MAINT/API: Fix Table references in latest version of cogent3, simplify API of model for build and fit tree apps

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "piqtree"
-dependencies = ["cogent3>=2025.3.22a2", "pyyaml", "requests"]
+dependencies = ["cogent3>=2025.5.8a2", "pyyaml", "requests"]
 requires-python = ">=3.11, <3.14"
 
 authors = [{name="Gavin Huttley"}, {name="Robert McArthur"}, {name="Bui Quang Minh "}, {name="Richard Morris"}, {name="Thomas Wong"}]

src/piqtree/_app/__init__.py

@@ -23,21 +23,13 @@ class piqtree_phylo:
     @extend_docstring_from(build_tree)
     def __init__(
         self,
-        submod_type: str,
-        freq_type: str | None = None,
-        rate_model: str | None = None,
+        model: Model | str,
         *,
-        invariant_sites: bool = False,
         rand_seed: int | None = None,
         bootstrap_reps: int | None = None,
         num_threads: int | None = None,
     ) -> None:
-        self._model = Model(
-            submod_type=submod_type,
-            invariant_sites=invariant_sites,
-            rate_model=rate_model,
-            freq_type=freq_type,
-        )
+        self._model = model
         self._rand_seed = rand_seed
         self._bootstrap_reps = bootstrap_reps
         self._num_threads = num_threads
@@ -61,21 +53,13 @@ class piqtree_fit:
     def __init__(
         self,
         tree: cogent3.PhyloNode,
-        submod_type: str,
-        freq_type: str | None = None,
-        rate_model: str | None = None,
+        model: Model | str,
         *,
         rand_seed: int | None = None,
         num_threads: int | None = None,
-        invariant_sites: bool = False,
     ) -> None:
         self._tree = tree
-        self._model = Model(
-            submod_type=submod_type,
-            invariant_sites=invariant_sites,
-            rate_model=rate_model,
-            freq_type=freq_type,
-        )
+        self._model = model
         self._rand_seed = rand_seed
         self._num_threads = num_threads
 

src/piqtree/iqtree/_tree.py

@@ -11,7 +11,7 @@
 
 from piqtree.exceptions import ParseIqTreeError
 from piqtree.iqtree._decorator import iqtree_func
-from piqtree.model import DnaModel, Model
+from piqtree.model import DnaModel, Model, make_model
 
 iq_build_tree = iqtree_func(iq_build_tree, hide_files=True)
 iq_fit_tree = iqtree_func(iq_fit_tree, hide_files=True)
@@ -196,7 +196,7 @@ def _process_tree_yaml(
 
 def build_tree(
     aln: c3_types.AlignedSeqsType,
-    model: Model,
+    model: Model | str,
     rand_seed: int | None = None,
     bootstrap_replicates: int | None = None,
     num_threads: int | None = None,
@@ -209,7 +209,7 @@ def build_tree(
     ----------
     aln : c3_types.AlignedSeqsType
         The sequence alignment.
-    model : Model
+    model : Model | str
         The substitution model with base frequencies and rate heterogeneity.
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
@@ -227,6 +227,9 @@ def build_tree(
         The IQ-TREE maximum likelihood tree from the given alignment.
 
     """
+    if isinstance(model, str):
+        model = make_model(model)
+
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
@@ -261,7 +264,7 @@ def build_tree(
 def fit_tree(
     aln: c3_types.AlignedSeqsType,
     tree: cogent3.PhyloNode,
-    model: Model,
+    model: Model | str,
     rand_seed: int | None = None,
     num_threads: int | None = None,
 ) -> cogent3.PhyloNode:
@@ -276,7 +279,7 @@ def fit_tree(
         The sequence alignment.
     tree : cogent3.PhyloNode
         The topology to fit branch lengths to.
-    model : Model
+    model : Model | str
         The substitution model with base frequencies and rate heterogeneity.
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
@@ -290,6 +293,9 @@ def fit_tree(
         A phylogenetic tree with same given topology fitted with branch lengths.
 
     """
+    if isinstance(model, str):
+        model = make_model(model)
+
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 

src/piqtree/model/_options.py

@@ -3,7 +3,7 @@
 import functools
 from typing import Literal
 
-from cogent3 import _Table, make_table
+from cogent3.core.table import Table, make_table
 
 from piqtree.model._freq_type import FreqType
 from piqtree.model._rate_type import ALL_BASE_RATE_TYPES, get_description
@@ -40,7 +40,7 @@ def available_models(
     model_type: Literal["dna", "protein"] | None = None,
     *,
     show_all: bool = True,
-) -> _Table:
+) -> Table:
     """Return a table showing available substitution models.
 
     Parameters
@@ -52,7 +52,7 @@ def available_models(
 
     Returns
     -------
-    _Table
+    Table
         Table with all available models.
 
     """
@@ -78,7 +78,7 @@ def available_models(
     return table
 
 
-def available_freq_type() -> _Table:
+def available_freq_type() -> Table:
     """Return a table showing available freq type options."""
     data: dict[str, list[str]] = {"Freq Type": [], "Description": []}
 
@@ -89,7 +89,7 @@ def available_freq_type() -> _Table:
     return make_table(data=data, title="Available frequency types")
 
 
-def available_rate_type() -> _Table:
+def available_rate_type() -> Table:
     """Return a table showing available rate type options."""
     data: dict[str, list[str]] = {"Rate Type": [], "Description": []}
 

tests/test_app/test_app.py

@@ -3,18 +3,18 @@
 from cogent3.core.new_alignment import Alignment
 
 import piqtree
-from piqtree import jc_distances
+from piqtree import jc_distances, make_model
 
 
 def test_piqtree_phylo(four_otu: Alignment) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
-    app = get_app("piqtree_phylo", submod_type="JC")
+    app = get_app("piqtree_phylo", model="JC")
     got = app(four_otu)
     assert expected.same_topology(got)
 
 
 def test_piqtree_phylo_support(four_otu: Alignment) -> None:
-    app = get_app("piqtree_phylo", submod_type="JC", bootstrap_reps=1000)
+    app = get_app("piqtree_phylo", model=make_model("JC"), bootstrap_reps=1000)
     got = app(four_otu)
     supports = [
         node.params.get("support", None)
@@ -28,7 +28,7 @@ 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)
-    piphylo = get_app("piqtree_fit", tree=tree, submod_type="JC")
+    piphylo = get_app("piqtree_fit", tree=tree, model="JC")
     got = piphylo(three_otu)
     assert got.params["lnL"] == pytest.approx(expected.lnL)
 

tests/test_iqtree/test_build_tree.py

@@ -22,6 +22,7 @@ def check_build_tree(
     rate_model: RateModel | None = None,
     *,
     invariant_sites: bool = False,
+    coerce_str: bool = False,
 ) -> None:
     expected = make_tree("(Human,Chimpanzee,(Rhesus,Mouse));")
 
@@ -32,7 +33,11 @@ def check_build_tree(
         rate_model=rate_model,
     )
 
-    got1 = piqtree.build_tree(four_otu, model, rand_seed=1)
+    got1 = piqtree.build_tree(
+        four_otu,
+        str(model) if coerce_str else model,
+        rand_seed=1,
+    )
     got1 = got1.unrooted()
     # Check topology
     assert expected.same_topology(got1.unrooted())
@@ -61,6 +66,11 @@ def test_lie_build_tree(four_otu: Alignment, dna_model: DnaModel) -> None:
     check_build_tree(four_otu, dna_model)
 
 
+@pytest.mark.parametrize("dna_model", list(DnaModel)[-3:])
+def test_str_build_tree(four_otu: Alignment, dna_model: DnaModel) -> None:
+    check_build_tree(four_otu, dna_model, coerce_str=True)
+
+
 @pytest.mark.parametrize("dna_model", list(DnaModel)[:5])
 @pytest.mark.parametrize("invariant_sites", [False, True])
 @pytest.mark.parametrize(

tests/test_iqtree/test_fit_tree.py

@@ -83,14 +83,52 @@ def test_fit_tree(three_otu: Alignment, iq_model: DnaModel, c3_model: str) -> No
     app = get_app("model", c3_model, tree=tree_topology)
     expected = app(three_otu)
 
-    got1 = piqtree.fit_tree(three_otu, tree_topology, Model(iq_model), rand_seed=1)
+    model = Model(iq_model)
+
+    got1 = piqtree.fit_tree(three_otu, tree_topology, model, rand_seed=1)
+    check_likelihood(got1, expected)
+    check_motif_probs(got1, expected.tree)
+    check_rate_parameters(got1, expected.tree)
+    check_branch_lengths(got1, expected.tree)
+
+    # Should be within an approximation for any seed
+    got2 = piqtree.fit_tree(three_otu, tree_topology, model, rand_seed=None)
+    check_likelihood(got2, expected)
+    check_motif_probs(got2, expected.tree)
+    check_rate_parameters(got2, expected.tree)
+    check_branch_lengths(got2, expected.tree)
+
+
+@pytest.mark.parametrize(
+    ("iq_model", "c3_model"),
+    [
+        (DnaModel.JC, "JC69"),
+        (DnaModel.K80, "K80"),
+        (DnaModel.GTR, "GTR"),
+        (DnaModel.TN, "TN93"),
+        (DnaModel.HKY, "HKY85"),
+        (DnaModel.F81, "F81"),
+    ],
+)
+def test_fit_tree_str_model(
+    three_otu: Alignment,
+    iq_model: DnaModel,
+    c3_model: str,
+) -> None:
+    tree_topology = make_tree(tip_names=three_otu.names)
+    app = get_app("model", c3_model, tree=tree_topology)
+    expected = app(three_otu)
+
+    model = str(Model(iq_model))
+
+    got1 = piqtree.fit_tree(three_otu, tree_topology, model, rand_seed=1)
     check_likelihood(got1, expected)
     check_motif_probs(got1, expected.tree)
     check_rate_parameters(got1, expected.tree)
     check_branch_lengths(got1, expected.tree)
 
     # Should be within an approximation for any seed
-    got2 = piqtree.fit_tree(three_otu, tree_topology, Model(iq_model), rand_seed=None)
+    got2 = piqtree.fit_tree(three_otu, tree_topology, model, rand_seed=None)
     check_likelihood(got2, expected)
     check_motif_probs(got2, expected.tree)
     check_rate_parameters(got2, expected.tree)