scipy >= 0.13.0 windows refactoring. Closes #753

Author: oliche

brainbox/population/cca.py

@@ -1,11 +1,14 @@
 import numpy as np
 import matplotlib.pylab as plt
+from scipy.signal.windows import gaussian
+from scipy.signal import convolve
+from sklearn.decomposition import PCA
+
 from iblutil.numerical import bincount2D
 
 
 def _smooth(data, sd):
-    from scipy.signal import gaussian
-    from scipy.signal import convolve
+
     n_bins = data.shape[0]
     w = n_bins - 1 if n_bins % 2 == 0 else n_bins
     window = gaussian(w, std=sd)
@@ -15,7 +18,6 @@ def _smooth(data, sd):
 
 
 def _pca(data, n_pcs):
-    from sklearn.decomposition import PCA
     pca = PCA(n_components=n_pcs)
     pca.fit(data)
     data_pc = pca.transform(data)

brainbox/singlecell.py

@@ -3,7 +3,8 @@
 '''
 
 import numpy as np
-from scipy.signal import convolve, gaussian
+from scipy.signal import convolve
+from scipy.signal.windows import gaussian
 from iblutil.util import Bunch
 from brainbox.population.decode import xcorr
 

requirements.txt

@@ -15,7 +15,7 @@ pynrrd>=0.4.0
 pytest
 requests>=2.22.0
 scikit-learn>=0.22.1
-scipy>=1.7.0,<1.13 # scipy gaussian missing April 2024
+scipy>=1.7.0
 scikit-image  # this is a widefield requirement missing as of July 2023, we may remove it once wfield has this figured out
 sparse
 seaborn>=0.9.0