TST: add fit_tree and build_tree tests

tests/test_build_tree.py

@@ -0,0 +1,16 @@
+import piqtree2
+import pytest
+from cogent3 import load_aligned_seqs, make_tree
+
+
+@pytest.fixture()
+def four_otu(DATA_DIR):
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna")
+    aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
+    return aln.omit_gap_pos(allowed_gap_frac=0)
+
+
+def test_phylogenetic_analysis(four_otu):
+    expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
+    got = piqtree2.build_tree(four_otu, "JC", rand_seed=1)
+    assert expected.same_topology(got)

tests/test_fit_tree.py

@@ -0,0 +1,18 @@
+import piqtree2
+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_topology = make_tree(tip_names=three_otu.names)
+    app = get_app("model", "JC69", tree=tree_topology)
+    expected = app(three_otu)
+    got = piqtree2.fit_tree(three_otu, tree_topology, "JC", rand_seed=1)
+    assert got.params["lnL"] == pytest.approx(expected.lnL)