🗑️ Remove shapely.speedups (#622)

- Remove `shapely.speedups`.
- [The shapely.speedups module (the enable and disable functions) is deprecated and will be removed in the future. The module no longer has any affect in Shapely >=2.0.](https://shapely.readthedocs.io/en/stable/release/2.x.html#shapely-2-0-api-changes-deprecated-in-1-8)

Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>

tiatoolbox/annotation/storage.py

@@ -58,7 +58,7 @@
 
 import numpy as np
 import pandas as pd
-from shapely import speedups, wkb, wkt
+from shapely import wkb, wkt
 from shapely.affinity import scale, translate
 from shapely.geometry import LineString, Point, Polygon
 from shapely.geometry import mapping as geometry2feature
@@ -76,9 +76,6 @@
 
 sqlite3.enable_callback_tracebacks(True)
 
-if speedups.available:  # pragma: no branch
-    speedups.enable()
-
 Geometry = Union[Point, Polygon, LineString]
 Properties = Dict[str, Union[Dict, List, Number, str]]
 BBox = Tuple[Number, Number, Number, Number]

tiatoolbox/utils/visualization.py

@@ -10,15 +10,11 @@
 from matplotlib import colormaps
 from numpy.typing import ArrayLike
 from PIL import Image, ImageFilter, ImageOps
-from shapely import speedups
 from shapely.geometry import Polygon
 
 from tiatoolbox import logger
 from tiatoolbox.annotation.storage import Annotation, AnnotationStore
 
-if speedups.available:  # pragma: no branch
-    speedups.enable()
-
 
 def random_colors(num_colors, bright=True):
     """Generate a number of random colors.