From 1f4004c6576b74ce02e4837d1458e45f64e78a49 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 21:47:04 +0100
Subject: [PATCH 1/7] Enable ruff/bugbear rules (B)

As suggested by Repo-Review.
---
 pyproject.toml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 904c974424..ea57fa0478 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -103,6 +103,11 @@ exclude = [
     "docs"
 ]
 
+[tool.ruff.lint]
+extend-select = [
+    "B"
+]
+
 [tool.black]
 line-length = 100
 exclude = '''

From 4abb3cd12d3b396aebdeedfba0c6264a9579dfd6 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 21:34:13 +0100
Subject: [PATCH 2/7] 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/
---
 zarr/tests/test_meta.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/zarr/tests/test_meta.py b/zarr/tests/test_meta.py
index c85d3f923f..a91e07b531 100644
--- a/zarr/tests/test_meta.py
+++ b/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)

From 381b7b00431062b24ee1b5466ede22a22c4cbd04 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 21:36:04 +0100
Subject: [PATCH 3/7] 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/
---
 zarr/tests/test_storage_v3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/zarr/tests/test_storage_v3.py b/zarr/tests/test_storage_v3.py
index c096f9cb02..e8675786e0 100644
--- a/zarr/tests/test_storage_v3.py
+++ b/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))])

From 80399234fd8d0bb137725b9b7e416a1ccdbe841a Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 21:53:22 +0100
Subject: [PATCH 4/7] Fix ruff/bugbear issues (B028)

B028 No explicit `stacklevel` keyword argument found

https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/
---
 zarr/creation.py |  2 +-
 zarr/n5.py       | 18 +++++++++++++++---
 zarr/storage.py  |  6 +++++-
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/zarr/creation.py b/zarr/creation.py
index c541531d54..9b2b1d6d4c 100644
--- a/zarr/creation.py
+++ b/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
 
diff --git a/zarr/n5.py b/zarr/n5.py
index fdd3d5babf..bb80dba3cc 100644
--- a/zarr/n5.py
+++ b/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()):
@@ -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"]
diff --git a/zarr/storage.py b/zarr/storage.py
index 10f55f0ba3..a3ee8d87d9 100644
--- a/zarr/storage.py
+++ b/zarr/storage.py
@@ -588,11 +588,15 @@ 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:

From e3ceb5c010097ef22103d97d40b1a2b2666468ce Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 21:43:45 +0100
Subject: [PATCH 5/7] 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/
---
 zarr/_storage/absstore.py                |  8 ++++----
 zarr/_storage/v3_storage_transformers.py |  8 ++++----
 zarr/core.py                             |  4 ++--
 zarr/hierarchy.py                        | 10 +++++-----
 zarr/indexing.py                         |  2 +-
 zarr/meta.py                             |  6 +++---
 zarr/meta_v1.py                          |  2 +-
 zarr/n5.py                               |  4 ++--
 zarr/storage.py                          | 10 +++++-----
 zarr/util.py                             | 12 ++++++------
 10 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/zarr/_storage/absstore.py b/zarr/_storage/absstore.py
index 217b2a29e0..ce3d32cac2 100644
--- a/zarr/_storage/absstore.py
+++ b/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 (
diff --git a/zarr/_storage/v3_storage_transformers.py b/zarr/_storage/v3_storage_transformers.py
index 37e56f8ecd..00467d44f9 100644
--- a/zarr/_storage/v3_storage_transformers.py
+++ b/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)
 
diff --git a/zarr/core.py b/zarr/core.py
index 1bd081acee..6aa86b6465 100644
--- a/zarr/core.py
+++ b/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)
diff --git a/zarr/hierarchy.py b/zarr/hierarchy.py
index 0fb07dd620..8894a5ed57 100644
--- a/zarr/hierarchy.py
+++ b/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
diff --git a/zarr/indexing.py b/zarr/indexing.py
index 9889fcadad..2f2402fe27 100644
--- a/zarr/indexing.py
+++ b/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:
diff --git a/zarr/meta.py b/zarr/meta.py
index 4b360270de..d8aefa3273 100644
--- a/zarr/meta.py
+++ b/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
 
diff --git a/zarr/meta_v1.py b/zarr/meta_v1.py
index 65bfd3488e..714f55f477 100644
--- a/zarr/meta_v1.py
+++ b/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
 
diff --git a/zarr/n5.py b/zarr/n5.py
index bb80dba3cc..3d3e9afa26 100644
--- a/zarr/n5.py
+++ b/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]
diff --git a/zarr/storage.py b/zarr/storage.py
index a3ee8d87d9..73a5f5be71 100644
--- a/zarr/storage.py
+++ b/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
diff --git a/zarr/util.py b/zarr/util.py
index e58aed80ab..8a96f92c24 100644
--- a/zarr/util.py
+++ b/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)

From 0e84d1f107b95ad6466e8e5d13ecbb1c1be81a9d Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 11 Mar 2024 22:04:49 +0100
Subject: [PATCH 6/7] Document changes in docs/release.rst

---
 docs/release.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/release.rst b/docs/release.rst
index 811ede3d58..f5f6b25adc 100644
--- a/docs/release.rst
+++ b/docs/release.rst
@@ -35,6 +35,9 @@ Docs
 
 Maintenance
 ~~~~~~~~~~~
+* Enable ruff/bugbear rules (B) and fix issues.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1702`.
+
 
 Deprecations
 ~~~~~~~~~~~~

From 2c392172dbe1d07e065ee7873175e67a6723d298 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Sun, 5 May 2024 18:36:09 +0200
Subject: [PATCH 7/7] Disable ruff/bugbear rule (B017)

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

https://docs.astral.sh/ruff/rules/assert-raises-exception/
---
 zarr/tests/test_storage.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/zarr/tests/test_storage.py b/zarr/tests/test_storage.py
index ae8a56fa61..da690f5959 100644
--- a/zarr/tests/test_storage.py
+++ b/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[...]