Bump iqtree2 from 18fa5a3 to ea7a080 (#114) (allows specifying a …

…number of threads #42)

* Bump iqtree2 from `18fa5a3` to `ea7a080`

Bumps [iqtree2](https://github.com/iqtree/iqtree2) from `18fa5a3` to `ea7a080`.
- [Release notes](https://github.com/iqtree/iqtree2/releases)
- [Commits](iqtree/iqtree2@18fa5a3...ea7a080)

---
updated-dependencies:
- dependency-name: iqtree2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>

* MAINT: propogate num_threads to python side

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Robert McArthur <[email protected]>

src/piqtree2/_app/__init__.py

@@ -30,6 +30,7 @@ def __init__(
         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,
@@ -39,6 +40,7 @@ def __init__(
         )
         self._rand_seed = rand_seed
         self._bootstrap_reps = bootstrap_reps
+        self._num_threads = num_threads
 
     def main(
         self,
@@ -49,6 +51,7 @@ def main(
             self._model,
             self._rand_seed,
             bootstrap_replicates=self._bootstrap_reps,
+            num_threads=self._num_threads,
         )
 
 
@@ -63,6 +66,7 @@ def __init__(
         rate_model: str | None = None,
         *,
         rand_seed: int | None = None,
+        num_threads: int | None = None,
         invariant_sites: bool = False,
     ) -> None:
         self._tree = tree
@@ -73,12 +77,19 @@ def __init__(
             freq_type=freq_type,
         )
         self._rand_seed = rand_seed
+        self._num_threads = num_threads
 
     def main(
         self,
         aln: c3_types.AlignedSeqsType,
     ) -> cogent3.PhyloNode | cogent3.app.typing.SerialisableType:
-        return fit_tree(aln, self._tree, self._model, self._rand_seed)
+        return fit_tree(
+            aln,
+            self._tree,
+            self._model,
+            self._rand_seed,
+            self._num_threads,
+        )
 
 
 @composable.define_app

src/piqtree2/_libiqtree/_piqtree2.cpp

@@ -32,7 +32,8 @@ extern string build_tree(vector<string>& names,
                          vector<string>& seqs,
                          string model,
                          int rand_seed = 0,
-                         int bootstrap_rep = 0);
+                         int bootstrap_rep = 0,
+                         int num_thres = 1);
 
 /*
  * Perform phylogenetic analysis on the input alignment
@@ -43,7 +44,8 @@ extern string fit_tree(vector<string>& names,
                        vector<string>& seqs,
                        string model,
                        string intree,
-                       int rand_seed = 0);
+                       int rand_seed = 0,
+                       int num_thres = 1);
 
 /*
  * Perform phylogenetic analysis with ModelFinder
@@ -59,7 +61,8 @@ extern string modelfinder(vector<string>& names,
                           int rand_seed = 0,
                           string model_set = "",
                           string freq_set = "",
-                          string rate_set = "");
+                          string rate_set = "",
+                          int num_thres = 1);
 
 /*
  * Build pairwise JC distance matrix

src/piqtree2/iqtree/_model_finder.py

@@ -88,11 +88,15 @@ def model_finder(
     freq_set: Iterable[str] | None = None,
     rate_set: Iterable[str] | None = None,
     rand_seed: int | None = None,
+    num_threads: int | None = None,
 ) -> ModelFinderResult | c3_types.SerialisableType:
     source = aln.info.source
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
+    if num_threads is None:
+        num_threads = 1
+
     if model_set is None:
         model_set = set()
     if freq_set is None:
@@ -111,6 +115,7 @@ def model_finder(
             ",".join(model_set),
             ",".join(freq_set),
             ",".join(rate_set),
+            num_threads,
         ),
     )
     return ModelFinderResult(raw_data=raw, source=source)

src/piqtree2/iqtree/_tree.py

@@ -199,6 +199,7 @@ def build_tree(
     model: Model,
     rand_seed: int | None = None,
     bootstrap_replicates: int | None = None,
+    num_threads: int | None = None,
 ) -> cogent3.PhyloNode:
     """Reconstruct a phylogenetic tree.
 
@@ -216,6 +217,8 @@ def build_tree(
         The number of bootstrap replicates to perform, by default None.
         If 0 is provided, then no bootstrapping is performed.
         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).
 
     Returns
     -------
@@ -229,11 +232,21 @@ def build_tree(
     if bootstrap_replicates is None:
         bootstrap_replicates = 0
 
+    if num_threads is None:
+        num_threads = 1
+
     names = aln.names
     seqs = [str(seq) for seq in aln.iter_seqs(names)]
 
     yaml_result = yaml.safe_load(
-        iq_build_tree(names, seqs, str(model), rand_seed, bootstrap_replicates),
+        iq_build_tree(
+            names,
+            seqs,
+            str(model),
+            rand_seed,
+            bootstrap_replicates,
+            num_threads,
+        ),
     )
     tree = _process_tree_yaml(yaml_result, names)
 
@@ -249,6 +262,7 @@ def fit_tree(
     tree: cogent3.PhyloNode,
     model: Model,
     rand_seed: int | None = None,
+    num_threads: int | None = None,
 ) -> cogent3.PhyloNode:
     """Fit branch lengths to a tree.
 
@@ -265,6 +279,8 @@ def fit_tree(
         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.
+    num_threads: int | None, optional
+        Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
 
     Returns
     -------
@@ -275,12 +291,15 @@ def fit_tree(
     if rand_seed is None:
         rand_seed = 0  # The default rand_seed in IQ-TREE
 
+    if num_threads is None:
+        num_threads = 1
+
     names = aln.names
     seqs = [str(seq) for seq in aln.iter_seqs(names)]
     newick = str(tree)
 
     yaml_result = yaml.safe_load(
-        iq_fit_tree(names, seqs, str(model), newick, rand_seed),
+        iq_fit_tree(names, seqs, str(model), newick, rand_seed, num_threads),
     )
     tree = _process_tree_yaml(yaml_result, names)
 

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)
-    # internal nodes are now named by default
-    supported_node = tree.get_node_matching_name("node1")
+
+    supported_node = max(tree.children, key=lambda x: len(x.children))
     assert "support" in supported_node.params