Merge pull request #112 from klausweinbauer/master

make RandomWalk kernel compatible with SciPy version >= 1.12.0
ysig · Oct 24, 2024 · 6a9cebf · 6a9cebf
2 parents 2a49dc7 + 25f7926
commit 6a9cebf
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Showing 3 changed files with 15 additions and 4 deletions.
diff --git a/grakel/kernels/random_walk.py b/grakel/kernels/random_walk.py
@@ -268,7 +268,7 @@ def lsf(x, lamda):
             # A*x=b
             A = LinearOperator((mn, mn), matvec=lambda x: lsf(x, self.lamda))
             b = np.ones(mn)
-            x_sol, _ = cg(A, b, tol=1.0e-6, maxiter=20, atol='legacy')
+            x_sol, _ = cg(A, b, rtol=1.0e-6, maxiter=20)
             return np.sum(x_sol)
 
 
@@ -467,7 +467,7 @@ def lsf(x, lamda):
             # A*x=b
             A = LinearOperator((mn, mn), matvec=lambda x: lsf(x, self.lamda))
             b = np.ones(mn)
-            x_sol, _ = cg(A, b, tol=1.0e-6, maxiter=20, atol='legacy')
+            x_sol, _ = cg(A, b, rtol=1.0e-6, maxiter=20)
             return np.sum(x_sol)
 
 

diff --git a/grakel/kernels/vertex_histogram.py b/grakel/kernels/vertex_histogram.py
@@ -132,15 +132,25 @@ def parse_input(self, X):
                     self.sparse_ = bool(self.sparse)
 
             if self.sparse_:
-                features = csr_matrix((data, (rows, cols)), shape=(ni, len(labels)), copy=False)
+                features = csr_matrix(
+                    (data, (rows, cols)),
+                    shape=(ni, len(labels)),
+                    copy=False,
+                    dtype=">f8",
+                )
             else:
                 # Initialise the feature matrix
                 try:
                     features = zeros(shape=(ni, len(labels)))
                     features[rows, cols] = data
                 except MemoryError:
                     warn('memory-error: switching to sparse')
-                    self.sparse_, features = True, csr_matrix((data, (rows, cols)), shape=(ni, len(labels)), copy=False)
+                    self.sparse_, features = True, csr_matrix(
+                        (data, (rows, cols)),
+                        shape=(ni, len(labels)),
+                        copy=False,
+                        dtype=">f8",
+                    )
 
             if ni == 0:
                 raise ValueError('parsed input is empty')

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,7 @@
 numpy>=1.14.0
 cython>=0.27.3
 scikit-learn>=0.19
+scipy>=1.12.0
 six>=1.11.0
 future>=0.16.0
 joblib