,8 +156,6 @@ def test_stack(self):
 
 @pytest.mark.skip(reason="Not implemented")
 class TestSerializeManifest:
-    def test_serialize_manifest_to_zarr(self):
-        ...
+    def test_serialize_manifest_to_zarr(self): ...
 
-    def test_deserialize_manifest_from_zarr(self):
-        ...
+    def test_deserialize_manifest_from_zarr(self): ...
diff --git a/virtualizarr/tests/test_xarray.py b/virtualizarr/tests/test_xarray.py
index 22d1ce5e..a13977ff 100644
--- a/virtualizarr/tests/test_xarray.py
+++ b/virtualizarr/tests/test_xarray.py
@@ -225,9 +225,6 @@ def test_concat_dim_coords_along_existing_dim(self):
         assert result.data.zarray.zarr_format == zarray.zarr_format
 
 
-
-
-
 class TestOpenVirtualDatasetIndexes:
     def test_no_indexes(self, netcdf4_file):
         vds = open_virtual_dataset(netcdf4_file, indexes={})
@@ -273,7 +270,7 @@ def test_combine_by_coords(self, netcdf4_files):
 
 class TestLoadVirtualDataset:
     def test_loadable_variables(self, netcdf4_file):
-        vars_to_load = ['air', 'time']
+        vars_to_load = ["air", "time"]
         vds = open_virtual_dataset(netcdf4_file, loadable_variables=vars_to_load)
 
         for name in vds.variables:
diff --git a/virtualizarr/tests/test_zarr.py b/virtualizarr/tests/test_zarr.py
index 2faf43c7..71bec981 100644
--- a/virtualizarr/tests/test_zarr.py
+++ b/virtualizarr/tests/test_zarr.py
@@ -1,27 +1,30 @@
-import xarray as xr
 import numpy as np
+import xarray as xr
 import xarray.testing as xrt
-from virtualizarr import open_virtual_dataset, ManifestArray
+
+from virtualizarr import ManifestArray, open_virtual_dataset
 from virtualizarr.manifests.manifest import ChunkEntry
 
 
 def test_zarr_v3_roundtrip(tmpdir):
     arr = ManifestArray(
-            chunkmanifest={"0.0": ChunkEntry(path="test.nc", offset=6144, length=48)},
-            zarray=dict(
-                shape=(2, 3),
-                dtype=np.dtype("<i8"),
-                chunks=(2, 3),
-                compressor=None,
-                filters=None,
-                fill_value=None,
-                order="C",
-                zarr_format=3,
-            ),
-        )
+        chunkmanifest={"0.0": ChunkEntry(path="test.nc", offset=6144, length=48)},
+        zarray=dict(
+            shape=(2, 3),
+            dtype=np.dtype("<i8"),
+            chunks=(2, 3),
+            compressor=None,
+            filters=None,
+            fill_value=None,
+            order="C",
+            zarr_format=3,
+        ),
+    )
     original = xr.Dataset({"a": (["x", "y"], arr)}, attrs={"something": 0})
 
     original.virtualize.to_zarr(tmpdir / "store.zarr")
-    roundtrip = open_virtual_dataset(tmpdir / "store.zarr", filetype="zarr_v3", indexes={})
+    roundtrip = open_virtual_dataset(
+        tmpdir / "store.zarr", filetype="zarr_v3", indexes={}
+    )
 
     xrt.assert_identical(roundtrip, original)
diff --git a/virtualizarr/vendor/zarr/utils.py b/virtualizarr/vendor/zarr/utils.py
index 918d6b57..32986793 100644
--- a/virtualizarr/vendor/zarr/utils.py
+++ b/virtualizarr/vendor/zarr/utils.py
@@ -1,6 +1,5 @@
 import json
 import numbers
-
 from typing import Any
 
 
@@ -18,5 +17,10 @@ def default(self, o):
 def json_dumps(o: Any) -> bytes:
     """Write JSON in a consistent, human-readable way."""
     return json.dumps(
-        o, indent=4, sort_keys=True, ensure_ascii=True, separators=(",", ": "), cls=NumberEncoder
+        o,
+        indent=4,
+        sort_keys=True,
+        ensure_ascii=True,
+        separators=(",", ": "),
+        cls=NumberEncoder,
     ).encode("ascii")
diff --git a/virtualizarr/xarray.py b/virtualizarr/xarray.py
index 1fa83577..8ab69d09 100644
--- a/virtualizarr/xarray.py
+++ b/virtualizarr/xarray.py
@@ -1,5 +1,14 @@
 from pathlib import Path
-from typing import List, Literal, Mapping, Optional, Union, overload, MutableMapping, Iterable
+from typing import (
+    Iterable,
+    List,
+    Literal,
+    Mapping,
+    MutableMapping,
+    Optional,
+    Union,
+    overload,
+)
 
 import ujson  # type: ignore
 import xarray as xr
@@ -9,9 +18,13 @@
 from xarray.core.variable import IndexVariable
 
 import virtualizarr.kerchunk as kerchunk
-from virtualizarr.kerchunk import KerchunkStoreRefs, FileType
+from virtualizarr.kerchunk import FileType, KerchunkStoreRefs
 from virtualizarr.manifests import ChunkManifest, ManifestArray
-from virtualizarr.zarr import dataset_to_zarr, attrs_from_zarr_group_json, metadata_from_zarr_json
+from virtualizarr.zarr import (
+    attrs_from_zarr_group_json,
+    dataset_to_zarr,
+    metadata_from_zarr_json,
+)
 
 
 class ManifestBackendArray(ManifestArray, BackendArray):
@@ -78,13 +91,14 @@ def open_virtual_dataset(
     if common:
         raise ValueError(f"Cannot both load and drop variables {common}")
 
-
     if virtual_array_class is not ManifestArray:
         raise NotImplementedError()
 
     if filetype == "zarr_v3":
         # TODO is there a neat way of auto-detecting this?
-        return open_virtual_dataset_from_v3_store(storepath=filepath, drop_variables=drop_variables, indexes=indexes)
+        return open_virtual_dataset_from_v3_store(
+            storepath=filepath, drop_variables=drop_variables, indexes=indexes
+        )
     else:
         # this is the only place we actually always need to use kerchunk directly
         # TODO avoid even reading byte ranges for variables that will be dropped later anyway?
@@ -114,7 +128,11 @@ def open_virtual_dataset(
             else:
                 indexes = dict(**indexes)  # for type hinting: to allow mutation
 
-            loadable_vars = {name: var for name, var in ds.variables.items() if name in loadable_variables}
+            loadable_vars = {
+                name: var
+                for name, var in ds.variables.items()
+                if name in loadable_variables
+            }
 
             # if we only read the indexes we can just close the file right away as nothing is lazy
             if loadable_vars == {}:
@@ -212,14 +230,14 @@ def virtual_vars_from_kerchunk_refs(
         var_name for var_name in var_names if var_name not in drop_variables
     ]
 
-    vars = {var_name: variable_from_kerchunk_refs(
-            refs, var_name, virtual_array_class
-        ) for var_name in var_names_to_keep}
+    vars = {
+        var_name: variable_from_kerchunk_refs(refs, var_name, virtual_array_class)
+        for var_name in var_names_to_keep
+    }
 
     return vars
 
 
-
 def dataset_from_kerchunk_refs(
     refs: KerchunkStoreRefs,
     drop_variables: List[str] = [],
@@ -336,16 +354,15 @@ def to_zarr(self, storepath: str) -> None:
         dataset_to_zarr(self.ds, storepath)
 
     @overload
-    def to_kerchunk(self, filepath: None, format: Literal["dict"]) -> KerchunkStoreRefs:
-        ...
+    def to_kerchunk(
+        self, filepath: None, format: Literal["dict"]
+    ) -> KerchunkStoreRefs: ...
 
     @overload
-    def to_kerchunk(self, filepath: str, format: Literal["json"]) -> None:
-        ...
+    def to_kerchunk(self, filepath: str, format: Literal["json"]) -> None: ...
 
     @overload
-    def to_kerchunk(self, filepath: str, format: Literal["parquet"]) -> None:
-        ...
+    def to_kerchunk(self, filepath: str, format: Literal["parquet"]) -> None: ...
 
     def to_kerchunk(
         self,
diff --git a/virtualizarr/zarr.py b/virtualizarr/zarr.py
index 54774131..ac3c2c45 100644
--- a/virtualizarr/zarr.py
+++ b/virtualizarr/zarr.py
@@ -1,12 +1,22 @@
-
-from pathlib import Path
-from typing import Any, Literal, NewType, Optional, Tuple, Union, List, Dict, TYPE_CHECKING
 import json
+from pathlib import Path
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Dict,
+    List,
+    Literal,
+    NewType,
+    Optional,
+    Tuple,
+    Union,
+)
 
 import numpy as np
 import ujson  # type: ignore
 import xarray as xr
 from pydantic import BaseModel, ConfigDict, field_validator
+
 from virtualizarr.vendor.zarr.utils import json_dumps
 
 if TYPE_CHECKING:
@@ -134,12 +144,8 @@ def dataset_to_zarr(ds: xr.Dataset, storepath: str) -> None:
     Path.mkdir(_storepath, exist_ok=False)
 
     # should techically loop over groups in a tree but a dataset corresponds to only one group
-    group_metadata = {
-        "zarr_format": 3,
-        "node_type": "group",
-        "attributes": ds.attrs
-    }
-    with open(_storepath / 'zarr.json', "wb") as group_metadata_file:
+    group_metadata = {"zarr_format": 3, "node_type": "group", "attributes": ds.attrs}
+    with open(_storepath / "zarr.json", "wb") as group_metadata_file:
         group_metadata_file.write(json_dumps(group_metadata))
 
     for name, var in ds.variables.items():
@@ -177,10 +183,10 @@ def to_zarr_json(var: xr.Variable, array_dir: Path) -> None:
 
     marr = var.data
 
-    marr.manifest.to_zarr_json(array_dir / 'manifest.json')
+    marr.manifest.to_zarr_json(array_dir / "manifest.json")
 
     metadata = zarr_v3_array_metadata(marr.zarray, list(var.dims), var.attrs)
-    with open(array_dir / 'zarr.json', "wb") as metadata_file:
+    with open(array_dir / "zarr.json", "wb") as metadata_file:
         metadata_file.write(json_dumps(metadata))
 
 
@@ -194,12 +200,13 @@ def zarr_v3_array_metadata(zarray: ZArray, dim_names: List[str], attrs: dict) ->
     metadata["zarr_format"] = 3
     metadata["node_type"] = "array"
     metadata["data_type"] = str(np.dtype(metadata.pop("dtype")))
-    metadata["chunk_grid"] = {"name": "regular", "configuration": {"chunk_shape": metadata.pop("chunks")}}
+    metadata["chunk_grid"] = {
+        "name": "regular",
+        "configuration": {"chunk_shape": metadata.pop("chunks")},
+    }
     metadata["chunk_key_encoding"] = {
         "name": "default",
-        "configuration": {
-            "separator": "/"
-        }
+        "configuration": {"separator": "/"},
     }
     metadata["codecs"] = metadata.pop("filters")
     metadata.pop("compressor")  # TODO this should be entered in codecs somehow
@@ -209,9 +216,7 @@ def zarr_v3_array_metadata(zarray: ZArray, dim_names: List[str], attrs: dict) ->
     metadata["storage_transformers"] = [
         {
             "name": "chunk-manifest-json",
-            "configuration": {
-                "manifest": "./manifest.json"
-            }
+            "configuration": {"manifest": "./manifest.json"},
         }
     ]
 
@@ -233,12 +238,14 @@ def metadata_from_zarr_json(filepath: Path) -> Tuple[ZArray, List[str], dict]:
         metadata = json.load(metadata_file)
 
     if {
-            "name": "chunk-manifest-json",
-            "configuration": {
-                "manifest": "./manifest.json",
-            }
-       } not in metadata.get("storage_transformers", []):
-        raise ValueError("Can only read byte ranges from Zarr v3 stores which implement the manifest storage transformer ZEP.")
+        "name": "chunk-manifest-json",
+        "configuration": {
+            "manifest": "./manifest.json",
+        },
+    } not in metadata.get("storage_transformers", []):
+        raise ValueError(
+            "Can only read byte ranges from Zarr v3 stores which implement the manifest storage transformer ZEP."
+        )
 
     attrs = metadata.pop("attributes")
     dim_names = metadata.pop("dimension_names")