Merge pull request #17 from Advestis/refactoring

Replace np.int (deprecated) by np.int_
Advestis · Nov 29, 2023 · 526e61d · 526e61d
2 parents ea0d552 + fc39719
commit 526e61d
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Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/adnmtf/nmtf_base.py b/adnmtf/nmtf_base.py
@@ -25,14 +25,14 @@
 
 def init(m, mmis, nc):
     n, p = m.shape
-    mmis = mmis.astype(np.int)
+    mmis = mmis.astype(np.int_)
     n_mmis = mmis.shape[0]
     if n_mmis == 0:
         missing_values_indexes = np.where(np.isnan(m) == 1)
         n_mmis = missing_values_indexes[0].size
         if n_mmis > 0:
             mmis = np.isnan(m) == 0
-            mmis = mmis.astype(np.int)
+            mmis = mmis.astype(np.int_)
             m[mmis == 0] = 0
     else:
         m[mmis == 0] = 0
@@ -443,14 +443,14 @@ def r_ntf_solve(
             cancel_pressed,
         )
 
-    mmis = mmis.astype(np.int)
+    mmis = mmis.astype(np.int_)
     n_mmis = mmis.shape[0]
     if n_mmis == 0:
         missing_values_indexes = np.where(np.isnan(m) == 1)
         n_mmis = missing_values_indexes[0].size
         if n_mmis > 0:
             mmis = np.isnan(m) == 0
-            mmis = mmis.astype(np.int)
+            mmis = mmis.astype(np.int_)
             m[mmis == 0] = 0
     else:
         m[mmis == 0] = 0
@@ -646,12 +646,12 @@ def init_factorization(m, n_components):
     n, p = m.shape
     # Identify missing values
     mmis = np.array([])
-    mmis = mmis.astype(np.int)
+    mmis = mmis.astype(np.int_)
     missing_values_indexes = np.where(np.isnan(m) == 1)
     n_mmis = missing_values_indexes[0].size
     if n_mmis > 0:
         mmis = np.isnan(m) == 0
-        mmis = mmis.astype(np.int)
+        mmis = mmis.astype(np.int_)
         m[mmis == 0] = 0
     else:
         m[mmis == 0] = 0

diff --git a/adnmtf/nmtf_core.py b/adnmtf/nmtf_core.py
@@ -23,7 +23,7 @@ def ntf_stack(m, mmis, n_blocks):
     for future use with NMF
     """
     n, p = m.shape
-    mmis = mmis.astype(np.int)
+    mmis = mmis.astype(np.int_)
     n_mmis = mmis.shape[0]
     n_blocks = int(n_blocks)
 

diff --git a/adnmtf/nmtf_utils.py b/adnmtf/nmtf_utils.py
@@ -495,10 +495,10 @@ def build_clusters(
 def cluster_pvalues(cluster_size, nb_groups, mt, r_ct, n_ct, row_groups, list_groups, ngroup):
     """Calculate Pvalue of each group versus cluster"""
     n, nc = mt.shape
-    cluster_size = cluster_size.astype(np.int)
+    cluster_size = cluster_size.astype(np.int_)
     nb_groups = int(nb_groups)
-    r_ct = r_ct.astype(np.int)
-    n_ct = n_ct.astype(np.int)
+    r_ct = r_ct.astype(np.int_)
+    n_ct = n_ct.astype(np.int_)
     cluster_size = np.reshape(cluster_size, nc)
     r_ct = np.reshape(r_ct, (n,))
     n_ct = np.reshape(n_ct, (nc,))
@@ -569,8 +569,8 @@ def global_sign(nrun, nb_groups, mt, r_ct, n_ct, row_groups, list_groups, ngroup
     n, nc = mt.shape
     nrun = int(nrun)
     nb_groups = int(nb_groups)
-    r_ct = r_ct.astype(np.int)
-    n_ct = n_ct.astype(np.int)
+    r_ct = r_ct.astype(np.int_)
+    n_ct = n_ct.astype(np.int_)
     cluster_size = np.zeros(nc)
     r_ct = np.reshape(r_ct, n)
     n_ct = np.reshape(n_ct, nc)