deprecations: replaced np.str -> str, np.int -> int; pd.testing.asser…

…t_frame_equal: check_less_precise -> rtol=1e-3

evcouplings/align/alignment.py

@@ -422,7 +422,7 @@ def sequences_to_matrix(sequences):
 
     N = len(sequences)
     L = len(next(iter(sequences)))
-    matrix = np.empty((N, L), dtype=np.str)
+    matrix = np.empty((N, L), dtype=str)
 
     for i, seq in enumerate(sequences):
         if len(seq) != L:

evcouplings/couplings/model.py

@@ -609,7 +609,7 @@ def convert_sequences(self, sequences):
                 )
             )
 
-        S = np.empty((len(sequences), L_seq), dtype=np.int)
+        S = np.empty((len(sequences), L_seq), dtype=int)
 
         try:
             for i, s in enumerate(sequences):
@@ -689,8 +689,8 @@ def delta_hamiltonian(self, substitutions, verify_mutants=True):
             2) delta J_ij, 3) delta h_i
 
         """
-        pos = np.empty(len(substitutions), dtype=np.int)
-        subs = np.empty(len(substitutions), dtype=np.int)
+        pos = np.empty(len(substitutions), dtype=int)
+        subs = np.empty(len(substitutions), dtype=int)
 
         try:
             for i, (subs_pos, subs_from, subs_to) in enumerate(substitutions):

test/TestComplex.py

@@ -402,7 +402,9 @@ def test_find_possible_partners(self):
 
         pd.testing.assert_frame_equal(
             self.possible_partners, _possible_partners,
-            check_less_precise=True, check_like=True,
+            check_exact=False,
+            rtol=1e-3,
+            check_like=True,
             check_names=False
         )
 

test/TestMutation.py

@@ -98,7 +98,7 @@ def test_single_mutant_matrix(self):
         # gotta round to account for this
         _singles = _singles.round(3)
         singles = singles.round(3)
-        pd.testing.assert_frame_equal(singles, _singles, check_exact=False, check_less_precise=True)
+        pd.testing.assert_frame_equal(singles, _singles, check_exact=False, rtol=1e-3)
 
     def test_split_mutants_single(self):
         """
@@ -228,7 +228,7 @@ def test_predict_mutation_table_segment_column(self):
             self.c0, self.singles, output_column="prediction_independent"
         )
 
-        pd.testing.assert_frame_equal(self.singles, _singles, check_less_precise=True)
+        pd.testing.assert_frame_equal(self.singles, _singles, check_exact=False, rtol=1e-3)
 
     def test_predict_mutation_table_empty_segment(self):
         """