ENH: add piqtree_nj as a cogent3 quick_tree hook

pyproject.toml

@@ -68,6 +68,9 @@ piqtree_jc_dists = "piqtree._app:piqtree_jc_dists"
 piqtree_nj = "piqtree._app:piqtree_nj"
 piqtree_mfinder = "piqtree._app:piqtree_mfinder"
 
+[project.entry-points."cogent3.hook"]
+quick_tree = "piqtree._app:piqtree_nj"
+
 [tool.setuptools.dynamic]
 version = {attr = "piqtree.__version__"}
 

src/piqtree/_app/__init__.py

@@ -125,7 +125,9 @@ def main(
 @composable.define_app
 @extend_docstring_from(nj_tree)
 def piqtree_nj(dists: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
-    return nj_tree(dists)
+    tree = nj_tree(dists)
+    tree.params |= {"provenance": "piqtree"}
+    return tree
 
 
 @composable.define_app

tests/conftest.py

@@ -11,20 +11,20 @@ def DATA_DIR() -> pathlib.Path:
 
 @pytest.fixture
 def three_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
 def four_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
 def five_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
-    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Manatee", "Dugong"])
     return aln.omit_gap_pos(allowed_gap_frac=0)

tests/test_app/test_app.py

@@ -1,18 +1,20 @@
 import pytest
-from cogent3 import ArrayAlignment, get_app, make_tree
+from cogent3 import __version__ as cogent3_vers
+from cogent3 import get_app, make_tree
+from cogent3.core.new_alignment import Alignment
 
 import piqtree
 from piqtree import jc_distances
 
 
-def test_piqtree_phylo(four_otu: ArrayAlignment) -> None:
+def test_piqtree_phylo(four_otu: Alignment) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
     app = get_app("piqtree_phylo", submod_type="JC")
     got = app(four_otu)
     assert expected.same_topology(got)
 
 
-def test_piqtree_phylo_support(four_otu: ArrayAlignment) -> None:
+def test_piqtree_phylo_support(four_otu: Alignment) -> None:
     app = get_app("piqtree_phylo", submod_type="JC", bootstrap_reps=1000)
     got = app(four_otu)
     supports = [
@@ -23,7 +25,7 @@ def test_piqtree_phylo_support(four_otu: ArrayAlignment) -> None:
     assert all(supports)
 
 
-def test_piqtree_fit(three_otu: ArrayAlignment) -> None:
+def test_piqtree_fit(three_otu: Alignment) -> None:
     tree = make_tree(tip_names=three_otu.names)
     app = get_app("model", "JC69", tree=tree)
     expected = app(three_otu)
@@ -53,7 +55,7 @@ def test_piqtree_random_trees(
         assert len(tree.tips()) == num_taxa
 
 
-def test_piqtree_jc_distances(five_otu: ArrayAlignment) -> None:
+def test_piqtree_jc_distances(five_otu: Alignment) -> None:
     app = get_app("piqtree_jc_dists")
     dists = app(five_otu)
 
@@ -79,7 +81,7 @@ def test_piqtree_jc_distances(five_otu: ArrayAlignment) -> None:
     )  # dugong closer than rhesus
 
 
-def test_piqtree_nj(five_otu: ArrayAlignment) -> None:
+def test_piqtree_nj(five_otu: Alignment) -> None:
     dists = jc_distances(five_otu)
 
     expected = make_tree("(((Human, Chimpanzee), Rhesus), Manatee, Dugong);")
@@ -91,15 +93,15 @@ def test_piqtree_nj(five_otu: ArrayAlignment) -> None:
     assert expected.same_topology(actual)
 
 
-def test_mfinder(five_otu: ArrayAlignment) -> None:
+def test_mfinder(five_otu: Alignment) -> None:
     from piqtree.iqtree import ModelFinderResult
 
     app = get_app("piqtree_mfinder")
     got = app(five_otu)
     assert isinstance(got, ModelFinderResult)
 
 
-def test_mfinder_result_roundtrip(five_otu: ArrayAlignment) -> None:
+def test_mfinder_result_roundtrip(five_otu: Alignment) -> None:
     from piqtree.iqtree import ModelFinderResult
 
     app = get_app("piqtree_mfinder")
@@ -108,3 +110,9 @@ def test_mfinder_result_roundtrip(five_otu: ArrayAlignment) -> None:
     inflated = ModelFinderResult.from_rich_dict(rd)
     assert isinstance(inflated, ModelFinderResult)
     assert str(got.best_aicc) == str(inflated.best_aicc)
+
+@pytest.mark.skipif(cogent3_vers < "2025.3.1", reason="requires cogent3 >= 2025.3.1")
+@pytest.mark.parametrize("use_hook", [None, "piqtree"])
+def test_quick_tree_hook(four_otu: Alignment, use_hook: str | None) -> None:
+    tree = four_otu.quick_tree(use_hook=use_hook)
+    assert tree.params["provenance"] == "piqtree"