Changed dtype to int32 and added plot

.gitignore

@@ -3,3 +3,4 @@ balibase/
 __pycache__/
 balibase.zip
 atlas
+timings.png

.gitlab-ci.yml

@@ -11,3 +11,6 @@ test:
 test_performance:
         script:
                 - python3 -m unittest alignementseq_tests.PerformanceTestCase
+        artifacts:
+                paths:
+                        - timings.png

alignementseq.py

@@ -159,7 +159,7 @@ def vec_align(seq1, seq2, mat=dict_to_weight(Bio.SubsMat.MatrixInfo.blosum62), g
     x = np.array(list(ord(c)-ord('A') for c in seq1.seq))
     y = np.array(list(ord(c)-ord('A') for c in seq2.seq))
     mat = mat.flatten()
-    S = [ np.zeros(min(s,n,m,n+m-s)+1, dtype=np.int) for s in range(n+m+1) ]
+    S = [ np.zeros(min(s,n,m,n+m-s)+1, dtype=np.int32) for s in range(n+m+1) ]
 
     S[0][0] = 0
     S[1][0] = gap

alignementseq_tests.py

@@ -8,6 +8,7 @@ import warnings
 import timeit
 import multiprocessing
 import pandas as pd
+import matplotlib.pyplot
 
 import Bio.SeqIO
 import Bio.pairwise2
@@ -144,7 +145,8 @@ class PerformanceTestCase(AlignmentSeqTestCase):
         from alignementseq import align, vec_align
 
         methods = (vec_align, align)
-        times = pd.DataFrame(columns=("length1", "length2", "method", "time"))
+        times = pd.DataFrame(columns=("length1", "length2", "method", "time"),
+                dtype=float)
         for s1, s2, filename in self.get_dataset_heads():
             for method in methods:
                 def to_time():
@@ -153,7 +155,17 @@ class PerformanceTestCase(AlignmentSeqTestCase):
                 times.loc[len(times)] = (
                         len(s1.seq), len(s2.seq), method.__name__, t
                         )
+        times['length_product'] = times.length1 * times.length2
         print(times)
+        
+        ax = None
+        cmap = matplotlib.cm.inferno
+        colors = [ cmap(i/2) for i in range(2) ]
+        for im, method in enumerate(methods):
+            ax = times.loc[times.method == method.__name__].plot.scatter(
+                    'length_product', 'time', c=colors[im],
+                    label=method.__name__, ax=ax)
+        matplotlib.pyplot.savefig("timings.png")
 
     def test_titin(self):
         from alignementseq import align, vec_align