debug (removed njit)

caretta/msa_numba.py

@@ -52,6 +52,9 @@ def make_pairwise_rmsd_score_matrix(coords_array, secondary_array, lengths_array
     pairwise_matrix = np.zeros((coords_array.shape[0], coords_array.shape[0]))
     for i in nb.prange(pairwise_matrix.shape[0] - 1):
         for j in range(i + 1, pairwise_matrix.shape[1]):
+            print(i, j)
+            print(coords_array[i, :lengths_array[i]], coords_array[j, :lengths_array[j]],
+                  secondary_array[i, :lengths_array[i]], secondary_array[j, :lengths_array[j]])
             dtw_aln_1, dtw_aln_2, score = psa.get_pairwise_alignment(coords_array[i, :lengths_array[i]], coords_array[j, :lengths_array[j]],
                                                                      secondary_array[i, :lengths_array[i]], secondary_array[j, :lengths_array[j]],
                                                                      gamma,

caretta/psa_numba.py

@@ -46,7 +46,7 @@ def dtw_signals_index(coords_1, coords_2, index, size=30, overlap=1):
     return coords_1, coords_2
 
 
-# @nb.njit
+@nb.njit
 # @numba_cc.export('get_dtw_signal_score_pos', '(f64[:], f64[:], f64, i64, f64, f64)')
 def get_dtw_signal_score_pos(coords_1, coords_2, gamma, index, gap_open_penalty, gap_extend_penalty):
     coords_1[:, :3], coords_2[:, :3] = dtw_signals_index(coords_1[:, :3], coords_2[:, :3], index)
@@ -75,7 +75,7 @@ def get_secondary_distance_matrix(secondary_1, secondary_2, gap=0):
     return score_matrix
 
 
-# @nb.njit
+@nb.njit
 # @numba_cc.export('get_secondary_rmsd_pos', '(i8[:], i8[:], f64[:], f64[:], f64, f64, f64)')
 def get_secondary_rmsd_pos(secondary_1, secondary_2, coords_1, coords_2, gamma, gap_open_sec, gap_extend_sec):
     distance_matrix = get_secondary_distance_matrix(secondary_1, secondary_2)