double speed of expand subpaths

Author: verginer

pathpy/classes/paths.py

@@ -559,7 +559,8 @@ def expand_subpaths(self):
                     for s in range(path_length - k + 1):
                         # Add frequency as a subpath to *first* entry of occurrence
                         # counter
-                        self.paths[k][path[s:s + k + 1]] += np.array([frequency, 0])
+                        path_slice = path[s:s + k + 1]
+                        self.paths[k][path_slice][0] += frequency
 
     def add_path_tuple(self, path, expand_subpaths=True, frequency=np.array([0, 1])):
         """Adds a tuple of elements as a path. If the elements are not strings,
@@ -583,8 +584,9 @@ def add_path_tuple(self, path, expand_subpaths=True, frequency=np.array([0, 1]))
         assert path, 'Error: paths needs to contain at least one element'
 
         for x in path:
-            if self.separator in x:
-                raise PathpyError('Error: Node name contains separator character. Choose different separator.')
+            if isinstance(x, str) and self.separator in x:
+                raise PathpyError('Error: Node name contains separator character. '
+                                  'Choose different separator.')
 
         path_str = path if isinstance(path, str) else tuple(map(str, path))
 
@@ -629,8 +631,9 @@ def add_path_ngram(self, ngram, separator=',', expand_subpaths=True, frequency=N
         """
         path = tuple(ngram.split(separator))
         for x in path:
-            if self.separator in x:
-                raise PathpyError('Error: Node name contains separator character. Choose different separator.')
+            if isinstance(x, str) and self.separator in x:
+                raise PathpyError('Error: Node name contains separator character.'
+                                  'Choose different separator.')
 
         path_length = len(path) - 1
 

tests/test_DAG.py

@@ -88,19 +88,16 @@ def test_dag_path_mapping_to_many(dag_object):
     dag.topsort()
 
     mapping = {
-        'a': {1, 2},
-        'b': {2, 5},
-        'c': {5},
-        'e': {1, 2},
-        'f': {2, 3},
-        'g': {2, 5},
-        'h': {1},
-        'i': {1, 5},
+        'a': {1, 2}, 'b': {2, 5},
+        'c': {5}, 'e': {1, 2},
+        'f': {2, 3}, 'g': {2, 5},
+        'h': {1}, 'i': {1, 5},
         'j': {4}
     }
     paths_mapped2 = pp.path_extraction.paths_from_dag(dag, node_mapping=mapping)
 
-    assert paths_mapped2.observation_count is None
+    assert paths_mapped2.observation_count == 55
+    assert set(paths_mapped2.nodes()) == {'1', '2', '3', '4', '5'}
 
 
 edges1, types1 = [(1, 2), (1, 3), (2, 3)], ({1}, {2}, {3})
@@ -150,27 +147,6 @@ def test_remove_edge(dag_object: pp.DAG):
     assert 'e' in dag_object.isolate_nodes()
 
 
-def test_set_path_expansion(dag_object: pp.DAG):
-    from collections import defaultdict
-    mapping = {'a': {1, 2},
-               'b': {2, 5},
-               'c': {5},
-               'e': {1, 2},
-               'f': {2, 3},
-               'g': {2, 5},
-               'h': {1},
-               'i': {1, 5},
-               'j': {4}
-               }
-
-    path_count = defaultdict(lambda: 0)
-    # for root in dag_object.roots:
-        # for set_path in dag_object.routes_from_node(root):
-
-
-
-
-
 
 
 

tests/test_Path.py

@@ -250,5 +250,13 @@ def test_pickle(random_paths, tmpdir):
     assert paths.observation_count == paths.observation_count
 
 
+# def test_expand_subpaths(random_paths):
+#     paths = random_paths(2000, 0, 400)
+#     paths.expand_subpaths()
+#
+#
+# import pytest
+# pytest.main(__file__)
+