Fix ruff/bugbear issues (B904)

B904 Within an `except` clause, raise exceptions with `raise ... from err` or
     `raise ... from None` to distinguish them from errors in exception handling

https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/

Author: DimitriPapadopoulos

zarr/_storage/absstore.py

@@ -143,8 +143,8 @@ 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)
@@ -156,8 +156,8 @@ 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

@@ -196,8 +196,8 @@ 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/hierarchy.py

@@ -186,16 +186,16 @@ 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)
 
@@ -518,8 +518,8 @@ 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

@@ -608,8 +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]

zarr/storage.py

@@ -872,8 +872,8 @@ 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)
@@ -891,8 +891,8 @@ 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:
@@ -1140,7 +1140,7 @@ 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/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)
@@ -323,7 +323,7 @@ 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
 
@@ -484,13 +484,13 @@ 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)