Enable ruff/bugbear rules (B) and fix issues

docs/release.rst

@@ -34,6 +34,9 @@ Docs
 
 Maintenance
 ~~~~~~~~~~~
+* Enable ruff/bugbear rules (B) and fix issues.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1702`.
+
 * Minor updates to use `np.inf` instead of `np.PINF` / `np.NINF` in preparation for NumPy 2.0.0 release. 
   By :user:`Joe Hamman <jhamman>` :issue:`1842`.
 

pyproject.toml

@@ -103,6 +103,11 @@ exclude = [
     "docs"
 ]
 
+[tool.ruff.lint]
+extend-select = [
+    "B"
+]
+
 [tool.black]
 line-length = 100
 exclude = '''

zarr/_storage/absstore.py

@@ -156,8 +156,8 @@ def __getitem__(self, key):
         blob_name = self._append_path_to_prefix(key)
         try:
             return self.client.download_blob(blob_name).readall()
-        except ResourceNotFoundError:
-            raise KeyError(f"Blob {blob_name} not found")
+        except ResourceNotFoundError as e:
+            raise KeyError(f"Blob {blob_name} not found") from e
 
     def __setitem__(self, key, value):
         value = ensure_bytes(value)
@@ -169,8 +169,8 @@ def __delitem__(self, key):
 
         try:
             self.client.delete_blob(self._append_path_to_prefix(key))
-        except ResourceNotFoundError:
-            raise KeyError(f"Blob {key} not found")
+        except ResourceNotFoundError as e:
+            raise KeyError(f"Blob {key} not found") from e
 
     def __eq__(self, other):
         return (

zarr/_storage/v3_storage_transformers.py

@@ -183,8 +183,8 @@ def __getitem__(self, key):
             shard_key, chunk_subkey = self._key_to_shard(key)
             try:
                 full_shard_value = self.inner_store[shard_key]
-            except KeyError:
-                raise KeyError(key)
+            except KeyError as e:
+                raise KeyError(key) from e
             index = self._get_index_from_buffer(full_shard_value)
             chunk_slice = index.get_chunk_slice(chunk_subkey)
             if chunk_slice is not None:
@@ -265,8 +265,8 @@ def __delitem__(self, key):
             shard_key, chunk_subkey = self._key_to_shard(key)
             try:
                 index = self._get_index_from_store(shard_key)
-            except KeyError:
-                raise KeyError(key)
+            except KeyError as e:
+                raise KeyError(key) from e
 
             index.set_chunk_slice(chunk_subkey, None)
 

zarr/core.py

@@ -200,8 +200,8 @@ def _load_metadata_nosync(self):
         try:
             mkey = _prefix_to_array_key(self._store, self._key_prefix)
             meta_bytes = self._store[mkey]
-        except KeyError:
-            raise ArrayNotFoundError(self._path)
+        except KeyError as e:
+            raise ArrayNotFoundError(self._path) from e
         else:
             # decode and store metadata as instance members
             meta = self._store._metadata_class.decode_array_metadata(meta_bytes)

zarr/creation.py

@@ -297,7 +297,7 @@ def _kwargs_compat(compressor, fill_value, kwargs):
 
     # ignore other keyword arguments
     for k in kwargs:
-        warn(f"ignoring keyword argument {k!r}")
+        warn(f"ignoring keyword argument {k!r}", stacklevel=2)
 
     return compressor, fill_value
 

zarr/hierarchy.py

@@ -187,16 +187,16 @@ def __init__(
             mkey = _prefix_to_group_key(self._store, self._key_prefix)
             assert not mkey.endswith("root/.group")
             meta_bytes = store[mkey]
-        except KeyError:
+        except KeyError as e:
             if self._version == 2:
-                raise GroupNotFoundError(path)
+                raise GroupNotFoundError(path) from e
             else:
                 implicit_prefix = meta_root + self._key_prefix
                 if self._store.list_prefix(implicit_prefix):
                     # implicit group does not have any metadata
                     self._meta = None
                 else:
-                    raise GroupNotFoundError(path)
+                    raise GroupNotFoundError(path) from e
         else:
             self._meta = self._store._metadata_class.decode_group_metadata(meta_bytes)
 
@@ -536,8 +536,8 @@ def __getattr__(self, item):
         # allow access to group members via dot notation
         try:
             return self.__getitem__(item)
-        except KeyError:
-            raise AttributeError
+        except KeyError as e:
+            raise AttributeError from e
 
     def __dir__(self):
         # noinspection PyUnresolvedReferences

zarr/indexing.py

@@ -932,7 +932,7 @@ def check_fields(fields, dtype):
                 # multiple field selection
                 out_dtype = np.dtype([(f, dtype[f]) for f in fields])
         except KeyError as e:
-            raise IndexError(f"invalid 'fields' argument, field not found: {e!r}")
+            raise IndexError(f"invalid 'fields' argument, field not found: {e!r}") from e
         else:
             return out_dtype
     else:

zarr/meta.py

@@ -310,8 +310,8 @@ def decode_dtype(cls, d, validate=True):
             # extract the type from the extension info
             try:
                 d = d["type"]
-            except KeyError:
-                raise KeyError("Extended dtype info must provide a key named 'type'.")
+            except KeyError as e:
+                raise KeyError("Extended dtype info must provide a key named 'type'.") from e
         d = cls._decode_dtype_descr(d)
         dtype = np.dtype(d)
         if validate:
@@ -518,7 +518,7 @@ def decode_array_metadata(cls, s: Union[MappingType, bytes, str]) -> MappingType
                 meta["storage_transformers"] = storage_transformers
 
         except Exception as e:
-            raise MetadataError(f"error decoding metadata: {e}")
+            raise MetadataError(f"error decoding metadata: {e}") from e
         else:
             return meta
 

zarr/meta_v1.py

@@ -23,7 +23,7 @@ def decode_metadata(b):
             order=meta["order"],
         )
     except Exception as e:
-        raise MetadataError(f"error decoding metadata: {e}")
+        raise MetadataError(f"error decoding metadata: {e}") from e
     else:
         return meta
 

zarr/n5.py

@@ -125,7 +125,11 @@ def __setitem__(self, key: str, value: Any):
 
             for k in n5_keywords:
                 if k in zarr_attrs:
-                    warnings.warn(f"Attribute {k} is a reserved N5 keyword", UserWarning)
+                    warnings.warn(
+                        f"Attribute {k} is a reserved N5 keyword",
+                        UserWarning,
+                        stacklevel=2,
+                    )
 
             # remove previous user attributes
             for k in list(n5_attrs.keys()):
@@ -327,7 +331,10 @@ class N5FSStore(FSStore):
     def __init__(self, *args, **kwargs):
         if "dimension_separator" in kwargs:
             kwargs.pop("dimension_separator")
-            warnings.warn("Keyword argument `dimension_separator` will be ignored")
+            warnings.warn(
+                "Keyword argument `dimension_separator` will be ignored",
+                stacklevel=2,
+            )
         dimension_separator = "."
         super().__init__(*args, dimension_separator=dimension_separator, **kwargs)
 
@@ -411,7 +418,11 @@ def __setitem__(self, key: str, value: Any):
 
             for k in n5_keywords:
                 if k in zarr_attrs.keys():
-                    warnings.warn(f"Attribute {k} is a reserved N5 keyword", UserWarning)
+                    warnings.warn(
+                        f"Attribute {k} is a reserved N5 keyword",
+                        UserWarning,
+                        stacklevel=2,
+                    )
 
             # replace previous user attributes
             for k in list(n5_attrs.keys()):
@@ -597,8 +608,8 @@ def array_metadata_to_n5(array_metadata: Dict[str, Any], top_level=False) -> Dic
         array_metadata["n5"] = N5_FORMAT
     try:
         dtype = np.dtype(array_metadata["dataType"])
-    except TypeError:
-        raise TypeError(f"Data type {array_metadata['dataType']} is not supported by N5")
+    except TypeError as e:
+        raise TypeError(f"Data type {array_metadata['dataType']} is not supported by N5") from e
 
     array_metadata["dataType"] = dtype.name
     array_metadata["dimensions"] = array_metadata["dimensions"][::-1]
@@ -711,6 +722,7 @@ def compressor_config_to_n5(compressor_config: Optional[Dict[str, Any]]) -> Dict
                 "Not all N5 implementations support lzma compression (yet). You "
                 "might not be able to open the dataset with another N5 library.",
                 RuntimeWarning,
+                stacklevel=2,
             )
             n5_config["format"] = _compressor_config["format"]
             n5_config["check"] = _compressor_config["check"]

zarr/storage.py

@@ -589,11 +589,15 @@ def _init_array_metadata(
                     "missing object_codec for object array; this will raise a "
                     "ValueError in version 3.0",
                     FutureWarning,
+                    stacklevel=2,
                 )
         else:
             filters_config.insert(0, object_codec.get_config())
     elif object_codec is not None:
-        warnings.warn("an object_codec is only needed for object arrays")
+        warnings.warn(
+            "an object_codec is only needed for object arrays",
+            stacklevel=2,
+        )
 
     # use null to indicate no filters
     if not filters_config:
@@ -869,8 +873,8 @@ def __getitem__(self, item: str):
         parent, key = self._get_parent(item)
         try:
             value = parent[key]
-        except KeyError:
-            raise KeyError(item)
+        except KeyError as e:
+            raise KeyError(item) from e
         else:
             if isinstance(value, self.cls):
                 raise KeyError(item)
@@ -888,8 +892,8 @@ def __delitem__(self, item: str):
             parent, key = self._get_parent(item)
             try:
                 del parent[key]
-            except KeyError:
-                raise KeyError(item)
+            except KeyError as e:
+                raise KeyError(item) from e
 
     def __contains__(self, item: str):  # type: ignore[override]
         try:
@@ -1137,7 +1141,7 @@ def __setitem__(self, key, value):
                 os.makedirs(dir_path)
             except OSError as e:
                 if e.errno != errno.EEXIST:
-                    raise KeyError(key)
+                    raise KeyError(key) from e
 
         # write to temporary file
         # note we're not using tempfile.NamedTemporaryFile to avoid restrictive file permissions

zarr/tests/test_meta.py

@@ -601,7 +601,7 @@ def test_metadata3_exceptions():
     required = ["zarr_format", "metadata_encoding", "metadata_key_suffix", "extensions"]
     for key in required:
         meta = copy.copy(_default_entry_point_metadata_v3)
-        meta.pop("zarr_format")
+        meta.pop(key)
         with pytest.raises(ValueError):
             # cannot encode metadata that is missing a required key
             Metadata3.encode_hierarchy_metadata(meta)

zarr/tests/test_storage.py

@@ -1353,13 +1353,13 @@ def test_exceptions(self, memory_store):
         # no exception from FSStore.getitems getting KeyError
         assert group.store.getitems(["foo"], contexts={}) == {}
         # exception from FSStore.getitems getting AttributeError
-        with pytest.raises(Exception):
+        with pytest.raises(Exception):  # noqa: B017
             group.store.getitems(["x/0"], contexts={})
         # exception from FSStore.getitems getting AttributeError
-        with pytest.raises(Exception):
+        with pytest.raises(Exception):  # noqa: B017
             x[...]
         # exception from FSStore.__getitem__ getting AttributeError
-        with pytest.raises(Exception):
+        with pytest.raises(Exception):  # noqa: B017
             y[...]
 
 

zarr/tests/test_storage_v3.py

@@ -286,7 +286,7 @@ def test_rename_nonexisting(self):
 
     def test_get_partial_values(self):
         store = self.create_store()
-        store.supports_efficient_get_partial_values in [True, False]
+        assert store.supports_efficient_get_partial_values in [True, False]
         store[data_root + "foo"] = b"abcdefg"
         store[data_root + "baz"] = b"z"
         assert [b"a"] == store.get_partial_values([(data_root + "foo", (0, 1))])

zarr/util.py

@@ -198,11 +198,11 @@ def normalize_dtype(dtype: Union[str, np.dtype], object_codec) -> Tuple[np.dtype
                     args = []
                 try:
                     object_codec = codec_registry[codec_id](*args)
-                except KeyError:  # pragma: no cover
+                except KeyError as e:  # pragma: no cover
                     raise ValueError(
                         f"codec {codec_id!r} for object type {key!r} is not "
                         f"available; please provide an object_codec manually"
-                    )
+                    ) from e
             return dtype, object_codec
 
     dtype = np.dtype(dtype)
@@ -332,7 +332,7 @@ def normalize_fill_value(fill_value, dtype: np.dtype):
             raise ValueError(
                 f"fill_value {fill_value!r} is not valid for dtype {dtype}; "
                 f"nested exception: {e}"
-            )
+            ) from e
 
     return fill_value
 
@@ -492,13 +492,13 @@ def tree_widget_sublist(node, root=False, expand=False):
 def tree_widget(group, expand, level):
     try:
         import ipytree
-    except ImportError as error:
+    except ImportError as e:
         raise ImportError(
-            f"{error}: Run `pip install zarr[jupyter]` or `conda install ipytree`"
+            f"{e}: Run `pip install zarr[jupyter]` or `conda install ipytree`"
             f"to get the required ipytree dependency for displaying the tree "
             f"widget. If using jupyterlab<3, you also need to run "
             f"`jupyter labextension install ipytree`"
-        )
+        ) from e
 
     result = ipytree.Tree()
     root = TreeNode(group, level=level)