Merge branch 'main' into dependabot/pip/fsspec-2023.12.2

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/releases.yml

@@ -16,7 +16,7 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4.7.1
+      - uses: actions/setup-python@v5.0.0
         name: Install Python
         with:
           python-version: '3.8'

.pre-commit-config.yaml

@@ -6,27 +6,25 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.224'
+    rev: 'v0.1.8'
     hooks:
     - id: ruff
-      # Respect `exclude` and `extend-exclude` settings.
-      args: ["--force-exclude"]
   - repo: https://github.com/psf/black
-    rev: 23.10.1
+    rev: 23.12.0
     hooks:
     - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.7.1
     hooks:
       - id: mypy
         files: zarr

pyproject.toml

@@ -120,9 +120,10 @@ exclude = '''
 '''
 
 [tool.mypy]
-python_version = "3.8"
 ignore_missing_imports = true
-follow_imports = "silent"
+warn_unused_configs = true
+warn_redundant_casts = true
+warn_unused_ignores = true
 
 [tool.pytest.ini_options]
 doctest_optionflags = [

zarr/_storage/store.py

@@ -642,10 +642,10 @@ def _rmdir_from_keys_v3(store: StoreV3, path: str = "") -> None:
     sfx = _get_metadata_suffix(store)
     array_meta_file = meta_dir + ".array" + sfx
     if array_meta_file in store:
-        store.erase(array_meta_file)  # type: ignore
+        store.erase(array_meta_file)
     group_meta_file = meta_dir + ".group" + sfx
     if group_meta_file in store:
-        store.erase(group_meta_file)  # type: ignore
+        store.erase(group_meta_file)
 
 
 def _listdir_from_keys(store: BaseStore, path: Optional[str] = None) -> List[str]:

zarr/_storage/v3_storage_transformers.py

@@ -351,7 +351,7 @@ def erase_prefix(self, prefix):
 
     def rmdir(self, path=None):
         path = normalize_storage_path(path)
-        _rmdir_from_keys_v3(self, path)  # type: ignore
+        _rmdir_from_keys_v3(self, path)
 
     def __contains__(self, key):
         if self._is_data_key(key):

zarr/core.py

@@ -2536,7 +2536,7 @@ def hexdigest(self, hashname="sha1"):
         checksum = binascii.hexlify(self.digest(hashname=hashname))
 
         # This is a bytes object on Python 3 and we want a str.
-        if type(checksum) is not str:
+        if not isinstance(checksum, str):
             checksum = checksum.decode("utf8")
 
         return checksum

zarr/meta.py

@@ -234,8 +234,8 @@ def decode_fill_value(cls, v: Any, dtype: np.dtype, object_codec: Any = None) ->
                 return np.array(v, dtype=dtype)[()]
         elif dtype.kind in "c":
             v = (
-                cls.decode_fill_value(v[0], dtype.type().real.dtype),  # type: ignore
-                cls.decode_fill_value(v[1], dtype.type().imag.dtype),  # type: ignore
+                cls.decode_fill_value(v[0], dtype.type().real.dtype),
+                cls.decode_fill_value(v[1], dtype.type().imag.dtype),
             )
             v = v[0] + 1j * v[1]
             return np.array(v, dtype=dtype)[()]

zarr/storage.py

@@ -206,7 +206,7 @@ def rmdir(store: StoreLike, path: Path = None):
     store_version = getattr(store, "_store_version", 2)
     if hasattr(store, "rmdir") and store.is_erasable():  # type: ignore
         # pass through
-        store.rmdir(path)  # type: ignore
+        store.rmdir(path)
     else:
         # slow version, delete one key at a time
         if store_version == 2:
@@ -236,7 +236,7 @@ def listdir(store: BaseStore, path: Path = None):
     path = normalize_storage_path(path)
     if hasattr(store, "listdir"):
         # pass through
-        return store.listdir(path)  # type: ignore
+        return store.listdir(path)
     else:
         # slow version, iterate through all keys
         warnings.warn(
@@ -289,7 +289,7 @@ def getsize(store: BaseStore, path: Path = None) -> int:
     if hasattr(store, "getsize"):
         # pass through
         path = normalize_storage_path(path)
-        return store.getsize(path)  # type: ignore
+        return store.getsize(path)
     elif isinstance(store, MutableMapping):
         return _getsize(store, path)
     else:
@@ -627,7 +627,7 @@ def _init_array_metadata(
 
     key = _prefix_to_array_key(store, _path_to_prefix(path))
     if hasattr(store, "_metadata_class"):
-        store[key] = store._metadata_class.encode_array_metadata(meta)  # type: ignore
+        store[key] = store._metadata_class.encode_array_metadata(meta)
     else:
         store[key] = encode_array_metadata(meta)
 
@@ -730,10 +730,10 @@ def _init_group_metadata(
     if store_version == 3:
         meta = {"attributes": {}}  # type: ignore
     else:
-        meta = {}  # type: ignore
+        meta = {}
     key = _prefix_to_group_key(store, _path_to_prefix(path))
     if hasattr(store, "_metadata_class"):
-        store[key] = store._metadata_class.encode_group_metadata(meta)  # type: ignore
+        store[key] = store._metadata_class.encode_group_metadata(meta)
     else:
         store[key] = encode_group_metadata(meta)
 

zarr/util.py

@@ -183,7 +183,7 @@ def normalize_chunks(chunks: Any, shape: Tuple[int, ...], typesize: int) -> Tupl
 def normalize_dtype(dtype: Union[str, np.dtype], object_codec) -> Tuple[np.dtype, Any]:
     # convenience API for object arrays
     if inspect.isclass(dtype):
-        dtype = dtype.__name__  # type: ignore
+        dtype = dtype.__name__
     if isinstance(dtype, str):
         # allow ':' to delimit class from codec arguments
         tokens = dtype.split(":")