Add type hint checking with mypy

Author: dstansby

.pre-commit-config.yaml

@@ -25,3 +25,10 @@ repos:
     rev: 2024.08.19
     hooks:
     - id: sp-repo-review
+
+  -   repo: https://github.com/pre-commit/mirrors-mypy
+      rev: 'v1.4.0'
+      hooks:
+      -   id: mypy
+          args: [--config-file, pyproject.toml]
+          additional_dependencies: [numpy, pytest, zfpy]

docs/conf.py

@@ -232,7 +232,7 @@ def __getattr__(cls, name):
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict[str, str] = {
     # The paper size ('letterpaper' or 'a4paper').
     #'papersize': 'letterpaper',
     # The font size ('10pt', '11pt' or '12pt').

numcodecs/abc.py

@@ -29,13 +29,14 @@
 """
 
 from abc import ABC, abstractmethod
+from typing import Optional
 
 
 class Codec(ABC):
     """Codec abstract base class."""
 
     # override in sub-class
-    codec_id = None
+    codec_id: Optional[str] = None
     """Codec identifier."""
 
     @abstractmethod

numcodecs/checksum32.py

@@ -1,19 +1,23 @@
 import struct
 import zlib
-from typing import Literal
+from collections.abc import Callable
+from typing import TYPE_CHECKING, Literal
 
 import numpy as np
 
 from .abc import Codec
 from .compat import ensure_contiguous_ndarray, ndarray_copy
 from .jenkins import jenkins_lookup3
 
+if TYPE_CHECKING:
+    from typing_extensions import Buffer
+
 CHECKSUM_LOCATION = Literal['start', 'end']
 
 
 class Checksum32(Codec):
     # override in sub-class
-    checksum = None
+    checksum: Callable[["Buffer", int], int] | None = None
     location: CHECKSUM_LOCATION = 'start'
 
     def __init__(self, location: CHECKSUM_LOCATION | None = None):

numcodecs/compat.py

@@ -100,7 +100,7 @@ def ensure_contiguous_ndarray_like(buf, max_buffer_size=None, flatten=True) -> N
 
     # check for datetime or timedelta ndarray, the buffer interface doesn't support those
     if arr.dtype.kind in "Mm":
-        arr = arr.view(np.int64)
+        arr = arr.view(np.int64)  # type: ignore[arg-type]
 
     # check memory is contiguous, if so flatten
     if arr.flags.c_contiguous or arr.flags.f_contiguous:
@@ -117,7 +117,7 @@ def ensure_contiguous_ndarray_like(buf, max_buffer_size=None, flatten=True) -> N
     return arr
 
 
-def ensure_contiguous_ndarray(buf, max_buffer_size=None, flatten=True) -> np.array:
+def ensure_contiguous_ndarray(buf, max_buffer_size=None, flatten=True) -> np.ndarray:
     """Convenience function to coerce `buf` to a numpy array, if it is not already a
     numpy array. Also ensures that the returned value exports fully contiguous memory,
     and supports the new-style buffer interface. If the optional max_buffer_size is

numcodecs/lzma.py

@@ -1,11 +1,14 @@
-import contextlib
+from types import ModuleType
+from typing import Optional
 
-_lzma = None
+_lzma: Optional[ModuleType] = None
 try:
     import lzma as _lzma
 except ImportError:  # pragma: no cover
-    with contextlib.suppress(ImportError):
-        from backports import lzma as _lzma
+    try:
+        from backports import lzma as _lzma  # type: ignore[no-redef]
+    except ImportError:
+        pass
 
 
 if _lzma:

numcodecs/ndarray_like.py

@@ -1,7 +1,7 @@
 from typing import Any, ClassVar, Optional, Protocol, runtime_checkable
 
 
-class _CachedProtocolMeta(Protocol.__class__):
+class _CachedProtocolMeta(type):
     """Custom implementation of @runtime_checkable
 
     The native implementation of @runtime_checkable is slow,

numcodecs/registry.py

@@ -2,11 +2,13 @@
 applications to dynamically register and look-up codec classes."""
 
 import logging
-from importlib.metadata import entry_points
+from importlib.metadata import EntryPoints, entry_points
+
+from numcodecs.abc import Codec
 
 logger = logging.getLogger("numcodecs")
-codec_registry = {}
-entries = {}
+codec_registry: dict[str, Codec] = {}
+entries: dict[str, EntryPoints] = {}
 
 
 def run_entrypoints():

numcodecs/tests/test_lzma.py

@@ -1,5 +1,7 @@
 import itertools
 import unittest
+from types import ModuleType
+from typing import cast
 
 import numpy as np
 import pytest
@@ -20,6 +22,8 @@
     check_repr,
 )
 
+_lzma = cast(ModuleType, _lzma)
+
 codecs = [
     LZMA(),
     LZMA(preset=1),

numcodecs/tests/test_zfpy.py

@@ -1,3 +1,6 @@
+from types import ModuleType
+from typing import cast
+
 import numpy as np
 import pytest
 
@@ -17,6 +20,9 @@
     check_repr,
 )
 
+_zfpy = cast(ModuleType, _zfpy)
+
+
 codecs = [
     ZFPY(mode=_zfpy.mode_fixed_rate, rate=-1),
     ZFPY(),

numcodecs/zfpy.py

@@ -1,8 +1,10 @@
 import warnings
 from contextlib import suppress
 from importlib.metadata import PackageNotFoundError, version
+from types import ModuleType
+from typing import Optional
 
-_zfpy = None
+_zfpy: Optional[ModuleType] = None
 
 _zfpy_version: tuple = ()
 with suppress(PackageNotFoundError):
@@ -21,7 +23,7 @@
         )
     else:
         with suppress(ImportError):
-            import zfpy as _zfpy
+            import zfpy as _zfpy  # type: ignore[no-redef]
 
 if _zfpy:
     import numpy as np

pyproject.toml

@@ -177,3 +177,7 @@ ignore = [
 
 [tool.ruff.format]
 quote-style = "preserve"
+
+[tool.mypy]
+ignore_errors = false
+ignore_missing_imports = true