ci: update typing, pre-commit, and add all kwargs to decon func (#48)

* update typing

* add all args

* style(pre-commit.ci): auto fixes [...]

* more typing

* fix mypy

* style(pre-commit.ci): auto fixes [...]

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -7,27 +7,27 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.262
+    rev: v0.0.289
     hooks:
       - id: ruff
         args: [--fix]
 
   - repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.9.1
     hooks:
       - id: black
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.2
+    rev: v0.14
     hooks:
       - id: validate-pyproject
 
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v1.2.0
-  #   hooks:
-  #     - id: mypy
-  #       files: "^src/"
-  #       # # you have to add the things you want to type check against here
-  #       additional_dependencies:
-  #         - numpy
-  #         - typing_extensions
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.5.1
+    hooks:
+      - id: mypy
+        files: "^src/"
+        # # you have to add the things you want to type check against here
+        additional_dependencies:
+          - numpy
+          - typing_extensions

pyproject.toml

@@ -11,7 +11,7 @@ readme = "README.md"
 requires-python = ">=3.7"
 license = { text = "MIT" }
 keywords = ["deconvolution", "microscopy", "CUDA"]
-authors = [{ email = "talley.lambert@gmail.com" }, { name = "Talley Lambert" }]
+authors = [{ email = "talley.lambert@gmail.com", name = "Talley Lambert" }]
 classifiers = [
   "Development Status :: 4 - Beta",
   "Environment :: GPU :: NVIDIA CUDA",

src/pycudadecon/__init__.py

@@ -1,7 +1,7 @@
 try:
     from importlib.metadata import PackageNotFoundError, version
 except ImportError:
-    from importlib_metadata import PackageNotFoundError, version
+    from importlib_metadata import PackageNotFoundError, version  # type: ignore
 
 try:
     __version__ = version("pycudadecon")
@@ -15,7 +15,7 @@
 
 
 try:
-    from . import _libwrap as lib  # noqa: F811
+    from . import _libwrap as lib
 except FileNotFoundError as e:
     import warnings
 
@@ -26,7 +26,7 @@ class _stub:
         def __getattr__(self, name):
             raise t
 
-    lib = _stub()
+    lib = _stub()  # type: ignore
 
 
 from .affine import affineGPU, deskewGPU, rotateGPU

src/pycudadecon/_ctyped.py

@@ -3,11 +3,19 @@
 import os
 from ctypes.util import find_library
 from inspect import Parameter, signature
-from typing import Callable, Optional, Tuple, Type
+from typing import TYPE_CHECKING, Callable, Optional, Tuple, Type
 
 import numpy as np
 from typing_extensions import Annotated, get_args, get_origin
 
+if TYPE_CHECKING:
+    from typing import TypeVar
+
+    from typing_extensions import ParamSpec
+
+    P = ParamSpec("P")
+    R = TypeVar("R")
+
 
 class Library:
     def __init__(self, name: str, version: Tuple[int, ...] = (0, 0, 0)):
@@ -24,7 +32,7 @@ def __init__(self, name: str, version: Tuple[int, ...] = (0, 0, 0)):
         if not self.lib._name:
             raise FileNotFoundError(f"Unable to find library: {self.name}")
 
-    def function(self, func: Callable) -> Callable:
+    def function(self, func: "Callable[P, R]") -> "Callable[P, R]":
         func_c = getattr(self.lib, func.__name__)
 
         sig = signature(func)
@@ -40,7 +48,7 @@ def __init__(self, func):
             def __signature__(self):
                 return sig
 
-            def __call__(self, *args, **kw):
+            def __call__(self, *args: "P.args", **kw: "P.kwargs") -> "R":
                 return self._func(*args, **kw)
 
             def __repr__(_self):
@@ -68,5 +76,6 @@ def cast_type(hint: Type) -> Optional[Type]:
         float: ctypes.c_float,
         int: ctypes.c_int,
         str: ctypes.c_char_p,
+        bytes: ctypes.c_char_p,
         np.ndarray: np.ctypeslib.ndpointer(ctypes.c_float, flags="C_CONTIGUOUS"),
     }[hint]

src/pycudadecon/_libwrap.py

@@ -1,11 +1,12 @@
 import os
 from pathlib import Path
+from typing import Tuple
 
 import numpy as np
 from typing_extensions import Annotated
 
 from ._ctyped import Library
-from typing import Tuple
+
 # FIXME: ugly... we should export version better from cudadecon
 _cudadecon_version: Tuple[int, ...] = (0, 0, 0)
 _conda_prefix = os.getenv("CONDA_PREFIX")
@@ -32,12 +33,14 @@
 
 
 @lib.function
-def camcor_interface_init(nx: int, ny: int, nz: int, camparam: np.ndarray) -> int:
+def camcor_interface_init(  # type: ignore [empty-body]
+    nx: int, ny: int, nz: int, camparam: np.ndarray
+) -> int:
     """Setup for camera corrections."""
 
 
 @lib.function
-def camcor_interface(
+def camcor_interface(  # type: ignore [empty-body]
     raw_data: ndarray_uint16, nx: int, ny: int, nz: int, result: ndarray_uint16
 ) -> int:
     """Execute camera corrections."""
@@ -46,7 +49,7 @@ def camcor_interface(
 if _cudadecon_version < (0, 6):
 
     @lib.function
-    def RL_interface_init(
+    def RL_interface_init(  # type: ignore [empty-body]
         nx: int,
         ny: int,
         nz: int,
@@ -75,10 +78,10 @@ def RL_interface_init(
         OTF_file_name: file name of OTF
         """
 
-else: # include "bSkewDecon" arguement
+else:  # include "bSkewDecon" arguement
 
     @lib.function
-    def RL_interface_init(
+    def RL_interface_init(  # type: ignore [empty-body]
         nx: int,
         ny: int,
         nz: int,
@@ -113,7 +116,7 @@ def RL_interface_init(
 if _cudadecon_version < (0, 6):
 
     @lib.function
-    def RL_interface(
+    def RL_interface(  # type: ignore [empty-body]
         raw_data: ndarray_uint16,
         nx: int,
         ny: int,
@@ -135,7 +138,7 @@ def RL_interface(
 else:
 
     @lib.function
-    def RL_interface(
+    def RL_interface(  # type: ignore [empty-body]
         raw_data: ndarray_uint16,
         nx: int,
         ny: int,
@@ -160,17 +163,17 @@ def RL_interface(
 # retrieve the post-deskewed image dimensions
 # can be used to allocate result buffer before calling RL_interface()
 @lib.function
-def get_output_nx() -> int:
+def get_output_nx() -> int:  # type: ignore [empty-body]
     ...
 
 
 @lib.function
-def get_output_ny() -> int:
+def get_output_ny() -> int:  # type: ignore [empty-body]
     ...
 
 
 @lib.function
-def get_output_nz() -> int:
+def get_output_nz() -> int:  # type: ignore [empty-body]
     ...
 
 
@@ -197,7 +200,7 @@ def cuda_reset() -> None:
 
 
 @lib.function
-def Deskew_interface(
+def Deskew_interface(  # type: ignore [empty-body]
     raw_data: np.ndarray,
     nx: int,
     ny: int,
@@ -214,7 +217,7 @@ def Deskew_interface(
 
 
 @lib.function
-def Affine_interface(
+def Affine_interface(  # type: ignore [empty-body]
     raw_data: np.ndarray,
     nx: int,
     ny: int,
@@ -226,7 +229,7 @@ def Affine_interface(
 
 
 @lib.function
-def Affine_interface_RA(
+def Affine_interface_RA(  # type: ignore [empty-body]
     raw_data: np.ndarray,
     nx: int,
     ny: int,
@@ -251,8 +254,8 @@ def Affine_interface_RA(
 
 @otf_lib.function
 def makeOTF(
-    ifiles: str,
-    ofiles: str,
+    ifiles: bytes,
+    ofiles: bytes,
     lambdanm: int = 520,
     dz: float = 0.102,
     interpkr: int = 10,

src/pycudadecon/affine.py

@@ -165,9 +165,9 @@ def affineGPU(
     # have to calculate this here to know the size of the return array
     result = np.empty((nz, ny, nx), dtype=np.float32)
     if isinstance(dzyx, (tuple, list)) and len(dzyx) == 3:
-        _dzyx = tuple(float(i) for i in dzyx[::-1])
+        dx, dy, dz = (float(i) for i in dzyx[::-1])
         # note, dzyx coordinate order is flipped when handing to Affine_interface_RA
-        lib.Affine_interface_RA(im, nx, ny, nz, *_dzyx, result, tmat)
+        lib.Affine_interface_RA(im, nx, ny, nz, dx, dy, dz, result, tmat)
     else:
         lib.Affine_interface(im, nx, ny, nz, result, tmat)
     return result