changed implementation to avoid the use of apc

hstrat/_auxiliary_lib/_alifestd_calc_triplet_distance_asexual.py

@@ -1,35 +1,28 @@
-import alifedata_phyloinformatics_convert as apc
 import pandas as pd
 import tqdist
 
+from . import (
+    alifestd_as_newick_asexual,
+    alifestd_collapse_unifurcations,
+)
+
 
 # adapted from https://github.com/mmore500/hstrat/blob/d23917cf03ba59061ff2f9b951efe79e995eb4d8/tests/test_hstrat/test_phylogenetic_inference/test_tree/_impl/_tree_quartet_distance.py
 def alifestd_calc_triplet_distance_asexual(
     ref: pd.DataFrame, cmp: pd.DataFrame
 ) -> float:
     """Calculate the triplet distance between two trees."""
-    tree_a = apc.RosettaTree(ref).as_dendropy
-    tree_b = apc.RosettaTree(cmp).as_dendropy
 
-    # must suppress root unifurcations or tqdist barfs
-    # see https://github.com/uym2/tripVote/issues/15
-    tree_a.unassign_taxa(exclude_leaves=True)
-    tree_a.suppress_unifurcations()
-    tree_b.unassign_taxa(exclude_leaves=True)
-    tree_b.suppress_unifurcations()
+    ref = alifestd_collapse_unifurcations(ref)
+    cmp = alifestd_collapse_unifurcations(cmp)
 
-    tree_a_taxon_labels = [
-        leaf.taxon.label for leaf in tree_a.leaf_node_iter()
-    ]
-    tree_b_taxon_labels = [
-        leaf.taxon.label for leaf in tree_b.leaf_node_iter()
-    ]
-    assert {*tree_a_taxon_labels} == {*tree_b_taxon_labels}
-    for taxon_label in tree_a_taxon_labels:
+    ref_labels = {*ref["taxon_label"]}
+    assert ref_labels == {*cmp["taxon_label"]}
+    for taxon_label in ref_labels:
         assert taxon_label
         assert taxon_label.strip()
 
     return tqdist.triplet_distance(
-        tree_a.as_string(schema="newick").removeprefix("[&R]").strip(),
-        tree_b.as_string(schema="newick").removeprefix("[&R]").strip(),
+        alifestd_as_newick_asexual(ref).removeprefix("[&R]").strip(),
+        alifestd_as_newick_asexual(cmp).removeprefix("[&R]").strip(),
     )