Fix some mypy issues

pyproject.toml

@@ -67,6 +67,7 @@ changelog = "https://github.com/instamatic-dev/instamatic/releases"
 develop = [
     "bump2version",
     "check-manifest",
+    "mypy",
     "pre-commit",
     "pytest >= 5.4.1",
     "coverage",
@@ -151,6 +152,11 @@ required-imports = ["from __future__ import annotations"]
 quote-style = "single"
 indent-style = "space"
 
+[tool.mypy]
+files = ["src", "tests"]
+allow_redefinition = true
+ignore_missing_imports = true
+
 [tool.bumpversion]
 current_version = "2.0.5"
 

src/instamatic/TEMController/TEMController.py

@@ -524,7 +524,9 @@ def from_dict(self, dct: dict):
             except TypeError:
                 func(v)
 
-    def get_raw_image(self, exposure: float = None, binsize: int = None) -> np.ndarray:
+    def get_raw_image(
+        self, exposure: Optional[float] = None, binsize: Optional[int] = None
+    ) -> np.ndarray:
         """Simplified function equivalent to `get_image` that only returns the
         raw data array.
 
@@ -542,7 +544,9 @@ def get_raw_image(self, exposure: float = None, binsize: int = None) -> np.ndarr
         """
         return self.cam.get_image(exposure=exposure, binsize=binsize)
 
-    def get_future_image(self, exposure: float = None, binsize: int = None) -> 'future':
+    def get_future_image(
+        self, exposure: Optional[float] = None, binsize: Optional[int] = None
+    ) -> 'future':
         """Simplified function equivalent to `get_image` that returns the raw
         image as a future. This makes the data acquisition call non-blocking.
 
@@ -566,7 +570,9 @@ def get_future_image(self, exposure: float = None, binsize: int = None) -> 'futu
         future = self._executor.submit(self.get_raw_image, exposure=exposure, binsize=binsize)
         return future
 
-    def get_rotated_image(self, exposure: float = None, binsize: int = None) -> np.ndarray:
+    def get_rotated_image(
+        self, exposure: Optional[float] = None, binsize: Optional[int] = None
+    ) -> np.ndarray:
         """Simplified function equivalent to `get_image` that returns the
         rotated image array.
 
@@ -598,13 +604,13 @@ def get_rotated_image(self, exposure: float = None, binsize: int = None) -> np.n
 
     def get_image(
         self,
-        exposure: float = None,
-        binsize: int = None,
+        exposure: Optional[float] = None,
+        binsize: Optional[int] = None,
         comment: str = '',
-        out: str = None,
+        out: Optional[str] = None,
         plot: bool = False,
         verbose: bool = False,
-        header_keys: Tuple[str] = 'all',
+        header_keys: Optional[Tuple[str]] = None,
     ) -> Tuple[np.ndarray, dict]:
         """Retrieve image as numpy array from camera. If the exposure and
         binsize are not given, the default values are read from the config
@@ -685,7 +691,12 @@ def get_image(
         return arr, h
 
     def get_movie(
-        self, n_frames: int, *, exposure: float = None, binsize: int = None, out: str = None
+        self,
+        n_frames: int,
+        *,
+        exposure: Optional[float] = None,
+        binsize: Optional[int] = None,
+        out: Optional[str] = None,
     ) -> Tuple[np.ndarray]:
         """Collect a stack of images using the camera's movie mode, if
         available.
@@ -740,7 +751,9 @@ def store_diff_beam(self, name: str = 'beam', save_to_file: bool = False):
         keys = 'FunctionMode', 'Brightness', 'GunTilt', 'DiffFocus', 'SpotSize'
         self.store(name=name, keys=keys, save_to_file=save_to_file)
 
-    def store(self, name: str = 'stash', keys: tuple = None, save_to_file: bool = False):
+    def store(
+        self, name: str = 'stash', keys: Optional[tuple] = None, save_to_file: bool = False
+    ):
         """Stores current settings to dictionary.
 
         Multiple settings can be stored under different names. Specify

src/instamatic/TEMController/jeol_microscope.py

@@ -3,7 +3,7 @@
 import atexit
 import logging
 import time
-from typing import Tuple
+from typing import Optional, Tuple
 
 import comtypes.client
 
@@ -279,7 +279,7 @@ def getImageShift2(self) -> Tuple[int, int]:
     def setImageShift2(self, x: int, y: int):
         self.def3.SetIS2(x, y)
 
-    def getStagePosition(self) -> Tuple[int, int, int, int, int]:
+    def getStagePosition(self) -> Tuple[float, float, float, float, float]:
         """X, y, z in nanometer a and b in degrees."""
         x, y, z, a, b, result = self.stage3.GetPos()
         return x, y, z, a, b
@@ -334,11 +334,11 @@ def stopStage(self):
 
     def setStagePosition(
         self,
-        x: int = None,
-        y: int = None,
-        z: int = None,
-        a: int = None,
-        b: int = None,
+        x: Optional[float] = None,
+        y: Optional[float] = None,
+        z: Optional[float] = None,
+        a: Optional[float] = None,
+        b: Optional[float] = None,
         wait: bool = True,
     ):
         if z is not None:

src/instamatic/TEMController/lenses.py

@@ -121,14 +121,14 @@ def __repr__(self):
     def index(self) -> int:
         return self._indexgetter()
 
-    @property
-    def absolute_index(self) -> int:
-        return self._tem.getMagnificationAbsoluteIndex()
-
     @index.setter
     def index(self, index: int):
         self._indexsetter(index)
 
+    @property
+    def absolute_index(self) -> int:
+        return self._tem.getMagnificationAbsoluteIndex()
+
     def increase(self) -> None:
         try:
             self.index += 1

src/instamatic/TEMController/microscope_base.py

@@ -86,7 +86,7 @@ def getSpotSize(self) -> int:
         pass
 
     @abstractmethod
-    def getStagePosition(self) -> Tuple[int, int, int, int, int]:
+    def getStagePosition(self) -> Tuple[float, float, float, float, float]:
         pass
 
     @abstractmethod
@@ -170,7 +170,9 @@ def setSpotSize(self, value: int) -> None:
         pass
 
     @abstractmethod
-    def setStagePosition(self, x: int, y: int, z: int, a: int, b: int, wait: bool) -> None:
+    def setStagePosition(
+        self, x: float, y: float, z: float, a: float, b: float, wait: bool
+    ) -> None:
         pass
 
     @abstractmethod

src/instamatic/TEMController/simu_microscope.py

@@ -2,7 +2,7 @@
 
 import random
 import time
-from typing import Tuple
+from typing import Optional, Tuple
 
 from instamatic import config
 from instamatic.exceptions import TEMValueError
@@ -87,8 +87,8 @@ def __init__(self, name: str = 'simulate'):
         self._HT = 200_000  # V
 
         # self.Magnification_value = random.choice(self.MAGNIFICATIONS)
-        self.Magnification_value = config.microscope.ranges['mag1'][10]
-        self.Magnification_value_diff = config.microscope.ranges['diff'][3]
+        self.Magnification_value: int = config.microscope.ranges['mag1'][10]  # type: ignore
+        self.Magnification_value_diff: int = config.microscope.ranges['diff'][3]  # type: ignore
 
         self.beamblank = False
 
@@ -372,7 +372,7 @@ def setImageShift2(self, x: int, y: int):
         self.ImageShift2_x = x
         self.ImageShift2_y = y
 
-    def getStagePosition(self) -> Tuple[int, int, int, int, int]:
+    def getStagePosition(self) -> Tuple[float, float, float, float, float]:
         return (
             self.StagePosition_x,
             self.StagePosition_y,
@@ -390,32 +390,32 @@ def waitForStage(self, delay: float = 0.1):
         while self.isStageMoving():
             time.sleep(delay)
 
-    def setStageX(self, value: int, wait: bool = True):
+    def setStageX(self, value: float, wait: bool = True):
         self.StagePosition_x = value
         if wait:
             self.waitForStage()
 
-    def setStageY(self, value: int, wait: bool = True):
+    def setStageY(self, value: float, wait: bool = True):
         self.StagePosition_y = value
         if wait:
             self.waitForStage()
 
-    def setStageZ(self, value: int, wait: bool = True):
+    def setStageZ(self, value: float, wait: bool = True):
         self.StagePosition_z = value
         if wait:
             self.waitForStage()
 
-    def setStageA(self, value: int, wait: bool = True):
+    def setStageA(self, value: float, wait: bool = True):
         self.StagePosition_a = value
         if wait:
             self.waitForStage()
 
-    def setStageB(self, value: int, wait: bool = True):
+    def setStageB(self, value: float, wait: bool = True):
         self.StagePosition_b = value
         if wait:
             self.waitForStage()
 
-    def setStageXY(self, x: int, y: int, wait: bool = True):
+    def setStageXY(self, x: float, y: float, wait: bool = True):
         self.StagePosition_x = x
         self.StagePosition_y = y
         if wait:
@@ -426,11 +426,11 @@ def stopStage(self):
 
     def setStagePosition(
         self,
-        x: int = None,
-        y: int = None,
-        z: int = None,
-        a: int = None,
-        b: int = None,
+        x: Optional[float] = None,
+        y: Optional[float] = None,
+        z: Optional[float] = None,
+        a: Optional[float] = None,
+        b: Optional[float] = None,
         speed: float = -1,
         wait: bool = True,
     ):