docs(eyepy.core): adds type annotations to all objects in the core su…

…bpackage

src/eyepy/core/annotations.py

@@ -29,7 +29,7 @@ class EyeVolumeLayerAnnotation:
     def __init__(
         self,
         volume: EyeVolume,
-        data: Optional[npt.NDArray[np.float32]] = None,
+        data: Optional[npt.NDArray[np.float_]] = None,
         meta: Optional[dict] = None,
         **kwargs,
     ) -> None:

src/eyepy/core/eyebscan.py

@@ -19,7 +19,7 @@
 class EyeBscan:
     """ """
 
-    def __init__(self, volume: EyeVolume, index: int):
+    def __init__(self, volume: EyeVolume, index: int) -> None:
         """
 
         Args:
@@ -84,7 +84,7 @@ def plot(
         layer_kwargs: Optional[dict] = None,
         area_kwargs: Optional[dict] = None,
         #ascan_kwargs=None,
-        annotations_only=False,
+        annotations_only: bool=False,
         region: Union[slice, Tuple[slice, slice]] = np.s_[:, :],
     ) -> None:
         """ Plot B-scan.

src/eyepy/core/eyeenface.py

@@ -1,16 +1,20 @@
-from typing import Optional, Tuple, Union
+from typing import Dict, Optional, Tuple, TYPE_CHECKING, Union
 
 import matplotlib.pyplot as plt
 from numpy import typing as npt
 import numpy as np
 
 from eyepy.core.annotations import EyeEnfacePixelAnnotation
 
+if TYPE_CHECKING:
+    from eyepy import EyeEnfaceMeta
+
 
 class EyeEnface:
     """ """
 
-    def __init__(self, data, meta):
+    def __init__(self, data: npt.NDArray[np.int_],
+                 meta: EyeEnfaceMeta) -> None:
         """
 
         Args:
@@ -22,7 +26,7 @@ def __init__(self, data, meta):
         self.meta = meta
 
     @property
-    def area_maps(self):
+    def area_maps(self) -> Dict[str, EyeEnfacePixelAnnotation]:
         """
 
         Returns:
@@ -31,7 +35,10 @@ def area_maps(self):
         # Create a dict to access area_maps by their name
         return {am.name: am for am in self._area_maps}
 
-    def add_area_annotation(self, area_map=None, meta=None, **kwargs):
+    def add_area_annotation(self,
+                            area_map: Optional[npt.NDArray[np.bool_]] = None,
+                            meta: Optional[Dict] = None,
+                            **kwargs) -> EyeEnfacePixelAnnotation:
         """
 
         Args:
@@ -50,7 +57,7 @@ def add_area_annotation(self, area_map=None, meta=None, **kwargs):
         return area_annotation
 
     @property
-    def scale_x(self):
+    def scale_x(self) -> float:
         """
 
         Returns:
@@ -59,7 +66,7 @@ def scale_x(self):
         return self.meta["scale_x"]
 
     @property
-    def scale_y(self):
+    def scale_y(self) -> float:
         """
 
         Returns:
@@ -68,7 +75,7 @@ def scale_y(self):
         return self.meta["scale_y"]
 
     @property
-    def size_x(self):
+    def size_x(self) -> int:
         """
 
         Returns:
@@ -77,7 +84,7 @@ def size_x(self):
         return self.shape[1]
 
     @property
-    def size_y(self):
+    def size_y(self) -> int:
         """
 
         Returns:
@@ -86,7 +93,7 @@ def size_y(self):
         return self.shape[0]
 
     @property
-    def laterality(self):
+    def laterality(self) -> str:
         """
 
         Returns:
@@ -95,7 +102,7 @@ def laterality(self):
         return self.meta["laterality"]
 
     @property
-    def shape(self):
+    def shape(self) -> Tuple[int, int]:
         """
 
         Returns:
@@ -115,8 +122,7 @@ def plot(self,
         Returns:
 
         """
-        if ax is None:
-            ax = plt.gca()
+        ax = plt.gca() if ax is None else ax
         ax.imshow(self.data[region], cmap="gray")
 
         # Make sure tick labels match the image region

src/eyepy/core/eyemeta.py

@@ -1,13 +1,13 @@
 import datetime
 import json
 import os
-from typing import List, MutableMapping, Tuple
+from typing import Any, Dict, Iterable, List, MutableMapping, Tuple, Union
 
 
 class EyeMeta(MutableMapping):
     """ """
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self, *args, **kwargs) -> None:
         """
 
         Args:
@@ -17,7 +17,7 @@ def __init__(self, *args, **kwargs):
         self._store = dict()
         self.update(dict(*args, **kwargs))  # use the free update to set keys
 
-    def as_dict(self):
+    def as_dict(self) -> Dict:
         """
 
         Returns:
@@ -29,32 +29,32 @@ def as_dict(self):
                 data[key] = data[key].isoformat()
         return data
 
-    def __getitem__(self, key):
+    def __getitem__(self, key: str) -> Any:
         return self._store[key]
 
-    def __setitem__(self, key, value):
+    def __setitem__(self, key: str, value) -> None:
         self._store[key] = value
 
-    def __delitem__(self, key):
+    def __delitem__(self, key: str) -> None:
         del self._store[key]
 
     def __iter__(self):
         return iter(self._store)
 
-    def __len__(self):
+    def __len__(self) -> int:
         return len(self._store)
 
-    def __str__(self):
+    def __str__(self) -> str:
         return f"{os.linesep}".join([f"{f}: {self[f]}" for f in self if f != "__empty"])
 
-    def __repr__(self):
+    def __repr__(self) -> str:
         return self.__str__()
 
 
 class EyeEnfaceMeta(EyeMeta):
     """ """
 
-    def __init__(self, scale_x: float, scale_y: float, scale_unit: str, **kwargs):
+    def __init__(self, scale_x: float, scale_y: float, scale_unit: str, **kwargs) -> None:
         """A dict with required keys to hold meta data for enface images of the eye
 
         Args:
@@ -68,7 +68,7 @@ def __init__(self, scale_x: float, scale_y: float, scale_unit: str, **kwargs):
         )
 
     @classmethod
-    def from_dict(cls, data: dict):
+    def from_dict(cls, data: dict) -> "EyeEnfaceMeta":
         """
 
         Args:
@@ -92,7 +92,7 @@ def __init__(
         end_pos: Tuple[float, float],
         pos_unit: str,
         **kwargs,
-    ):
+    ) -> None:
         """A dict with required keys to hold meta data for OCT B-scans
 
         Args:
@@ -137,7 +137,7 @@ def __init__(
             **kwargs,
         )
 
-    def as_dict(self):
+    def as_dict(self) -> Dict:
         """
 
         Returns:
@@ -148,7 +148,7 @@ def as_dict(self):
         return data
 
     @classmethod
-    def from_dict(cls, data: dict):
+    def from_dict(cls, data: dict) -> "EyeVolumeMeta":
         """
 
         Args: