ENH: define cogent3 apps and add test stub

setup.py

@@ -12,4 +12,15 @@
     ),
 ]
 
-setup(ext_modules=ext_modules, cmdclass={"build_ext": build_ext}, zip_safe=False)
+setup(
+    ext_modules=ext_modules,
+    cmdclass={"build_ext": build_ext},
+    zip_safe=False,
+    entry_points={
+        "cogent3.app": [
+            "piqtree_phylo = piqtree2._app:piqtree_phylo",
+            "piqtree_fit = piqtree2._app:piqtree_fit",
+            "piqtree_random_trees = piqtree2._app:piqtree_random_trees",
+        ]
+    },
+)

src/piqtree2/_app.py

@@ -0,0 +1,6 @@
+from piqtree2 import _iq_wrappers as iqtree
+from cogent3.app.composable import define_app
+
+piqtree_phylo = define_app(iqtree.build_tree)
+piqtree_fit = define_app(iqtree.fit_tree)
+piqtree_random_trees = define_app(iqtree.random_trees)

src/piqtree2/_iq_wrappers.py

@@ -54,7 +54,9 @@ def _rename_iq_tree(tree: cogent3.PhyloNode, names: list[str]) -> None:
 
 
 def build_tree(
-    aln: cogent3.Alignment, model: str, rand_seed: int | None = None
+    aln: cogent3.Alignment | cogent3.ArrayAlignment,
+    model: str,
+    rand_seed: int | None = None,
 ) -> cogent3.PhyloNode:
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE

tests/conftest.py

@@ -0,0 +1,13 @@
+import pathlib
+
+import pytest
+
+
+@pytest.fixture(scope="session")
+def DATA_DIR():
+    return pathlib.Path(__file__).parent / "data"
+
+
+@pytest.fixture(scope="function")
+def tmp_dir(tmp_path_factory):
+    return tmp_path_factory.mktemp("cli")

tests/test_app.py

@@ -0,0 +1,18 @@
+import pytest
+from cogent3 import get_app, load_aligned_seqs, make_tree
+
+
+@pytest.fixture
+def three_otu(DATA_DIR):
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
+    return aln.omit_gap_pos(allowed_gap_frac=0)
+
+
+def test_piqtree_fit(three_otu):
+    tree = make_tree(tip_names=three_otu.names)
+    app = get_app("model", "JC69", tree=tree)
+    expect = app(three_otu)
+    piphylo = get_app("piqtree_fit", tree=tree, model="JC")
+    got = piphylo(three_otu)
+    assert got.lnL == expect.lnL