Bump iqtree2 from ea7a080 to da38244

src/piqtree2/_app/__init__.py

@@ -104,11 +104,22 @@ def piqtree_random_trees(
 
 
 @composable.define_app
-@extend_docstring_from(jc_distances)
-def piqtree_jc_dists(
-    aln: c3_types.AlignedSeqsType,
-) -> c3_types.PairwiseDistanceType:
-    return jc_distances(aln)
+class piqtree_jc_dists:
+    @extend_docstring_from(jc_distances)
+    def __init__(
+        self,
+        num_threads: int | None = None,
+    ) -> None:
+        self._num_threads = num_threads
+
+    def main(
+        self,
+        aln: c3_types.AlignedSeqsType,
+    ) -> cogent3.PhyloNode | cogent3.app.typing.SerialisableType:
+        return jc_distances(
+            aln,
+            num_threads=self._num_threads,
+        )
 
 
 @composable.define_app

src/piqtree2/_libiqtree/_piqtree2.cpp

@@ -71,7 +71,8 @@ extern string modelfinder(vector<string>& names,
  * j-th sequence, where n is the number of sequences
  */
 extern vector<double> build_distmatrix(vector<string>& names,
-                                       vector<string>& seqs);
+                                       vector<string>& seqs,
+                                       int num_thres);
 
 /*
  * Using Rapid-NJ to build tree from a distance matrix

src/piqtree2/iqtree/_jc_distance.py

@@ -38,22 +38,30 @@ def _dists_to_distmatrix(
 
 def jc_distances(
     aln: c3_types.AlignedSeqsType,
+    num_threads: int | None = None,
 ) -> c3_types.PairwiseDistanceType:
     """Compute pairwise JC distances for a given alignemnt.
 
     Parameters
     ----------
     aln : c3_types.AlignedSeqsType
         alignment to compute pairwise JC distances for.
+    num_threads: int | None, optional
+        Number of threads for IQ-TREE 2 to use, by default None (all available threads).
 
     Returns
     -------
     c3_types.PairwiseDistanceType
         Pairwise JC distance matrix.
 
     """
+    if num_threads is None:
+        num_threads = 0
+
     names = aln.names
     seqs = [str(seq) for seq in aln.iter_seqs(names)]
 
-    distances = np.array(iq_jc_distances(names, seqs)).reshape((len(names), len(names)))
+    distances = np.array(iq_jc_distances(names, seqs, num_threads)).reshape(
+        (len(names), len(names)),
+    )
     return _dists_to_distmatrix(distances, names)

src/piqtree2/iqtree/_tree.py

@@ -219,6 +219,7 @@ def build_tree(
         At least 1000 is required to perform bootstrapping.
     num_threads: int | None, optional
         Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
+        If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
 
     Returns
     -------
@@ -281,6 +282,7 @@ def fit_tree(
         The random seed - 0 or None means no seed, by default None.
     num_threads: int | None, optional
         Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
+        If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
 
     Returns
     -------

tests/test_app/test_app.py

@@ -58,24 +58,24 @@ def test_piqtree_jc_distances(five_otu: ArrayAlignment) -> None:
     dists = app(five_otu)
 
     assert (
-        dists["Human", "Chimpanzee"] < dists["Human", "Dugong"]
+        0 < dists["Human", "Chimpanzee"] < dists["Human", "Dugong"]
     )  # chimpanzee closer than rhesus
     assert (
-        dists["Human", "Rhesus"] < dists["Human", "Manatee"]
+        0 < dists["Human", "Rhesus"] < dists["Human", "Manatee"]
     )  # rhesus closer than manatee
     assert (
-        dists["Human", "Rhesus"] < dists["Human", "Dugong"]
+        0 < dists["Human", "Rhesus"] < dists["Human", "Dugong"]
     )  # rhesus closer than dugong
 
     assert (
-        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Manatee"]
+        0 < dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Manatee"]
     )  # rhesus closer than manatee
     assert (
-        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Dugong"]
+        0 < dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Dugong"]
     )  # rhesus closer than dugong
 
     assert (
-        dists["Manatee", "Dugong"] < dists["Manatee", "Rhesus"]
+        0 < dists["Manatee", "Dugong"] < dists["Manatee", "Rhesus"]
     )  # dugong closer than rhesus
 
 

tests/test_iqtree/test_distance.py

@@ -7,22 +7,22 @@ def test_jc_distance(five_otu: ArrayAlignment) -> None:
     dists = jc_distances(five_otu)
 
     assert (
-        dists["Human", "Chimpanzee"] < dists["Human", "Dugong"]
+        0 < dists["Human", "Chimpanzee"] < dists["Human", "Dugong"]
     )  # chimpanzee closer than rhesus
     assert (
-        dists["Human", "Rhesus"] < dists["Human", "Manatee"]
+        0 < dists["Human", "Rhesus"] < dists["Human", "Manatee"]
     )  # rhesus closer than manatee
     assert (
-        dists["Human", "Rhesus"] < dists["Human", "Dugong"]
+        0 < dists["Human", "Rhesus"] < dists["Human", "Dugong"]
     )  # rhesus closer than dugong
 
     assert (
-        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Manatee"]
+        0 < dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Manatee"]
     )  # rhesus closer than manatee
     assert (
-        dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Dugong"]
+        0 < dists["Chimpanzee", "Rhesus"] < dists["Chimpanzee", "Dugong"]
     )  # rhesus closer than dugong
 
     assert (
-        dists["Manatee", "Dugong"] < dists["Manatee", "Rhesus"]
+        0 < dists["Manatee", "Dugong"] < dists["Manatee", "Rhesus"]
     )  # dugong closer than rhesus