ENH: add jc distance app

Author: rmcar17

pyproject.toml

@@ -46,6 +46,7 @@ test = ["pytest", "pytest-cov", "nox"]
 piqtree_phylo = "piqtree2._app:piqtree_phylo"
 piqtree_fit = "piqtree2._app:piqtree_fit"
 piqtree_random_trees = "piqtree2._app:piqtree_random_trees"
+piqtree_jc_distances = "piqtree2._app:piqtree_jc_distances"
 piqtree_nj = "piqtree2._app:piqtree_nj"
 
 [tool.setuptools.dynamic]

src/piqtree2/_app/__init__.py

@@ -5,7 +5,14 @@
 from cogent3.app import composable
 from cogent3.util.misc import extend_docstring_from
 
-from piqtree2 import TreeGenMode, build_tree, fit_tree, nj_tree, random_trees
+from piqtree2 import (
+    TreeGenMode,
+    build_tree,
+    fit_tree,
+    jc_distances,
+    nj_tree,
+    random_trees,
+)
 from piqtree2.model import Model
 
 
@@ -76,6 +83,14 @@ def piqtree_random_trees(
     return random_trees(num_taxa, tree_mode, num_trees, rand_seed)
 
 
+@composable.define_app
+@extend_docstring_from(nj_tree)
+def piqtree_jc_distances(
+    aln: cogent3.Alignment | cogent3.ArrayAlignment,
+) -> c3_types.PairwiseDistanceType:
+    return jc_distances(aln)
+
+
 @composable.define_app
 @extend_docstring_from(nj_tree)
 def piqtree_nj(dists: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
@@ -86,5 +101,6 @@ def piqtree_nj(dists: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
     "piqtree_phylo",
     "piqtree_fit",
     "piqtree_random_trees",
+    "piqtree_jc_distances",
     "piqtree_nj",
 ]

tests/test_app/test_app.py

@@ -42,6 +42,32 @@ def test_piqtree_random_trees(
         assert len(tree.tips()) == num_taxa
 
 
+def test_piqtree_jc_distances(five_otu: ArrayAlignment) -> None:
+    app = get_app("piqtree_jc_distances")
+    dists = app(five_otu)
+
+    assert (
+        dists["Human", "Chimpanzee"] < dists["Human", "Dugong"]
+    )  # chimpanzee closer than rhesus
+    assert (
+        dists["Human", "Rhesus"] < dists["Human", "Manatee"]
+    )  # rhesus closer than manatee
+    assert (
+        dists["Human", "Rhesus"] < dists["Human", "Dugong"]
+    )  # rhesus closer than dugong
+
+    assert (
+        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Manatee"]
+    )  # rhesus closer than manatee
+    assert (
+        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Dugong"]
+    )  # rhesus closer than dugong
+
+    assert (
+        dists["Manatee", "Dugong"] < dists["Manatee", "Rhesus"]
+    )  # dugong closer than rhesus
+
+
 def test_piqtree_nj(five_otu: ArrayAlignment) -> None:
     dists = jc_distances(five_otu)