Enable ruff/bugbear rules (B) and fix issues (#1702)

* Enable ruff/bugbear rules (B)

As suggested by Repo-Review.

* Fix ruff/bugbear issue (B007)

B007 Loop control variable `key` not used within loop body

https://docs.astral.sh/ruff/rules/unused-loop-control-variable/

* Fix ruff/bugbear issue (B015)

B015 Pointless comparison. Did you mean to assign a value?
     Otherwise, prepend `assert` or remove it.

https://docs.astral.sh/ruff/rules/useless-comparison/

* Fix ruff/bugbear issues (B028)

B028 No explicit `stacklevel` keyword argument found

https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/

* 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/

* Document changes in docs/release.rst

* Disable ruff/bugbear rule (B017)

B017 `pytest.raises(Exception)` should be considered evil

https://docs.astral.sh/ruff/rules/assert-raises-exception/

---------

Co-authored-by: Joe Hamman <joe@earthmover.io>

Author: DimitriPapadopoulos

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