Updating code, removing deprecated patterns, general future compat (#87)

* Modify scipy import pattern for future compat.

* Rm scipy lower bound.

* Update for numpy 2.0.

* Unpin numpy.

deepcell_spots/decoding_functions.py

@@ -96,7 +96,7 @@ class MatrixSquareRoot(Function):
     """
     @staticmethod
     def forward(ctx, input):
-        m = input.detach().cpu().numpy().astype(np.float_)
+        m = input.detach().cpu().numpy().astype(np.float64)
         sqrtm = torch.from_numpy(scipy.linalg.sqrtm(m).real).to(input)
         ctx.save_for_backward(sqrtm)
         return sqrtm
@@ -106,8 +106,8 @@ def backward(ctx, grad_output):
         grad_input = None
         if ctx.needs_input_grad[0]:
             sqrtm, = ctx.saved_tensors
-            sqrtm = sqrtm.data.cpu().numpy().astype(np.float_)
-            gm = grad_output.data.cpu().numpy().astype(np.float_)
+            sqrtm = sqrtm.data.cpu().numpy().astype(np.float64)
+            gm = grad_output.data.cpu().numpy().astype(np.float64)
 
             # Given a positive semi-definite matrix X,
             # since X = X^{1/2}X^{1/2}, we can compute the gradient of the

deepcell_spots/utils/augmentation_utils.py

@@ -29,7 +29,7 @@
 import numpy as np
 from keras_preprocessing.image.affine_transformations import \
     transform_matrix_offset_center
-from scipy.ndimage.morphology import distance_transform_edt
+from scipy.ndimage import distance_transform_edt
 
 
 def subpixel_distance_transform(point_list, image_shape, dy=1, dx=1):

requirements.txt

@@ -1,6 +1,6 @@
 pandas<2
-numpy>=1.16.6
-scipy>=1.2.3,<2
+numpy
+scipy<2
 scikit-image>=0.19.3
 scikit-learn
 tensorflow~=2.8.0  # manually matched to deepcell-tf

setup.py

@@ -53,8 +53,8 @@
     long_description_content_type='text/markdown',
     install_requires=[
         'pandas<2',
-        'numpy>=1.16.6',
-        'scipy>=1.2.3,<2',
+        'numpy',
+        'scipy<2',
         'scikit-image>=0.19.3',
         'scikit-learn',
         'tensorflow~=2.8.0',