Merge pull request #2931 from PMEAL/patch-1

Fixed deprecation error coming from new Scipy and Numpy versions #maint

openpnm/_skgraph/generators/tools/_funcs.py

@@ -85,7 +85,7 @@ def get_centroid(pts, mode='rigorous'):
  if mode == 'rigorous':
  tri = sptl.Delaunay(pts)
  CoM = center_of_mass(simplices=tri.simplices.astype(np.int_),
- points=tri.points.astype(np.float_))
+ points=tri.points.astype(float))
  elif mode == 'fast':
  CoM = pts.mean(axis=0)
  return CoM
@@ -99,11 +99,11 @@ def get_centroid(pts, mode='rigorous'):
 # @njit
 def center_of_mass(simplices, points):
  A = []
- centroids = np.zeros((simplices.shape[0], points.shape[1]), dtype=np.float_)
+ centroids = np.zeros((simplices.shape[0], points.shape[1]), dtype=float)
  for i, s in enumerate(simplices):
  xy = points[s]
  cen = np.sum(points[s], axis=0)/simplices.shape[1]
- centroids[i, :] = cen.astype(np.float_)
+ centroids[i, :] = cen.astype(float)
  if xy.shape[1] == 2: # In 2D
  # Use Heron's formula to find area of arbitrary triangle
  a = np.sqrt((xy[0, 0] - xy[1, 0])**2 + (xy[0, 1] - xy[1, 1])**2)
@@ -117,9 +117,9 @@ def center_of_mass(simplices, points):
  temp = np.abs(np.linalg.det(d))/6.0
  # temp = 0
  A.append(temp)
- A = np.array(A, dtype=np.float_)
+ A = np.array(A, dtype=float)
  CoM = np.array([(centroids[:, i]*A/A.sum()*len(A)).mean()
- for i in range(centroids.shape[1])], dtype=np.float_)
+ for i in range(centroids.shape[1])], dtype=float)
  return CoM
 
 

openpnm/algorithms/_reactive_transport.py

@@ -1,14 +1,16 @@
 import logging
 import sys
-
 import numpy as np
 from numpy.linalg import norm
-from scipy.optimize.nonlin import TerminationCondition
+try: # For scipy < 1.14
+ from scipy.optimize.nonlin import TerminationCondition
+except ImportError: # For newer Scipy
+ from scipy.optimize._nonlin import TerminationCondition
 from tqdm.auto import tqdm
-
 from openpnm.algorithms import Transport
 from openpnm.utils import Docorator, TypedList
 
+
 __all__ = ["ReactiveTransport"]
 
 

openpnm/solvers/_scipy.py

@@ -23,4 +23,7 @@ def solve(self, A, b, **kwargs):
  if not isinstance(A, (csr_matrix, csc_matrix)):
  A = A.tocsr()
  atol = self._get_atol(b)
- return cg(A, b, tol=self.tol, atol=atol, **kwargs)
+ try:
+ return cg(A, b, tol=self.tol, atol=atol, **kwargs)
+ except TypeError:
+ return cg(A, b, rtol=self.tol, atol=atol, **kwargs)

openpnm/visualization/_plottools.py

@@ -602,7 +602,7 @@ def plot_tutorial(network,
  fig = plt.gcf()
  fig.tight_layout()
  dims = op.topotools.dimensionality(network)
- xy_range = network.coords.ptp(axis=0)[dims]
+ xy_range = np.ptp(network.coords, axis=0)[dims]
  aspect_ratio = xy_range[0] / xy_range[1]
  fig.set_size_inches(5, 5 / aspect_ratio)
 
@@ -781,7 +781,7 @@ def _generate_voxel_image(network, pore_shape, throat_shape, max_dim=200):
  # Transform points to satisfy origin at (0, 0, 0)
  xyz0 = xyz.min(axis=0) - delta
  xyz += -xyz0
- res = (xyz.ptp(axis=0).max() + 2 * delta) / max_dim
+ res = (np.ptp(xyz, axis=0).max() + 2 * delta) / max_dim
  shape = np.rint((xyz.max(axis=0) + delta) / res).astype(int) + 2 * extra_clearance
 
  # Transforming from real coords to matrix coords