Misc changes

build_tools/before_all_mac.sh

@@ -1,4 +1,8 @@
-brew update
+# Check if running in GitHub Actions
+if [ "$GITHUB_ACTIONS" = "true" ]; then
+    brew update
+fi
+
 brew install eigen boost
 
 bash build_tools/build_iqtree.sh

src/piqtree2/_app/__init__.py

@@ -27,6 +27,7 @@ def __init__(
         *,
         invariant_sites: bool = False,
         rand_seed: int | None = None,
+        bootstrap_reps: int | None = None,
     ) -> None:
         self._model = Model(
             substitution_model=substitution_model,
@@ -35,12 +36,15 @@ def __init__(
             freq_type=freq_type,
         )
         self._rand_seed = rand_seed
+        self._bootstrap_reps = bootstrap_reps
 
     def main(
         self,
         aln: cogent3.Alignment | cogent3.ArrayAlignment,
     ) -> cogent3.PhyloNode | cogent3.app.typing.SerialisableType:
-        return build_tree(aln, self._model, self._rand_seed)
+        return build_tree(
+            aln, self._model, self._rand_seed, bootstrap_replicates=self._bootstrap_reps
+        )
 
 
 @composable.define_app

src/piqtree2/iqtree/_tree.py

@@ -189,14 +189,16 @@ def _process_tree_yaml(
 
     _rename_iq_tree(tree, names)
 
+    tree.name_unnamed_nodes()
+
     return tree
 
 
 def build_tree(
     aln: cogent3.Alignment | cogent3.ArrayAlignment,
     model: Model,
     rand_seed: int | None = None,
-    bootstrap_replicates: int = 0,
+    bootstrap_replicates: int | None = 0,
 ) -> cogent3.PhyloNode:
     """Reconstruct a phylogenetic tree.
 
@@ -224,6 +226,9 @@ def build_tree(
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
+    if bootstrap_replicates is None:
+        bootstrap_replicates = 0
+
     names = aln.names
     seqs = [str(seq) for seq in aln.iter_seqs(names)]
 

src/piqtree2/model/_options.py

@@ -35,14 +35,15 @@ def _make_models(model_type: type[SubstitutionModel]) -> dict[str, list[str]]:
     return data
 
 
-def available_models(model_type: str | None = None) -> _Table:
+def available_models(model_type: str | None = None, show_all: bool = True) -> _Table:
     """Return a table showing available substitution models.
 
     Parameters
     ----------
     model_type
         either "nucleotide", "protein" or None. If None, all models are returned.
-
+    show_all
+        if True, the representation of the table shows all records
     """
     template = "Available {}substitution models"
     if model_type == "dna":
@@ -61,6 +62,8 @@ def available_models(model_type: str | None = None) -> _Table:
             title=template.format(""),
         )
 
+    if show_all:
+        table.set_repr_policy(head=table.shape[0])
     return table
 
 

tests/test_app/test_app.py

@@ -12,6 +12,17 @@ def test_piqtree_phylo(four_otu: ArrayAlignment) -> None:
     assert expected.same_topology(got)
 
 
+def test_piqtree_phylo_support(four_otu: ArrayAlignment) -> None:
+    app = get_app("piqtree_phylo", substitution_model="JC", bootstrap_reps=1000)
+    got = app(four_otu)
+    supports = [
+        node.params.get("support", None)
+        for node in got.postorder()
+        if not node.is_tip() and node.name != "root"
+    ]
+    assert all(supports)
+
+
 def test_piqtree_fit(three_otu: ArrayAlignment) -> None:
     tree = make_tree(tip_names=three_otu.names)
     app = get_app("model", "JC69", tree=tree)

tests/test_iqtree/test_build_tree.py

@@ -94,6 +94,6 @@ def test_build_tree_inadequate_bootstrapping(four_otu: ArrayAlignment) -> None:
 
 def test_build_tree_bootstrapping(four_otu: ArrayAlignment) -> None:
     tree = piqtree2.build_tree(four_otu, Model(DnaModel.GTR), bootstrap_replicates=1000)
-    tree.name_unnamed_nodes()
+    # internal nodes are now named by default
     supported_node = tree.get_node_matching_name("node1")
     assert "support" in supported_node.params

tests/test_model/test_options.py

@@ -21,6 +21,12 @@ def test_num_available_models(
     )
     assert total_models > 0
     assert table.shape[0] == total_models
+    assert table._repr_policy["head"] == table.shape[0]
+
+
+def test_num_available_models_not_show_all() -> None:
+    table = available_models(show_all=False)
+    assert table._repr_policy["head"] != table.shape[0]
 
 
 @pytest.mark.parametrize(