format and lint

historydag/beast_loader.py

@@ -34,7 +34,6 @@ def dag_from_beast_trees(
         include_sequence_names_in_labels: If True, augment leaf node labels with a ``name`` attribute
             containing the name of the corresponding sequence. Useful for distinguishing leaves when
             observed sequences are not unique.
-
     """
     dp_trees = load_beast_trees(
         beast_xml_file,

historydag/dag.py

@@ -2315,7 +2315,7 @@ def trim_optimal_rf_distance(
             history,
             rooted=rooted,
             one_sided=one_sided,
-            one_sided_coefficients=one_sided_coefficients
+            one_sided_coefficients=one_sided_coefficients,
         )
         return self.trim_optimal_weight(**kwargs, optimal_func=optimal_func)
 
@@ -2339,7 +2339,7 @@ def optimal_rf_distance(
             history,
             rooted=rooted,
             one_sided=one_sided,
-            one_sided_coefficients=one_sided_coefficients
+            one_sided_coefficients=one_sided_coefficients,
         )
         return self.optimal_weight_annotate(**kwargs, optimal_func=optimal_func)
 
@@ -2363,7 +2363,7 @@ def count_rf_distances(
             history,
             rooted=rooted,
             one_sided=one_sided,
-            one_sided_coefficients=one_sided_coefficients
+            one_sided_coefficients=one_sided_coefficients,
         )
         return self.weight_count(**kwargs)
 

historydag/utils.py

@@ -665,27 +665,28 @@ def make_rfdistance_countfuncs(
     of the IntState is computed as `a + sign(b) + |B|`, which on the UA node of the hDAG gives RF distance.
     """
 
-    rf_type_suffix = 'distance'
-    if one_sided_coefficients != (1,1):
-        rf_type_suffix = 'nonstandard'
+    rf_type_suffix = "distance"
+    if one_sided_coefficients != (1, 1):
+        rf_type_suffix = "nonstandard"
 
     if one_sided is None:
         pass
-    elif one_sided.lower() == 'left':
+    elif one_sided.lower() == "left":
         one_sided_coefficients = (1, 0)
-        one_sided_suffix = 'left_difference'
-    elif one_sided.lower() == 'right':
+        rf_type_suffix = "left_difference"
+    elif one_sided.lower() == "right":
         one_sided_coefficients = (0, 1)
-        one_sided_suffix = 'right_difference'
+        rf_type_suffix = "right_difference"
     else:
-        raise ValueError(f"Argument `one_sided` must have value 'left', 'right', or None, not {one_sided}")
+        raise ValueError(
+            f"Argument `one_sided` must have value 'left', 'right', or None, not {one_sided}"
+        )
 
     s, t = one_sided_coefficients
 
     taxa = frozenset(n.label for n in ref_tree.get_leaves())
 
     if not rooted:
-        # TODO sidedness not tested for rooted
 
         def split(node):
             cu = node.clade_union()
@@ -742,10 +743,9 @@ def edge_func(n1, n2):
                     summer(w.state for w in wlist)
                 ),
             },
-            name="RF_unrooted_distance",
+            name="RF_unrooted_distance_" + rf_type_suffix,
         )
     else:
-        # TODO sidedness not tested for unrooted
         ref_cus = frozenset(
             node.clade_union() for node in ref_tree.preorder(skip_ua_node=True)
         )

tests/test_factory.py

@@ -493,18 +493,30 @@ def rooted_rf_distance(history1, history2):
     cladeset2 = {n.clade_union() for n in history2.preorder(skip_ua_node=True)}
     return len(cladeset1 ^ cladeset2)
 
+
 def test_right_left_rf_add_correctly():
     # In both the rooted and unrooted cases, left and right RF distances should
     # sum to the normal RF distance.
     for rooted in (True, False):
         for dag in dags:
             ref_tree = dag.sample()
-            left_kwargs = dagutils.make_rfdistance_countfuncs(ref_tree, rooted=rooted, one_sided='left')
-            right_kwargs = dagutils.make_rfdistance_countfuncs(ref_tree, rooted=rooted, one_sided='right')
+            left_kwargs = dagutils.make_rfdistance_countfuncs(
+                ref_tree, rooted=rooted, one_sided="left"
+            )
+            right_kwargs = dagutils.make_rfdistance_countfuncs(
+                ref_tree, rooted=rooted, one_sided="right"
+            )
             kwargs = dagutils.make_rfdistance_countfuncs(ref_tree, rooted=rooted)
 
             for tree in dag:
-                assert tree.optimal_weight_annotate(**left_kwargs) + tree.optimal_weight_annotate(**right_kwargs) == tree.optimal_weight_annotate(**kwargs)
+                assert tree.optimal_weight_annotate(
+                    **left_kwargs
+                ) + tree.optimal_weight_annotate(
+                    **right_kwargs
+                ) == tree.optimal_weight_annotate(
+                    **kwargs
+                )
+
 
 def test_right_left_rf_collapse():
     """
@@ -533,18 +545,25 @@ def test_right_left_rf_collapse():
                     continue
                 else:
                     count += 1
-                    left_kwargs = dagutils.make_rfdistance_countfuncs(ctree, rooted=rooted, one_sided='left')
+                    left_kwargs = dagutils.make_rfdistance_countfuncs(
+                        ctree, rooted=rooted, one_sided="left"
+                    )
                     assert tree.optimal_weight_annotate(**left_kwargs) == 0
-                    oleft_kwargs = dagutils.make_rfdistance_countfuncs(tree, rooted=rooted, one_sided='left')
+                    oleft_kwargs = dagutils.make_rfdistance_countfuncs(
+                        tree, rooted=rooted, one_sided="left"
+                    )
                     assert ctree.optimal_weight_annotate(**oleft_kwargs) > 0
-                    right_kwargs = dagutils.make_rfdistance_countfuncs(ctree, rooted=rooted, one_sided='right')
+                    right_kwargs = dagutils.make_rfdistance_countfuncs(
+                        ctree, rooted=rooted, one_sided="right"
+                    )
                     assert tree.optimal_weight_annotate(**right_kwargs) > 0
-                    oright_kwargs = dagutils.make_rfdistance_countfuncs(tree, rooted=rooted, one_sided='right')
+                    oright_kwargs = dagutils.make_rfdistance_countfuncs(
+                        tree, rooted=rooted, one_sided="right"
+                    )
                     assert ctree.optimal_weight_annotate(**oright_kwargs) == 0
         assert count > 0
 
 
-
 def test_rf_rooted_distances():
     for dag in dags:
         ref_tree = dag.sample()
@@ -642,8 +661,10 @@ def test_optimal_sum_rf_distance():
             calculated_sum = tree.optimal_sum_rf_distance(dag)
             assert calculated_sum == expected_sum
 
+
 # ############# END RF Distance Tests: ###############
 
+
 def test_trim_range():
     for curr_dag in [dags[-1], cdags[-1]]:
         history_dag = curr_dag.copy()