From 8e99db34ab4e6b9b73423b748bc76774df8a5aa8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 19 Mar 2025 06:39:33 +0000
Subject: [PATCH 01/44] Bump iqtree2 from `1320c4c` to `39cbee5`

Bumps [iqtree2](https://github.com/iqtree/iqtree2) from `1320c4c` to `39cbee5`.
- [Release notes](https://github.com/iqtree/iqtree2/releases)
- [Commits](https://github.com/iqtree/iqtree2/compare/1320c4cc360bbacacc592911459aaa06cd4a7961...39cbee547c4bfc6d2e78f063b4beb9095e15f812)

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

Signed-off-by: dependabot[bot] <support@github.com>
---
 iqtree2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iqtree2 b/iqtree2
index 1320c4c..39cbee5 160000
--- a/iqtree2
+++ b/iqtree2
@@ -1 +1 @@
-Subproject commit 1320c4cc360bbacacc592911459aaa06cd4a7961
+Subproject commit 39cbee547c4bfc6d2e78f063b4beb9095e15f812

From 6911d6a28c2116a326f075ce31932a416c8653e5 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:14:59 +1100
Subject: [PATCH 02/44] DEV: ignore dll files

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index 87df248..0ea37ac 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,9 @@
 
 # piqtree specific ignores
 src/piqtree/_libiqtree/**/*.a
+src/piqtree/_libiqtree/**/*.dll
+src/piqtree/_libiqtree/**/*.lib
+src/*.dll
 
 # docs
 data

From 52dab316bdcd14bdf96f02722677ac3e4296333e Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:16:40 +1100
Subject: [PATCH 03/44] DEV: update libiqtree function signatures and add
 custom type convertors for structs

---
 src/piqtree/_libiqtree/_piqtree.cpp | 158 ++++++++++++++--------------
 src/piqtree/_libiqtree/_piqtree.h   | 113 ++++++++++++++++++++
 2 files changed, 194 insertions(+), 77 deletions(-)
 create mode 100644 src/piqtree/_libiqtree/_piqtree.h

diff --git a/src/piqtree/_libiqtree/_piqtree.cpp b/src/piqtree/_libiqtree/_piqtree.cpp
index 52210fe..52697f8 100644
--- a/src/piqtree/_libiqtree/_piqtree.cpp
+++ b/src/piqtree/_libiqtree/_piqtree.cpp
@@ -1,3 +1,5 @@
+#include "_piqtree.h"
+#include <pybind11/numpy.h>
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 #include <iostream>
@@ -8,82 +10,84 @@ using namespace std;
 
 namespace py = pybind11;
 
-/*
- * Calculates the robinson fould distance between two trees
- */
-extern int robinson_fould(const string& tree1, const string& tree2);
-
-/*
- * Generates a set of random phylogenetic trees
- * tree_gen_mode allows:"YULE_HARDING", "UNIFORM", "CATERPILLAR", "BALANCED",
- * "BIRTH_DEATH", "STAR_TREE" output: a newick tree (in string format)
- */
-extern string random_tree(int num_taxa,
-                          string tree_gen_mode,
-                          int num_trees,
-                          int rand_seed = 0);
-
-/*
- * Perform phylogenetic analysis on the input alignment
- * With estimation of the best topology
- * output: results in YAML format with the tree and the details of parameters
- */
-extern string build_tree(vector<string>& names,
-                         vector<string>& seqs,
-                         string model,
-                         int rand_seed = 0,
-                         int bootstrap_rep = 0,
-                         int num_thres = 1);
-
-/*
- * Perform phylogenetic analysis on the input alignment
- * With restriction to the input toplogy
- * output: results in YAML format with the details of parameters
- */
-extern string fit_tree(vector<string>& names,
-                       vector<string>& seqs,
-                       string model,
-                       string intree,
-                       int rand_seed = 0,
-                       int num_thres = 1);
-
-/*
- * Perform phylogenetic analysis with ModelFinder
- * on the input alignment (in string format)
- * model_set -- a set of models to consider
- * freq_set -- a set of frequency types
- * rate_set -- a set of RHAS models
- * rand_seed -- random seed, if 0, then will generate a new random seed
- * output: modelfinder results in YAML format
- */
-extern string modelfinder(vector<string>& names,
-                          vector<string>& seqs,
-                          int rand_seed = 0,
-                          string model_set = "",
-                          string freq_set = "",
-                          string rate_set = "",
-                          int num_thres = 1);
-
-/*
- * Build pairwise JC distance matrix
- * output: set of distances
- * (n * i + j)-th element of the list represents the distance between i-th and
- * j-th sequence, where n is the number of sequences
- */
-extern vector<double> build_distmatrix(vector<string>& names,
-                                       vector<string>& seqs,
-                                       int num_thres);
-
-/*
- * Using Rapid-NJ to build tree from a distance matrix
- * output: a newick tree (in string format)
- */
-extern string build_njtree(vector<string>& names, vector<double>& distances);
-
-/*
- * verion number
- */
-extern string version();
+namespace PYBIND11_NAMESPACE {
+namespace detail {
+template <>
+struct type_caster<StringArray> {
+ public:
+  PYBIND11_TYPE_CASTER(StringArray, const_name("StringArray"));
+
+  // Conversion from Python to C++
+  bool load(handle src, bool) {
+    /* Extract PyObject from handle */
+    PyObject* source = src.ptr();
+    if (!py::isinstance<py::sequence>(source)) {
+      return false;
+    }
+
+    auto seq = reinterpret_borrow<py::sequence>(src);
+    value.length = seq.size();
+
+    tmpStrings.reserve(value.length);
+    tmpCStrs.reserve(value.length);
+
+    for (size_t i = 0; i < seq.size(); ++i) {
+      auto item = seq[i];
+      if (!py::isinstance<py::str>(item)) {
+        return false;
+      }
+
+      tmpStrings.push_back(item.cast<std::string>());
+      tmpCStrs.push_back(tmpStrings[i].c_str());
+    }
+
+    value.strings = tmpCStrs.data();
+
+    return true;
+  }
+
+  // Conversion from C++ to Python
+  static handle cast(StringArray src, return_value_policy, handle) {
+    throw std::runtime_error("Unsupported operation");
+  }
+
+ private:
+  vector<string> tmpStrings;
+  vector<const char*> tmpCStrs;
+};
+
+template <>
+struct type_caster<DoubleArray> {
+ public:
+  PYBIND11_TYPE_CASTER(DoubleArray, _("DoubleArray"));
+
+  // Conversion from Python to C++
+  bool load(handle src, bool) {
+    if (!py::isinstance<py::array_t<double>>(src)) {
+      return false;  // Only accept numpy arrays of float64
+    }
+
+    auto arr = py::cast<py::array_t<double>>(src);
+    if (arr.ndim() != 1) {
+      return false;  // Only accept 1D arrays
+    }
+
+    value.length = arr.size();
+    value.doubles = new double[value.length];
+    std::memcpy(value.doubles, arr.data(), value.length * sizeof(double));
+    return true;
+  }
+
+  // Conversion from C++ to Python
+  static handle cast(DoubleArray src, return_value_policy, handle) {
+    auto result = py::array_t<double>(src.length);
+    std::memcpy(result.mutable_data(), src.doubles,
+                src.length * sizeof(double));
+    return result.release();
+  }
+};
+}  // namespace detail
+}  // namespace PYBIND11_NAMESPACE
 
 int mine() {
   return 42;
@@ -112,5 +116,5 @@ PYBIND11_MODULE(_piqtree, m) {
         "Construct pairwise distance matrix for alignment.");
   m.def("iq_nj_tree", &build_njtree,
         "Build neighbour-joining tree from distance matrix.");
-  m.def("mine", &mine, "The meaning of life, the universe (and everything)!");
+  m.def("mine", &mine, "The meaning of life, the universe (and everything) !");
 }
diff --git a/src/piqtree/_libiqtree/_piqtree.h b/src/piqtree/_libiqtree/_piqtree.h
new file mode 100644
index 0000000..ed77708
--- /dev/null
+++ b/src/piqtree/_libiqtree/_piqtree.h
@@ -0,0 +1,113 @@
+#ifndef _PIQTREE_H
+#define _PIQTREE_H
+
+using namespace std;
+
+#ifdef _MSC_VER
+#pragma pack(push, 1)
+#else
+#pragma pack(1)
+#endif
+
+typedef struct {
+  const char** strings;
+  size_t length;
+} StringArray;
+
+typedef struct {
+  double* doubles;
+  size_t length;
+} DoubleArray;
+
+#ifdef _MSC_VER
+#pragma pack(pop)
+#else
+#pragma pack()
+#endif
+
+/*
+ * Calculates the robinson fould distance between two trees
+ */
+extern "C" int robinson_fould(const char* ctree1, const char* ctree2);
+
+/*
+ * Generates a set of random phylogenetic trees
+ * tree_gen_mode allows:"YULE_HARDING", "UNIFORM", "CATERPILLAR", "BALANCED",
+ * "BIRTH_DEATH", "STAR_TREE" output: a newick tree (in string format)
+ */
+extern "C" char* random_tree(int num_taxa,
+                             const char* tree_gen_mode,
+                             int num_trees,
+                             int rand_seed = 0);
+
+/*
+ * Perform phylogenetic analysis on the input alignment
+ * With estimation of the best topology
+ * num_thres -- number of cpu threads to be used, default: 1; 0 - auto detection
+ * of the optimal number of cpu threads output: results in YAML format with the
+ * tree and the details of parameters
+ */
+extern "C" char* build_tree(StringArray& names,
+                            StringArray& seqs,
+                            const char* model,
+                            int rand_seed = 0,
+                            int bootstrap_rep = 0,
+                            int num_thres = 1);
+
+/*
+ * Perform phylogenetic analysis on the input alignment
+ * With restriction to the input toplogy
+ * num_thres -- number of cpu threads to be used, default: 1; 0 - auto detection
+ * of the optimal number of cpu threads output: results in YAML format with the
+ * details of parameters
+ */
+extern "C" char* fit_tree(StringArray& names,
+                          StringArray& seqs,
+                          const char* model,
+                          const char* intree,
+                          int rand_seed = 0,
+                          int num_thres = 1);
+
+/*
+ * Perform phylogenetic analysis with ModelFinder
+ * on the input alignment (in string format)
+ * model_set -- a set of models to consider
+ * freq_set -- a set of frequency types
+ * rate_set -- a set of RHAS models
+ * rand_seed -- random seed, if 0, then will generate a new random seed
+ * num_thres -- number of cpu threads to be used, default: 1; 0 - auto detection
+ * of the optimal number of cpu threads output: modelfinder results in YAML
+ * format
+ */
+extern "C" char* modelfinder(StringArray& names,
+                             StringArray& seqs,
+                             int rand_seed = 0,
+                             const char* model_set = "",
+                             const char* freq_set = "",
+                             const char* rate_set = "",
+                             int num_thres = 1);
+
+/*
+ * Build pairwise JC distance matrix
+ * output: set of distances
+ * (n * i + j)-th element of the list represents the distance between i-th and
+ * j-th sequence, where n is the number of sequences num_thres -- number of cpu
+ * threads to be used, default: 1; 0 - use all available cpu threads on the
+ * machine
+ */
+extern "C" DoubleArray build_distmatrix(StringArray& names,
+                                        StringArray& seqs,
+                                        int num_thres = 1);
+
+/*
+ * Using Rapid-NJ to build tree from a distance matrix
+ * output: a newick tree (in string format)
+ */
+extern "C" char* build_njtree(StringArray& names, DoubleArray& distances);
+
+/*
+ * verion number
+ */
+extern "C" char* version();
+
+#endif /* LIBIQTREE2_FUN */

From 971bb3ecab355f66aa31fa545584e132e95e06ab Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:17:48 +1100
Subject: [PATCH 04/44] DEV: ensure DLLs are included in build on windows

---
 pyproject.toml          |  7 +++-
 setup.py                | 80 ++++++++++++++++++++++++++++++++---------
 src/piqtree/__init__.py | 13 +++++++
 3 files changed, 82 insertions(+), 18 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 28f4cb7..1987151 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 61.0", "pybind11 >= 2.12"]
+requires = ["setuptools >= 61.0", "pybind11 >= 2.12", "delvewheel >= 1.10"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -152,6 +152,11 @@ dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 "src/piqtree/_app/__init__.py" = [
     "N801", # apps follow function naming convention
 ]
+"src/piqtree/__init__.py" = [
+    "E402", # handle DLLs before imports
+    "PTH118", # os operations for DLL path
+    "PTH120", # os operations for DLL path
+]
 "src/piqtree/model/_substitution_model.py" = ["N815"] # use IQ-TREE naming scheme
 
 [tool.ruff.format]
diff --git a/setup.py b/setup.py
index fcd22a3..62a6b4c 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,8 @@
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 from setuptools import setup
 
-LIBRARY_DIR = "src/piqtree/_libiqtree"
+LIBRARY_DIR = "src/piqtree/_libiqtree/"
+IQTREE_LIB_NAME = "iqtree2"
 
 
 def get_brew_prefix(package: str) -> Path:
@@ -18,7 +19,36 @@ def get_brew_prefix(package: str) -> Path:
     )
 
 
-if platform.system() == "Darwin":
+extra_libs = []
+extra_compile_args = []
+include_dirs = []
+library_dirs = []
+
+
+def include_dlls() -> None:
+    import shutil
+
+    from delvewheel._dll_utils import get_all_needed
+
+    needed_dll_paths, _, _, _ = get_all_needed(
+        LIBRARY_DIR + f"{IQTREE_LIB_NAME}.dll",
+        set(),
+        None,
+        "raise",
+        False,  # noqa: FBT003
+        False,  # noqa: FBT003
+        0,
+    )
+
+    for dll_path in needed_dll_paths:
+        shutil.copy(dll_path, LIBRARY_DIR)
+
+
+def setup_windows() -> None:
+    include_dlls()
+
+
+def setup_macos() -> None:
     brew_prefix_llvm = get_brew_prefix("llvm")
     brew_prefix_libomp = get_brew_prefix("libomp")
 
@@ -27,20 +57,34 @@ def get_brew_prefix(package: str) -> Path:
     os.environ["CXX"] = str(brew_prefix_llvm / "bin" / "clang++")
 
     # Define OpenMP flags and libraries for macOS
-    openmp_flags = ["-Xpreprocessor", "-fopenmp"]
-    openmp_libs = ["omp"]
+    extra_compile_args.extend(["-Xpreprocessor", "-fopenmp"])
+    extra_libs.extend(["z", "omp"])
 
     # Use the paths from Homebrew for libomp
-    openmp_include = str(brew_prefix_libomp / "include")
-    library_dirs = [
-        str(brew_prefix_libomp / "lib"),
-        str(brew_prefix_llvm / "lib"),
-    ]
-else:
-    openmp_flags = ["-fopenmp"]
-    openmp_libs = ["gomp"]
-    openmp_include = None
-    library_dirs = []
+    include_dirs.extend([str(brew_prefix_libomp / "include")])
+    library_dirs.extend(
+        [
+            str(brew_prefix_libomp / "lib"),
+            str(brew_prefix_llvm / "lib"),
+        ],
+    )
+
+
+def setup_linux() -> None:
+    extra_compile_args.extend(["-fopenmp"])
+    extra_libs.extend(["z", "gomp"])
+
+
+match system := platform.system():
+    case "Windows":
+        setup_windows()
+    case "Darwin":
+        setup_macos()
+    case "Linux":
+        setup_linux()
+    case _:
+        msg = f"Unsupported platform: {system}"
+        raise ValueError(msg)
 
 ext_modules = [
     Pybind11Extension(
@@ -50,14 +94,16 @@ def get_brew_prefix(package: str) -> Path:
             *library_dirs,
             LIBRARY_DIR,
         ],
-        libraries=["iqtree2", "z", *openmp_libs],
-        extra_compile_args=openmp_flags,
-        include_dirs=[openmp_include] if openmp_include else [],
+        libraries=[IQTREE_LIB_NAME, *extra_libs],
+        extra_compile_args=extra_compile_args,
+        include_dirs=include_dirs,
     ),
 ]
 
 setup(
+    name="piqtree",
     ext_modules=ext_modules,
     cmdclass={"build_ext": build_ext},
     zip_safe=False,
+    package_data={"piqtree": ["_libiqtree/*.dll"]},
 )
diff --git a/src/piqtree/__init__.py b/src/piqtree/__init__.py
index 5461c95..d5392db 100644
--- a/src/piqtree/__init__.py
+++ b/src/piqtree/__init__.py
@@ -1,5 +1,18 @@
 """piqtree - access the power of IQ-TREE within Python."""
 
+
+def _add_dll_path() -> None:
+    import os
+
+    if "add_dll_directory" in dir(os):
+        dll_folder = os.path.join(os.path.dirname(__file__), "_libiqtree")
+        os.add_dll_directory(dll_folder)
+
+
+_add_dll_path()
+del _add_dll_path
+
+
 from _piqtree import __iqtree_version__
 
 from piqtree._data import dataset_names, download_dataset

From 4af4b53802a56336e5c4c9150f4c24ac9d2c83ee Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:18:25 +1100
Subject: [PATCH 05/44] BUG: on windows, change out of tmp directory before
 cleaning up

---
 src/piqtree/iqtree/_decorator.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/piqtree/iqtree/_decorator.py b/src/piqtree/iqtree/_decorator.py
index d7f4fd6..4d59e10 100644
--- a/src/piqtree/iqtree/_decorator.py
+++ b/src/piqtree/iqtree/_decorator.py
@@ -84,7 +84,7 @@ def wrapper_iqtree_func(*args: Param.args, **kwargs: Param.kwargs) -> RetType:
             os.close(devnull_fd)
 
             if hide_files:
-                tempdir.cleanup()
                 os.chdir(original_dir)
+                tempdir.cleanup()
 
     return wrapper_iqtree_func

From 48dcde49fcc0eb699a0ac69dd0e0b0e2d3a79014 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:18:56 +1100
Subject: [PATCH 06/44] TST: skip tests which throw error on IQ-TREE side on
 windows

---
 tests/test_iqtree/test_build_tree.py         |  5 +++++
 tests/test_iqtree/test_random_trees.py       |  6 ++++++
 tests/test_iqtree/test_segmentation_fault.py | 14 ++++++++++++++
 3 files changed, 25 insertions(+)

diff --git a/tests/test_iqtree/test_build_tree.py b/tests/test_iqtree/test_build_tree.py
index 90cbf8a..d8232d1 100644
--- a/tests/test_iqtree/test_build_tree.py
+++ b/tests/test_iqtree/test_build_tree.py
@@ -1,3 +1,4 @@
+import platform
 import re
 
 import pytest
@@ -87,6 +88,10 @@ def test_rate_model_build_tree(
     )
 
 
+@pytest.mark.skipif(
+    platform.system() == "Windows",
+    reason="IQ-TREE errors can't be caught yet on Windows",
+)
 def test_build_tree_inadequate_bootstrapping(four_otu: ArrayAlignment) -> None:
     with pytest.raises(IqTreeError, match=re.escape("#replicates must be >= 1000")):
         piqtree.build_tree(four_otu, Model(DnaModel.GTR), bootstrap_replicates=10)
diff --git a/tests/test_iqtree/test_random_trees.py b/tests/test_iqtree/test_random_trees.py
index 60c09ce..82ce8f4 100644
--- a/tests/test_iqtree/test_random_trees.py
+++ b/tests/test_iqtree/test_random_trees.py
@@ -1,3 +1,5 @@
+import platform
+
 import pytest
 
 import piqtree
@@ -45,6 +47,10 @@ def test_random_trees_no_seed(
 
 @pytest.mark.parametrize("num_taxa", [-1, 0, 1, 2])
 @pytest.mark.parametrize("tree_mode", list(piqtree.TreeGenMode))
+@pytest.mark.skipif(
+    platform.system() == "Windows",
+    reason="IQ-TREE errors can't be caught yet on Windows",
+)
 def test_invalid_taxa(
     num_taxa: int,
     tree_mode: piqtree.TreeGenMode,
diff --git a/tests/test_iqtree/test_segmentation_fault.py b/tests/test_iqtree/test_segmentation_fault.py
index 701cc40..1fb5857 100644
--- a/tests/test_iqtree/test_segmentation_fault.py
+++ b/tests/test_iqtree/test_segmentation_fault.py
@@ -1,5 +1,7 @@
 """Test combinations of calls which under previous versions resulted in a segmentation fault."""
 
+import platform
+
 import pytest
 from cogent3 import make_aligned_seqs, make_tree
 
@@ -8,6 +10,10 @@
 from piqtree.model import DiscreteGammaModel, DnaModel, FreeRateModel, Model
 
 
+@pytest.mark.skipif(
+    platform.system() == "Windows",
+    reason="IQ-TREE errors can't be caught yet on Windows",
+)
 def test_two_build_random_trees() -> None:
     """
     Calling build tree twice followed by random trees with a bad input
@@ -22,6 +28,10 @@ def test_two_build_random_trees() -> None:
         random_trees(3, 2, TreeGenMode.BALANCED, 1)
 
 
+@pytest.mark.skipif(
+    platform.system() == "Windows",
+    reason="IQ-TREE errors can't be caught yet on Windows",
+)
 def test_two_fit_random_trees() -> None:
     """
     Calling fit tree twice followed by random trees with a bad input
@@ -39,6 +49,10 @@ def test_two_fit_random_trees() -> None:
 
 @pytest.mark.parametrize("rate_model_class", [DiscreteGammaModel, FreeRateModel])
 @pytest.mark.parametrize("categories", [0, -4])
+@pytest.mark.skipif(
+    platform.system() == "Windows",
+    reason="IQ-TREE errors can't be caught yet on Windows",
+)
 def test_two_invalid_models(
     rate_model_class: type[DiscreteGammaModel] | type[FreeRateModel],
     categories: int,

From b2273f67bf45aaff0f3db9b5c4ef922929538e2f Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:21:38 +1100
Subject: [PATCH 07/44] ENH: include cstddef for other platforms

---
 src/piqtree/_libiqtree/_piqtree.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/piqtree/_libiqtree/_piqtree.h b/src/piqtree/_libiqtree/_piqtree.h
index ed77708..070c621 100644
--- a/src/piqtree/_libiqtree/_piqtree.h
+++ b/src/piqtree/_libiqtree/_piqtree.h
@@ -1,6 +1,8 @@
 #ifndef _PIQTREE_H
 #define _PIQTREE_H
 
+#include <cstddef>
+
 using namespace std;
 
 #ifdef _MSC_VER

From fbe6bba6c8fdaf54f8e26b207296494d0aa1b2d6 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Wed, 19 Mar 2025 18:25:48 +1100
Subject: [PATCH 08/44] MAINT: ignore attr-defined typing error for non-windows

---
 src/piqtree/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/piqtree/__init__.py b/src/piqtree/__init__.py
index d5392db..5a91c95 100644
--- a/src/piqtree/__init__.py
+++ b/src/piqtree/__init__.py
@@ -6,7 +6,7 @@ def _add_dll_path() -> None:
 
     if "add_dll_directory" in dir(os):
         dll_folder = os.path.join(os.path.dirname(__file__), "_libiqtree")
-        os.add_dll_directory(dll_folder)
+        os.add_dll_directory(dll_folder)  # type: ignore[attr-defined]
 
 
 _add_dll_path()

From e814a74172dc15552f6e429a159368c073ff20a5 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:06:34 +1100
Subject: [PATCH 09/44] DEV: add windows build scripts

---
 build_tools/before_all_windows.sh | 10 ++++++++++
 build_tools/build_iqtree.sh       | 19 +++++++++++++++++--
 2 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 build_tools/before_all_windows.sh

diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
new file mode 100644
index 0000000..4eac69f
--- /dev/null
+++ b/build_tools/before_all_windows.sh
@@ -0,0 +1,10 @@
+# Install dependencies using choco
+choco install -y llvm eigen boost libomp make
+
+# Set environment variables for LLVM
+export CMAKE_C_COMPILER="clang"
+export CMAKE_CXX_COMPILER="clang++"
+export CMAKE_MAKE_PROGRAM="make"
+
+# Build IQ-TREE
+bash build_tools/build_iqtree.sh
\ No newline at end of file
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index 38bb7af..e504878 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -9,11 +9,26 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
     echo $CXXFLAGS    
     cmake -DBUILD_LIB=ON -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
     gmake -j
+elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
+    echo "Building for Windows."
+    cmake -G "MinGW Makefiles" \
+        -DCMAKE_C_COMPILER=$CMAKE_C_COMPILER \
+        -DCMAKE_CXX_COMPILER=$CMAKE_CXX_COMPILER \
+        -DCMAKE_MAKE_PROGRAM=$CMAKE_MAKE_PROGRAM \
+        -DBUILD_LIB=ON \
+        ..
+    make -j
 else
-    echo "Building for linux."
+    echo "Building for Linux."
     cmake -DBUILD_LIB=ON ..
     make -j
 fi
 
 cd ../..
-mv iqtree2/build/libiqtree2.a src/piqtree/_libiqtree/
\ No newline at end of file
+
+if [[ "$OSTYPE" == "darwin"* || "$OSTYPE" == "linux"* ]]; then
+    mv iqtree2/build/libiqtree2.a src/piqtree/_libiqtree/
+elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
+    mv iqtree2/build/iqtree2.lib src/piqtree/_libiqtree/
+    mv iqtree2/build/iqtree2.dll src/piqtree/_libiqtree/
+fi

From 40196d3d75468648f80b729d5fbabfd5c46b55fa Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:07:41 +1100
Subject: [PATCH 10/44] DEV: build windows when building iqtree and cache
 correct files.

---
 .github/actions/build-iqtree/action.yml | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 6ce0372..d0fc1b7 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -23,7 +23,8 @@ runs:
       id: cache
       with:
         key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
-        path: src/piqtree/_libiqtree/libiqtree2.a
+        path: |
+          ${{ inputs.os == 'windows-latest' && 'src/piqtree/_libiqtree/iqtree2.lib\nsrc/piqtree/_libiqtree/iqtree2.dll' || 'src/piqtree/_libiqtree/libiqtree2.a' }}
         lookup-only: true
 
     - name: Build IQ-TREE
@@ -31,7 +32,12 @@ runs:
       if: steps.cache.outputs.cache-hit != 'true'
       run: |
         if [[ "${{ inputs.os }}" == "ubuntu-latest" ]]; then
-        sudo ./build_tools/before_all_linux.sh
+          sudo ./build_tools/before_all_linux.sh
+        elif [[ "${{ inputs.os }}" == "macOS-latest" ]]; then
+          ./build_tools/before_all_mac.sh
+        elif [[ "${{ inputs.os }}" == "windows-latest" ]]; then
+          ./build_tools/before_all_windows.sh
         else
-        ./build_tools/before_all_mac.sh
-        fi
+          echo "Unrecognized OS: '${{ inputs.os }}'."
+          exit 1
+        fi
\ No newline at end of file

From 5e65f8a304e6a2da5ce54855829b79847b88f12b Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:07:52 +1100
Subject: [PATCH 11/44] DEV: test build process on windows

---
 .github/workflows/ci.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 71e763b..e795b24 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,7 +13,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
+        os: [windows-latest]
+        # os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
 
     steps:
       - uses: "actions/checkout@v4"

From 29f586f64e211b36eeee5b3904a5ed5b739e2909 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:17:25 +1100
Subject: [PATCH 12/44] DEV: install boost through action on windows, remove
 non-available choco packages

---
 .github/actions/build-iqtree/action.yml | 9 +++++++++
 build_tools/before_all_windows.sh       | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index d0fc1b7..23c8e6f 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -27,6 +27,15 @@ runs:
           ${{ inputs.os == 'windows-latest' && 'src/piqtree/_libiqtree/iqtree2.lib\nsrc/piqtree/_libiqtree/iqtree2.dll' || 'src/piqtree/_libiqtree/libiqtree2.a' }}
         lookup-only: true
 
+    - name: Install Boost
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      uses: MarkusJx/install-boost@v2.4.5
+      id: install-boost
+      with:
+        boost_version: 1.84.0
+        platform_version: 2022
+        toolset: mingw
+
     - name: Build IQ-TREE
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'
diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 4eac69f..6cff446 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,5 +1,5 @@
 # Install dependencies using choco
-choco install -y llvm eigen boost libomp make
+choco install -y llvm eigen make
 
 # Set environment variables for LLVM
 export CMAKE_C_COMPILER="clang"

From 6d7cf298e2185a9f4bde73e7b305a17af83ca95e Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:27:12 +1100
Subject: [PATCH 13/44] DEV: set boost env variables

---
 .github/actions/build-iqtree/action.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 23c8e6f..5e03685 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -36,6 +36,13 @@ runs:
         platform_version: 2022
         toolset: mingw
 
+    - name: Set Boost Environment Variables
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+        echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+
     - name: Build IQ-TREE
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'

From 7792886b3df7160aaff4c7b3065a8925481b7974 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:33:27 +1100
Subject: [PATCH 14/44] DEV: debug boost env vars

---
 .github/actions/build-iqtree/action.yml | 9 +++++++++
 build_tools/before_all_windows.sh       | 5 +++++
 build_tools/build_iqtree.sh             | 5 +++++
 3 files changed, 19 insertions(+)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 5e03685..e016c0c 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -42,6 +42,15 @@ runs:
       run: |
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+    
+    - name: Debug Boost Variables
+      if: runner.os == 'Windows'
+      shell: bash
+      run: |
+        echo "BOOST_ROOT=$BOOST_ROOT"
+        echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
+        echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
+        echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
 
     - name: Build IQ-TREE
       shell: bash
diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 6cff446..8bf7885 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,3 +1,8 @@
+echo "BOOST_ROOT=$BOOST_ROOT"
+echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
+echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
+echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
+
 # Install dependencies using choco
 choco install -y llvm eigen make
 
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index e504878..6ae2ee8 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -1,3 +1,8 @@
+echo "BOOST_ROOT=$BOOST_ROOT"
+echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
+echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
+echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
+
 cd iqtree2
 rm -rf build
 mkdir build && cd build

From 14cef0a7bec4b321c1c6cada59eda8433afe5262 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:42:52 +1100
Subject: [PATCH 15/44] DEV: removed path debugs, manually specify boost dirs

---
 .github/actions/build-iqtree/action.yml | 9 ---------
 build_tools/before_all_windows.sh       | 5 -----
 build_tools/build_iqtree.sh             | 7 ++-----
 3 files changed, 2 insertions(+), 19 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index e016c0c..5e03685 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -42,15 +42,6 @@ runs:
       run: |
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
-    
-    - name: Debug Boost Variables
-      if: runner.os == 'Windows'
-      shell: bash
-      run: |
-        echo "BOOST_ROOT=$BOOST_ROOT"
-        echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
-        echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
-        echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
 
     - name: Build IQ-TREE
       shell: bash
diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 8bf7885..6cff446 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,8 +1,3 @@
-echo "BOOST_ROOT=$BOOST_ROOT"
-echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
-echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
-echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
-
 # Install dependencies using choco
 choco install -y llvm eigen make
 
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index 6ae2ee8..d1d882c 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -1,8 +1,3 @@
-echo "BOOST_ROOT=$BOOST_ROOT"
-echo "Boost_INCLUDE_DIR=$Boost_INCLUDE_DIR"
-echo "Boost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS"
-echo "CMAKE_PREFIX_PATH=$CMAKE_PREFIX_PATH"
-
 cd iqtree2
 rm -rf build
 mkdir build && cd build
@@ -20,6 +15,8 @@ elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
         -DCMAKE_C_COMPILER=$CMAKE_C_COMPILER \
         -DCMAKE_CXX_COMPILER=$CMAKE_CXX_COMPILER \
         -DCMAKE_MAKE_PROGRAM=$CMAKE_MAKE_PROGRAM \
+        -DBoost_INCLUDE_DIR=$Boost_INCLUDE_DIR \
+        -DBoost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS \
         -DBUILD_LIB=ON \
         ..
     make -j

From d570951d78982ab0f680b19b13102e5c8c3fe294 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 14:50:42 +1100
Subject: [PATCH 16/44] DEV: manually specify toolchain, downgrade llvm

---
 build_tools/before_all_windows.sh | 8 ++------
 build_tools/build_iqtree.sh       | 9 ++++++---
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 6cff446..763d3b2 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,10 +1,6 @@
 # Install dependencies using choco
-choco install -y llvm eigen make
-
-# Set environment variables for LLVM
-export CMAKE_C_COMPILER="clang"
-export CMAKE_CXX_COMPILER="clang++"
-export CMAKE_MAKE_PROGRAM="make"
+choco install -y llvm --version=14.0.6 --allow-downgrade
+choco install -y eigen 
 
 # Build IQ-TREE
 bash build_tools/build_iqtree.sh
\ No newline at end of file
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index d1d882c..60a36af 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -12,11 +12,14 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
 elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
     echo "Building for Windows."
     cmake -G "MinGW Makefiles" \
-        -DCMAKE_C_COMPILER=$CMAKE_C_COMPILER \
-        -DCMAKE_CXX_COMPILER=$CMAKE_CXX_COMPILER \
-        -DCMAKE_MAKE_PROGRAM=$CMAKE_MAKE_PROGRAM \
+        -DCMAKE_C_COMPILER=clang \
+        -DCMAKE_CXX_COMPILER=clang++ \
+        -DCMAKE_C_FLAGS=--target=x86_64-pc-windows-gnu \
+        -DCMAKE_CXX_FLAGS=--target=x86_64-pc-windows-gnu \
+        -DCMAKE_MAKE_PROGRAM=mingw32-make \
         -DBoost_INCLUDE_DIR=$Boost_INCLUDE_DIR \
         -DBoost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS \
+        -DIQTREE_FLAGS="cpp14" \
         -DBUILD_LIB=ON \
         ..
     make -j

From fca8540924b618a30654d5a0a9d0e783cbd7f5c6 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:07:32 +1100
Subject: [PATCH 17/44] DEV: add lib.exe to path

---
 .github/actions/build-iqtree/action.yml | 17 +++++++++++++++++
 .github/workflows/ci.yml                |  3 ++-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 5e03685..da23170 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -43,6 +43,23 @@ runs:
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
 
+    - name: Set Up MSVC for lib.exe
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        MSVC_BIN_PATH="C:\\Program Files\\Microsoft Visual Studio\\2022\\BuildTools\\VC\\Tools\\MSVC"
+        MSVC_VERSION=$(ls "$MSVC_BIN_PATH" | sort -V | tail -n 1)
+        LIB_PATH="$MSVC_BIN_PATH\\$MSVC_VERSION\\bin\\Hostx64\\x64"
+        
+        echo "Adding $LIB_PATH to PATH"
+        echo "PATH=$LIB_PATH:$PATH" >> "$GITHUB_ENV"
+
+    - name: Verify lib.exe
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      shell: bash
+      run: |
+        which lib.exe || echo "lib.exe not found"
+
     - name: Build IQ-TREE
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e795b24..bd46719 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,7 +36,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
+        os: [windows-latest]
+        # os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
         python-version: ["3.10", "3.11", "3.12"] 
     steps:
       - uses: "actions/checkout@v4"

From 688e589b60064ac2e8045343f55cc4548a17bbce Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:10:35 +1100
Subject: [PATCH 18/44] DEV: debug msvc path

---
 .github/actions/build-iqtree/action.yml | 29 ++++++++++++++++++++-----
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index da23170..a4a53fd 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -47,12 +47,29 @@ runs:
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       shell: bash
       run: |
-        MSVC_BIN_PATH="C:\\Program Files\\Microsoft Visual Studio\\2022\\BuildTools\\VC\\Tools\\MSVC"
-        MSVC_VERSION=$(ls "$MSVC_BIN_PATH" | sort -V | tail -n 1)
-        LIB_PATH="$MSVC_BIN_PATH\\$MSVC_VERSION\\bin\\Hostx64\\x64"
-        
-        echo "Adding $LIB_PATH to PATH"
-        echo "PATH=$LIB_PATH:$PATH" >> "$GITHUB_ENV"
+        # Check default VS installation paths
+        VSWHERE_PATH="/c/Program Files (x86)/Microsoft Visual Studio/Installer/vswhere.exe"
+
+        if [[ -f "$VSWHERE_PATH" ]]; then
+            echo "Finding latest MSVC installation..."
+            
+            MSVC_PATH=$("$VSWHERE_PATH" -latest -products * -requires Microsoft.VisualStudio.Component.VC.Tools.x86.x64 -property installationPath)
+            
+            if [[ -d "$MSVC_PATH" ]]; then
+                MSVC_BIN_PATH="$MSVC_PATH/VC/Tools/MSVC"
+                MSVC_VERSION=$(ls "$MSVC_BIN_PATH" | sort -V | tail -n 1)
+                LIB_PATH="$MSVC_BIN_PATH/$MSVC_VERSION/bin/Hostx64/x64"
+
+                echo "MSVC found at: $LIB_PATH"
+                echo "PATH=$LIB_PATH:$PATH" >> "$GITHUB_ENV"
+            else
+                echo "MSVC installation not found."
+                exit 1
+            fi
+        else
+            echo "vswhere.exe not found, unable to locate MSVC."
+            exit 1
+        fi
 
     - name: Verify lib.exe
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'

From d1e4d6194926d12ed8d3012143bd5f3bd1fd537d Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:13:35 +1100
Subject: [PATCH 19/44] DEV: try running wswhere through cmd

---
 .github/actions/build-iqtree/action.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index a4a53fd..788adc0 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -43,6 +43,12 @@ runs:
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
 
+    - name: Debug MSVC Installation
+      if: runner.os == 'Windows'
+      shell: cmd
+      run: |
+        "C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe" -all
+        
     - name: Set Up MSVC for lib.exe
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       shell: bash

From a189060481f0d57ad0eca1661ed49445b17c8ce5 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:20:41 +1100
Subject: [PATCH 20/44] DEV: try configuring MSVC

---
 .github/actions/build-iqtree/action.yml | 34 +++----------------------
 1 file changed, 4 insertions(+), 30 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 788adc0..5801e2c 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -43,45 +43,19 @@ runs:
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
 
-    - name: Debug MSVC Installation
-      if: runner.os == 'Windows'
-      shell: cmd
-      run: |
-        "C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe" -all
-        
-    - name: Set Up MSVC for lib.exe
+    - name: Setup Visual Studio Environment
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       shell: bash
       run: |
-        # Check default VS installation paths
-        VSWHERE_PATH="/c/Program Files (x86)/Microsoft Visual Studio/Installer/vswhere.exe"
-
-        if [[ -f "$VSWHERE_PATH" ]]; then
-            echo "Finding latest MSVC installation..."
-            
-            MSVC_PATH=$("$VSWHERE_PATH" -latest -products * -requires Microsoft.VisualStudio.Component.VC.Tools.x86.x64 -property installationPath)
-            
-            if [[ -d "$MSVC_PATH" ]]; then
-                MSVC_BIN_PATH="$MSVC_PATH/VC/Tools/MSVC"
-                MSVC_VERSION=$(ls "$MSVC_BIN_PATH" | sort -V | tail -n 1)
-                LIB_PATH="$MSVC_BIN_PATH/$MSVC_VERSION/bin/Hostx64/x64"
-
-                echo "MSVC found at: $LIB_PATH"
-                echo "PATH=$LIB_PATH:$PATH" >> "$GITHUB_ENV"
-            else
-                echo "MSVC installation not found."
-                exit 1
-            fi
-        else
-            echo "vswhere.exe not found, unable to locate MSVC."
-            exit 1
-        fi
+        source "C:/Program Files (x86)/Microsoft Visual Studio/2022/Enterprise/Common7/Tools/VsDevCmd.bat"
+        echo "Visual Studio environment configured"
 
     - name: Verify lib.exe
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       shell: bash
       run: |
         which lib.exe || echo "lib.exe not found"
+        exit 1
 
     - name: Build IQ-TREE
       shell: bash

From 26acfa1063177f4c5acc74b028ab15a4ab745ac1 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:27:21 +1100
Subject: [PATCH 21/44] DEV: use cmd to setup VS env

---
 .github/actions/build-iqtree/action.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 5801e2c..6cacd21 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -44,10 +44,9 @@ runs:
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
 
     - name: Setup Visual Studio Environment
-      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
-      shell: bash
+      shell: cmd
       run: |
-        source "C:/Program Files (x86)/Microsoft Visual Studio/2022/Enterprise/Common7/Tools/VsDevCmd.bat"
+        "C:\Program Files\Microsoft Visual Studio\2022\Community\Common7\Tools\VsDevCmd.bat"
         echo "Visual Studio environment configured"
 
     - name: Verify lib.exe

From b6d38b591441369290cad25c874d234607c94760 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:32:58 +1100
Subject: [PATCH 22/44] DEV: use action to setup msvc

---
 .github/actions/build-iqtree/action.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 6cacd21..694c98b 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -43,11 +43,9 @@ runs:
         echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
         echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
 
-    - name: Setup Visual Studio Environment
-      shell: cmd
-      run: |
-        "C:\Program Files\Microsoft Visual Studio\2022\Community\Common7\Tools\VsDevCmd.bat"
-        echo "Visual Studio environment configured"
+    - name: Setup MSVC Developer Command Prompt
+      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
+      uses: ilammy/msvc-dev-cmd@v1
 
     - name: Verify lib.exe
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'

From d52c8b4ee6fb571aed732bd5c63aa2fc9d0c5e5d Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 15:38:50 +1100
Subject: [PATCH 23/44] DEV: continue build process with found lib

---
 .github/actions/build-iqtree/action.yml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 694c98b..b252ecd 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -47,13 +47,6 @@ runs:
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       uses: ilammy/msvc-dev-cmd@v1
 
-    - name: Verify lib.exe
-      if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
-      shell: bash
-      run: |
-        which lib.exe || echo "lib.exe not found"
-        exit 1
-
     - name: Build IQ-TREE
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'

From 25611ac1d56f7025d6f7e16bb5ebcf0087acd512 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 16:05:02 +1100
Subject: [PATCH 24/44] DEV: only brew install on mac

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index bd46719..292f26d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -51,7 +51,7 @@ jobs:
           cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
       - name: Install llvm
-        if: matrix.os != 'ubuntu-latest'
+        if: runner.os == 'macOS'
         run: |
           brew install llvm
           

From ecb84ea96e495850484d3e8c00647eb4c5a95a67 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 16:05:32 +1100
Subject: [PATCH 25/44] DEV: use different caches on unix/windows

---
 .github/actions/build-iqtree/action.yml  | 29 +++++++++++++++++++++---
 .github/actions/setup-piqtree/action.yml | 25 ++++++++++++++++----
 2 files changed, 46 insertions(+), 8 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index b252ecd..f0ca238 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -19,14 +19,37 @@ runs:
         IQ_TREE_2_SHA=$(git rev-parse HEAD)
         echo "iqtree2-sha=${IQ_TREE_2_SHA}" >> "$GITHUB_OUTPUT"
 
-    - uses: actions/cache@v4
-      id: cache
+    - name: Cache IQ-TREE 2 (Windows)
+      if: runner.os == 'Windows'
+      uses: actions/cache@v4
+      id: cache-windows
+      with:
+        key: libiqtree-windows-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        path: |
+          src/piqtree/_libiqtree/iqtree2.lib
+          src/piqtree/_libiqtree/iqtree2.dll
+        lookup-only: true
+
+    - name: Cache IQ-TREE 2 (Linux/macOS)
+      if: runner.os != 'Windows'
+      uses: actions/cache@v4
+      id: cache-unix
       with:
         key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
         path: |
-          ${{ inputs.os == 'windows-latest' && 'src/piqtree/_libiqtree/iqtree2.lib\nsrc/piqtree/_libiqtree/iqtree2.dll' || 'src/piqtree/_libiqtree/libiqtree2.a' }}
+          src/piqtree/_libiqtree/libiqtree2.a
         lookup-only: true
 
+    - name: Combine Cache Hits
+      id: cache
+      shell: bash
+      run: |
+        if [[ "${{ steps.cache-windows.outputs.cache-hit }}" == 'true' || "${{ steps.cache-unix.outputs.cache-hit }}" == 'true' ]]; then
+          echo "cache-hit=true" >> "$GITHUB_OUTPUT"
+        else
+          echo "cache-hit=false" >> "$GITHUB_OUTPUT"
+        fi
+
     - name: Install Boost
       if: runner.os == 'Windows' && steps.cache.outputs.cache-hit != 'true'
       uses: MarkusJx/install-boost@v2.4.5
diff --git a/.github/actions/setup-piqtree/action.yml b/.github/actions/setup-piqtree/action.yml
index 00ae89b..01dffc5 100644
--- a/.github/actions/setup-piqtree/action.yml
+++ b/.github/actions/setup-piqtree/action.yml
@@ -13,9 +13,24 @@ runs:
     - uses: "actions/setup-python@v5"
       with:
         python-version: ${{ inputs.python-version }}
-      
-    - uses: actions/cache/restore@v4
+
+    - name: Cache IQ-TREE 2 (Windows)
+      if: runner.os == 'Windows'
+      uses: actions/cache/restore@v4
+      id: cache-windows
       with:
-        key: ${{ inputs.cache-key }}
-        path: src/piqtree/_libiqtree/libiqtree2.a
-        fail-on-cache-miss: true
\ No newline at end of file
+        key: libiqtree-windows-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        path: |
+          src/piqtree/_libiqtree/iqtree2.lib
+          src/piqtree/_libiqtree/iqtree2.dll
+        fail-on-cache-miss: true
+
+    - name: Cache IQ-TREE 2 (Linux/macOS)
+      if: runner.os != 'Windows'
+      uses: actions/cache/restore@v4
+      id: cache-unix
+      with:
+        key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        path: |
+          src/piqtree/_libiqtree/libiqtree2.a
+        fail-on-cache-miss: true

From fa7083dd49a837e70ef11be560135024cab0cbd6 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 16:48:39 +1100
Subject: [PATCH 26/44] DEV: Install llvm when testing windows ci, make
 build_iqtree compatible on local windows

---
 .github/workflows/ci.yml    | 7 ++++++-
 build_tools/build_iqtree.sh | 8 +++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 292f26d..4fce96f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -50,10 +50,15 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
-      - name: Install llvm
+      - name: Install llvm (macOS)
         if: runner.os == 'macOS'
         run: |
           brew install llvm
+
+      - name: Install llvm (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          choco install -y llvm --version=14.0.6 --allow-downgrade
           
       - name: Run Nox Testing
         run: |
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index 60a36af..5aedccd 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -11,12 +11,18 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
     gmake -j
 elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
     echo "Building for Windows."
+
+    if [[ -n "$BOOST_ROOT" ]]; then
+        export Boost_INCLUDE_DIR="${BOOST_ROOT}"
+        export Boost_LIBRARY_DIRS="${BOOST_ROOT}"
+    fi
+
     cmake -G "MinGW Makefiles" \
         -DCMAKE_C_COMPILER=clang \
         -DCMAKE_CXX_COMPILER=clang++ \
         -DCMAKE_C_FLAGS=--target=x86_64-pc-windows-gnu \
         -DCMAKE_CXX_FLAGS=--target=x86_64-pc-windows-gnu \
-        -DCMAKE_MAKE_PROGRAM=mingw32-make \
+        -DCMAKE_MAKE_PROGRAM=make \
         -DBoost_INCLUDE_DIR=$Boost_INCLUDE_DIR \
         -DBoost_LIBRARY_DIRS=$Boost_LIBRARY_DIRS \
         -DIQTREE_FLAGS="cpp14" \

From 289e9df11b07519ee89a1d06fe37fb6f02f5007b Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 17:17:17 +1100
Subject: [PATCH 27/44] DEV: re-enable full CI matrix

---
 .github/workflows/ci.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4fce96f..acf5078 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -13,8 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest]
-        # os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
+        os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
 
     steps:
       - uses: "actions/checkout@v4"
@@ -36,8 +35,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest]
-        # os: [ubuntu-latest, macos-13, macos-14] # Intel linux, Intel Mac, ARM Mac
+        os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
         python-version: ["3.10", "3.11", "3.12"] 
     steps:
       - uses: "actions/checkout@v4"

From 002f74e5f2608a6bda692e0507f9f393694d16e7 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 17:22:55 +1100
Subject: [PATCH 28/44] DEV: use runner.os for choosing before_all script

---
 .github/actions/build-iqtree/action.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index f0ca238..0a26c3a 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -74,11 +74,11 @@ runs:
       shell: bash
       if: steps.cache.outputs.cache-hit != 'true'
       run: |
-        if [[ "${{ inputs.os }}" == "ubuntu-latest" ]]; then
+        if [[ "${{ runner.os }}" == "Linux" ]]; then
           sudo ./build_tools/before_all_linux.sh
-        elif [[ "${{ inputs.os }}" == "macOS-latest" ]]; then
+        elif [[ "${{ runner.os }}" == "macOS" ]]; then
           ./build_tools/before_all_mac.sh
-        elif [[ "${{ inputs.os }}" == "windows-latest" ]]; then
+        elif [[ "${{ runner.os }}" == "Windows" ]]; then
           ./build_tools/before_all_windows.sh
         else
           echo "Unrecognized OS: '${{ inputs.os }}'."

From fec36ab4f54a91450ea75b3ff93e4ccbd8e8178e Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 17:40:11 +1100
Subject: [PATCH 29/44] DEV: standardise cache names

---
 .github/actions/build-iqtree/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/actions/build-iqtree/action.yml b/.github/actions/build-iqtree/action.yml
index 0a26c3a..9f45763 100644
--- a/.github/actions/build-iqtree/action.yml
+++ b/.github/actions/build-iqtree/action.yml
@@ -24,7 +24,7 @@ runs:
       uses: actions/cache@v4
       id: cache-windows
       with:
-        key: libiqtree-windows-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
         path: |
           src/piqtree/_libiqtree/iqtree2.lib
           src/piqtree/_libiqtree/iqtree2.dll

From 2d0f3b2cf6071d521211631b01e39d095db43b79 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 17:40:25 +1100
Subject: [PATCH 30/44] DEV: use correct input for cache key

---
 .github/actions/setup-piqtree/action.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/actions/setup-piqtree/action.yml b/.github/actions/setup-piqtree/action.yml
index 01dffc5..fb72ec8 100644
--- a/.github/actions/setup-piqtree/action.yml
+++ b/.github/actions/setup-piqtree/action.yml
@@ -19,7 +19,7 @@ runs:
       uses: actions/cache/restore@v4
       id: cache-windows
       with:
-        key: libiqtree-windows-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        key: ${{ inputs.cache-key }}
         path: |
           src/piqtree/_libiqtree/iqtree2.lib
           src/piqtree/_libiqtree/iqtree2.dll
@@ -30,7 +30,7 @@ runs:
       uses: actions/cache/restore@v4
       id: cache-unix
       with:
-        key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
+        key: ${{ inputs.cache-key }}
         path: |
           src/piqtree/_libiqtree/libiqtree2.a
         fail-on-cache-miss: true

From 631298f4f406c0d817ebe94e1023d521657885c3 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 17:56:51 +1100
Subject: [PATCH 31/44] DEV: add windows to cibuildwheel

---
 .github/workflows/build_wheels.yml | 30 ++++++++++++++++++++++++--
 .github/workflows/release.yml      | 34 +++++++++++++++++++++++++++---
 2 files changed, 59 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 66dc081..8b7537a 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        # manylinux (x86)
+        # manylinux x86_64
         - os: ubuntu-latest
           platform_id: manylinux_x86_64
         
@@ -22,6 +22,10 @@ jobs:
         - os: macos-14
           platform_id: macosx_arm64
 
+        # Windows x86_64
+        - os: windows-latest
+          platform_id: win_amd64
+
     steps:
       - uses: "actions/checkout@v4"
         with:
@@ -35,7 +39,7 @@ jobs:
           platforms: arm64
       
       - name: Set macOS Deployment Target
-        if: ${{startsWith(matrix.os, 'macos')}}
+        if: runner.os == 'macOS'
         run: |
           if [[ "${{ matrix.os }}" == "macos-13" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=13.0" >> $GITHUB_ENV
@@ -43,13 +47,35 @@ jobs:
             echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
           fi
 
+      - name: Install Boost
+        if: runner.os == 'Windows'
+        uses: MarkusJx/install-boost@v2.4.5
+        id: install-boost
+        with:
+          boost_version: 1.84.0
+          platform_version: 2022
+          toolset: mingw
+
+      - name: Set Boost Environment Variables
+        if: runner.os == 'Windows'
+        shell: bash
+        run: |
+          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+
+      - name: Setup MSVC Developer Command Prompt
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.23.0
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
+          CIBW_BEFORE_ALL_WINDOWS: ./build_tools/before_all_windows.sh
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
+          CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
           CIBW_BUILD: "*${{matrix.platform_id}}"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: pytest {package}/tests
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 17158bc..15c5a8e 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        # manylinux (x86)
+        # manylinux x86_64
         - os: ubuntu-latest
           platform_id: manylinux_x86_64
         
@@ -22,6 +22,10 @@ jobs:
         - os: macos-14
           platform_id: macosx_arm64
 
+        # Windows x86_64
+        - os: windows-latest
+          platform_id: win_amd64
+
     steps:
       - uses: "actions/checkout@v4"
         with:
@@ -35,23 +39,47 @@ jobs:
           platforms: arm64
 
       - name: Set macOS Deployment Target
-        if: ${{startsWith(matrix.os, 'macos')}}
+        if: runner.os == 'macOS'
         run: |
           if [[ "${{ matrix.os }}" == "macos-13" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=13.0" >> $GITHUB_ENV
           elif [[ "${{ matrix.os }}" == "macos-14" ]]; then
             echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
           fi
-  
+
+      - name: Install Boost
+        if: runner.os == 'Windows'
+        uses: MarkusJx/install-boost@v2.4.5
+        id: install-boost
+        with:
+          boost_version: 1.84.0
+          platform_version: 2022
+          toolset: mingw
+
+      - name: Set Boost Environment Variables
+        if: runner.os == 'Windows'
+        shell: bash
+        run: |
+          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+
+      - name: Setup MSVC Developer Command Prompt
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+    
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.23.0
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
+          CIBW_BEFORE_ALL_WINDOWS: ./build_tools/before_all_windows.sh
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
+          CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
+          CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
           CIBW_BUILD: "*${{matrix.platform_id}}"
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: pytest {package}/tests
+          CIBW_TEST_SKIP: "*-macosx_universal2:x86_64" # skip x86 on m1 mac
           CIBW_SKIP: pp* # Disable building PyPy wheels on all platforms
 
       - name: Upload wheels

From 19b06487c7bdb9fd289adf65a9517c5bd0b0d583 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 18:08:42 +1100
Subject: [PATCH 32/44] DEV: run before_all_windows script with bash

---
 .github/workflows/build_wheels.yml | 2 +-
 .github/workflows/release.yml      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 8b7537a..c078cd7 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -72,7 +72,7 @@ jobs:
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
-          CIBW_BEFORE_ALL_WINDOWS: ./build_tools/before_all_windows.sh
+          CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 15c5a8e..4b9fc0a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -72,7 +72,7 @@ jobs:
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
-          CIBW_BEFORE_ALL_WINDOWS: ./build_tools/before_all_windows.sh
+          CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 

From 2c221e444a8ac8d4c4fa610f2d1cbe3a3ec467f5 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 18:32:37 +1100
Subject: [PATCH 33/44] DEV: debug BOOST env vars

---
 .github/workflows/release.yml     | 1 +
 build_tools/before_all_windows.sh | 5 +++++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4b9fc0a..2158af1 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -73,6 +73,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
+          CIBW_ENVIRONMENT_WINDOWS: BOOST_ROOT='${{ steps.install-boost.outputs.BOOST_ROOT }}'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 763d3b2..5f81b9a 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,4 +1,9 @@
 # Install dependencies using choco
+
+echo "Boost_INCLUDE_DIR: " $Boost_INCLUDE_DIR
+echo "Boost_LIBRARY_DIRS: " $Boost_LIBRARY_DIRS
+echo "BOOST_ROOT: " $BOOST_ROOT
+
 choco install -y llvm --version=14.0.6 --allow-downgrade
 choco install -y eigen 
 

From 0914a962d8e1c9557c4900e81f089cbe6e5a772c Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 18:45:55 +1100
Subject: [PATCH 34/44] DEV: attempt hardcoding boost paths

---
 .github/workflows/build_wheels.yml | 1 +
 .github/workflows/release.yml      | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index c078cd7..41903b1 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -73,6 +73,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/include'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 2158af1..ff52508 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -73,7 +73,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: BOOST_ROOT='${{ steps.install-boost.outputs.BOOST_ROOT }}'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/include'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 

From 060b659e57773c7a7a20a2b92d73c7e8fff93c39 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 18:50:21 +1100
Subject: [PATCH 35/44] DEV: fix BOOST lib path

---
 .github/workflows/build_wheels.yml | 2 +-
 .github/workflows/release.yml      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 41903b1..28856ed 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -73,7 +73,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/include'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index ff52508..6ae48e8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -73,7 +73,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/include'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 

From d9673dea2fb76f7f5862761ce428e14d5fb1ec86 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 18:53:32 +1100
Subject: [PATCH 36/44] DEV: remove hardcoding of BOOST paths

---
 .github/workflows/build_wheels.yml | 9 +--------
 .github/workflows/release.yml      | 9 +--------
 2 files changed, 2 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 28856ed..a967611 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -56,13 +56,6 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
-      - name: Set Boost Environment Variables
-        if: runner.os == 'Windows'
-        shell: bash
-        run: |
-          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
-          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
-
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -73,7 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include"' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 6ae48e8..89e4c5d 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -56,13 +56,6 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
-      - name: Set Boost Environment Variables
-        if: runner.os == 'Windows'
-        shell: bash
-        run: |
-          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
-          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
-
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -73,7 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include"' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 

From a4d9bd192f130d8344654de8cb0f09f91557aaff Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 19:04:23 +1100
Subject: [PATCH 37/44] DEV: hardcode paths again

---
 .github/workflows/build_wheels.yml | 11 ++++++++++-
 .github/workflows/release.yml      | 11 ++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a967611..f89bea4 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -56,6 +56,15 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
+      - name: Set Boost Environment Variables
+        if: runner.os == 'Windows'
+        shell: bash
+        run: |
+          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+          echo $Boost_INCLUDE_DIR
+          echo $Boost_LIBRARY_DIRS
+
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -66,7 +75,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include"' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 89e4c5d..09657f3 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -56,6 +56,15 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
+      - name: Set Boost Environment Variables
+        if: runner.os == 'Windows'
+        shell: bash
+        run: |
+          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
+          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
+          echo $Boost_INCLUDE_DIR
+          echo $Boost_LIBRARY_DIRS
+
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -66,7 +75,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include"' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 

From a8e8476349aa4705586101a77f3d4da941f2fce4 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 19:16:15 +1100
Subject: [PATCH 38/44] DEV: normalise slashes in before_all_windows

---
 .github/workflows/build_wheels.yml | 11 +----------
 .github/workflows/release.yml      | 11 +----------
 build_tools/before_all_windows.sh  |  8 +++++---
 3 files changed, 7 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index f89bea4..5d56787 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -56,15 +56,6 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
-      - name: Set Boost Environment Variables
-        if: runner.os == 'Windows'
-        shell: bash
-        run: |
-          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
-          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
-          echo $Boost_INCLUDE_DIR
-          echo $Boost_LIBRARY_DIRS
-
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -75,7 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 09657f3..500c312 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -56,15 +56,6 @@ jobs:
           platform_version: 2022
           toolset: mingw
 
-      - name: Set Boost Environment Variables
-        if: runner.os == 'Windows'
-        shell: bash
-        run: |
-          echo "Boost_INCLUDE_DIR=${{ steps.install-boost.outputs.BOOST_ROOT }}/include" >> "$GITHUB_ENV"
-          echo "Boost_LIBRARY_DIRS=${{ steps.install-boost.outputs.BOOST_ROOT }}/lib" >> "$GITHUB_ENV"
-          echo $Boost_INCLUDE_DIR
-          echo $Boost_LIBRARY_DIRS
-
       - name: Setup MSVC Developer Command Prompt
         if: runner.os == 'Windows'
         uses: ilammy/msvc-dev-cmd@v1
@@ -75,7 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
           CIBW_BEFORE_ALL_WINDOWS: bash ./build_tools/before_all_windows.sh
-          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='D:/a/piqtree/piqtree/boost/boost/include' Boost_LIBRARY_DIRS='D:/a/piqtree/piqtree/boost/boost/lib'
+          CIBW_ENVIRONMENT_WINDOWS: Boost_INCLUDE_DIR='${{ steps.install-boost.outputs.BOOST_ROOT }}/include' Boost_LIBRARY_DIRS='${{ steps.install-boost.outputs.BOOST_ROOT }}/lib'
           CIBW_ARCHS_LINUX: ${{endsWith(matrix.platform_id, '_x86_64') && 'x86_64' || 'aarch64'}} 
           CIBW_ARCHS_MACOS: ${{endsWith(matrix.platform_id, 'universal2') && 'universal2' || 'auto'}} 
           CIBW_ARCHS_WINDOWS: ${{endsWith(matrix.platform_id, '_amd64') && 'AMD64' || 'ARM64'}} 
diff --git a/build_tools/before_all_windows.sh b/build_tools/before_all_windows.sh
index 5f81b9a..763536e 100644
--- a/build_tools/before_all_windows.sh
+++ b/build_tools/before_all_windows.sh
@@ -1,8 +1,10 @@
 # Install dependencies using choco
 
-echo "Boost_INCLUDE_DIR: " $Boost_INCLUDE_DIR
-echo "Boost_LIBRARY_DIRS: " $Boost_LIBRARY_DIRS
-echo "BOOST_ROOT: " $BOOST_ROOT
+export Boost_INCLUDE_DIR=$(echo $Boost_INCLUDE_DIR | sed 's|\\|/|g')
+export Boost_LIBRARY_DIRS=$(echo $Boost_LIBRARY_DIRS | sed 's|\\|/|g')
+
+echo "Boost_INCLUDE_DIR: $Boost_INCLUDE_DIR"
+echo "Boost_LIBRARY_DIRS: $Boost_LIBRARY_DIRS"
 
 choco install -y llvm --version=14.0.6 --allow-downgrade
 choco install -y eigen 

From 9f9669ccb5ff480a5b2d3b4c5448a31a131c3406 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 19:54:50 +1100
Subject: [PATCH 39/44] MAINT: remove extra space

---
 src/piqtree/_libiqtree/_piqtree.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/piqtree/_libiqtree/_piqtree.cpp b/src/piqtree/_libiqtree/_piqtree.cpp
index 52697f8..5101edd 100644
--- a/src/piqtree/_libiqtree/_piqtree.cpp
+++ b/src/piqtree/_libiqtree/_piqtree.cpp
@@ -116,5 +116,5 @@ PYBIND11_MODULE(_piqtree, m) {
         "Construct pairwise distance matrix for alignment.");
   m.def("iq_nj_tree", &build_njtree,
         "Build neighbour-joining tree from distance matrix.");
-  m.def("mine", &mine, "The meaning of life, the universe (and everything) !");
+  m.def("mine", &mine, "The meaning of life, the universe (and everything)!");
 }

From c0d4be70a20e214e0d53aeecff0ce8ecb6481a96 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Thu, 20 Mar 2025 21:03:14 +1100
Subject: [PATCH 40/44] MAINT: update python version (#4)

* MAINT: Add support for Python 3.13, drop for 3.10

* MAINT: Update nox supported python versions

* Bump pypa/cibuildwheel from 2.23.0 to 2.23.1

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.0 to 2.23.1.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/v2.23.1/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.23.0...v2.23.1)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/build_docs.yml   | 2 +-
 .github/workflows/build_wheels.yml | 2 +-
 .github/workflows/ci.yml           | 6 +++---
 .github/workflows/release.yml      | 4 ++--
 noxfile.py                         | 2 +-
 pyproject.toml                     | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index d4c0ec3..ad7ce76 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -32,7 +32,7 @@ jobs:
 
       - uses: ./.github/actions/setup-piqtree
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache-key: libiqtree-ubuntu-latest-${{ needs.build-iqtree.outputs.iqtree2-sha }}
       
       - name: Install Docs Dependencies
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 5d56787..a6f62be 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.0
+        uses: pypa/cibuildwheel@v2.23.1
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index acf5078..4fdb7fc 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -36,7 +36,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-13, macos-14, windows-latest] # Intel linux, Intel Mac, ARM Mac, Windows
-        python-version: ["3.10", "3.11", "3.12"] 
+        python-version: ["3.11", "3.12", "3.13"] 
     steps:
       - uses: "actions/checkout@v4"
         with:
@@ -90,7 +90,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         os: [ubuntu-latest]
 
     steps:
@@ -115,7 +115,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         os: [ubuntu-latest]
 
     steps:
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 500c312..faca30e 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
     
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.0
+        uses: pypa/cibuildwheel@v2.23.1
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
@@ -111,7 +111,7 @@ jobs:
 
       - uses: ./.github/actions/setup-piqtree
         with:
-          python-version: "3.12"
+          python-version: "3.13"
           cache-key: libiqtree-ubuntu-latest-${{ needs.build-iqtree.outputs.iqtree2-sha }}
       
       - name: Install Docs Dependencies
diff --git a/noxfile.py b/noxfile.py
index 42a3dd2..f4a2385 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -2,7 +2,7 @@
 
 import nox
 
-_py_versions = range(9, 13)
+_py_versions = range(11, 14)
 
 
 @nox.session(python=[f"3.{v}" for v in _py_versions])
diff --git a/pyproject.toml b/pyproject.toml
index 1987151..9460368 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "piqtree"
 dependencies = ["cogent3>=2024.11.29a2", "pyyaml", "requests"]
-requires-python = ">=3.10, <3.13"
+requires-python = ">=3.11, <3.14"
 
 authors = [{name="Gavin Huttley"}, {name="Robert McArthur"}, {name="Bui Quang Minh "}, {name="Richard Morris"}, {name="Thomas Wong"}]
 description="Python bindings for IQTree"

From 505c1d927ea9b58ae6f22ca1f47e75669d0c30f3 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Sun, 23 Mar 2025 23:34:43 +1100
Subject: [PATCH 41/44] DEV: update iqtree to error handling version

---
 iqtree2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/iqtree2 b/iqtree2
index 39cbee5..3ad863a 160000
--- a/iqtree2
+++ b/iqtree2
@@ -1 +1 @@
-Subproject commit 39cbee547c4bfc6d2e78f063b4beb9095e15f812
+Subproject commit 3ad863ad7e26d46aa549327e6c3003b75d288ff0

From e4ad032dc27b1ef5de0001cb691e48981ee990e6 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Mon, 24 Mar 2025 00:16:07 +1100
Subject: [PATCH 42/44] DEV: update return/arg types for calling IQ-TREE

---
 src/piqtree/_libiqtree/_piqtree.cpp | 67 +++++++++++++++++++++++--
 src/piqtree/_libiqtree/_piqtree.h   | 76 ++++++++++++++++++-----------
 2 files changed, 110 insertions(+), 33 deletions(-)

diff --git a/src/piqtree/_libiqtree/_piqtree.cpp b/src/piqtree/_libiqtree/_piqtree.cpp
index 5101edd..c76af49 100644
--- a/src/piqtree/_libiqtree/_piqtree.cpp
+++ b/src/piqtree/_libiqtree/_piqtree.cpp
@@ -5,11 +5,16 @@
 #include <iostream>
 #include <string>
 #include <vector>
-
-using namespace std;
+#include "_piqtree.h"
 
 namespace py = pybind11;
 
+void checkError(char* errorStr) {
+  if (errorStr && std::strlen(errorStr) > 0) {
+    throw std::runtime_error(errorStr);
+  }
+}
+
 namespace PYBIND11_NAMESPACE {
 namespace detail {
 template <>
@@ -80,9 +85,63 @@ struct type_caster<DoubleArray> {
 
   // Conversion from C++ to Python
   static handle cast(DoubleArray src, return_value_policy, handle) {
+    throw std::runtime_error("Unsupported operation");
+  }
+};
+
+template <>
+struct type_caster<IntegerResult> {
+ public:
+  PYBIND11_TYPE_CASTER(IntegerResult, _("IntegerResult"));
+
+  // Conversion from Python to C++
+  bool load(handle /* src */, bool /* convert */) {
+    throw std::runtime_error("Unsupported operation");
+  }
+
+  // Conversion from C++ to Python
+  static handle cast(const IntegerResult& src, return_value_policy, handle) {
+    checkError(src.errorStr);
+
+    return py::int_(src.value).release();
+  }
+};
+
+template <>
+struct type_caster<StringResult> {
+ public:
+  // Indicate that this caster only supports conversion from C++ to Python
+  PYBIND11_TYPE_CASTER(StringResult, _("StringResult"));
+
+  // Reject Python to C++ conversion
+  bool load(handle src, bool) {
+    throw std::runtime_error("Unsupported operation");
+  }
+
+  // Conversion from C++ to Python
+  static handle cast(const StringResult& src, return_value_policy, handle) {
+    checkError(src.errorStr);
+
+    return py::str(src.value).release();
+  }
+};
+
+template <>
+struct type_caster<DoubleArrayResult> {
+ public:
+  PYBIND11_TYPE_CASTER(DoubleArrayResult, _("DoubleArrayResult"));
+
+  // Conversion from Python to C++
+  bool load(handle src, bool) {
+    throw std::runtime_error("Unsupported operation");
+  }
+
+  // Conversion from C++ to Python
+  static handle cast(DoubleArrayResult src, return_value_policy, handle) {
+    checkError(src.errorStr);
+
     auto result = py::array_t<double>(src.length);
-    std::memcpy(result.mutable_data(), src.doubles,
-                src.length * sizeof(double));
+    std::memcpy(result.mutable_data(), src.value, src.length * sizeof(double));
     return result.release();
   }
 };
diff --git a/src/piqtree/_libiqtree/_piqtree.h b/src/piqtree/_libiqtree/_piqtree.h
index 070c621..5e37724 100644
--- a/src/piqtree/_libiqtree/_piqtree.h
+++ b/src/piqtree/_libiqtree/_piqtree.h
@@ -1,6 +1,7 @@
 #ifndef _PIQTREE_H
 #define _PIQTREE_H
 
+#include <pybind11/stl.h>
 #include <cstddef>
 
 using namespace std;
@@ -21,6 +22,22 @@ typedef struct {
   size_t length;
 } DoubleArray;
 
+typedef struct {
+  int value;
+  char* errorStr;
+} IntegerResult;
+
+typedef struct {
+  char* value;
+  char* errorStr;
+} StringResult;
+
+typedef struct {
+  double* value;
+  size_t length;
+  char* errorStr;
+} DoubleArrayResult;
+
 #ifdef _MSC_VER
 #pragma pack(pop)
 #else
@@ -30,17 +47,17 @@ typedef struct {
 /*
  * Calculates the robinson fould distance between two trees
  */
-extern "C" int robinson_fould(const char* ctree1, const char* ctree2);
+extern "C" IntegerResult robinson_fould(const char* ctree1, const char* ctree2);
 
 /*
  * Generates a set of random phylogenetic trees
  * tree_gen_mode allows:"YULE_HARDING", "UNIFORM", "CATERPILLAR", "BALANCED",
  * "BIRTH_DEATH", "STAR_TREE" output: a newick tree (in string format)
  */
-extern "C" char* random_tree(int num_taxa,
-                             const char* tree_gen_mode,
-                             int num_trees,
-                             int rand_seed = 0);
+extern "C" StringResult random_tree(int num_taxa,
+                                    const char* tree_gen_mode,
+                                    int num_trees,
+                                    int rand_seed = 0);
 
 /*
  * Perform phylogenetic analysis on the input alignment
@@ -49,12 +66,12 @@ extern "C" char* random_tree(int num_taxa,
  * of the optimal number of cpu threads output: results in YAML format with the
  * tree and the details of parameters
  */
-extern "C" char* build_tree(StringArray& names,
-                            StringArray& seqs,
-                            const char* model,
-                            int rand_seed = 0,
-                            int bootstrap_rep = 0,
-                            int num_thres = 1);
+extern "C" StringResult build_tree(StringArray& names,
+                                   StringArray& seqs,
+                                   const char* model,
+                                   int rand_seed = 0,
+                                   int bootstrap_rep = 0,
+                                   int num_thres = 1);
 
 /*
  * Perform phylogenetic analysis on the input alignment
@@ -63,12 +80,12 @@ extern "C" char* build_tree(StringArray& names,
  * of the optimal number of cpu threads output: results in YAML format with the
  * details of parameters
  */
-extern "C" char* fit_tree(StringArray& names,
-                          StringArray& seqs,
-                          const char* model,
-                          const char* intree,
-                          int rand_seed = 0,
-                          int num_thres = 1);
+extern "C" StringResult fit_tree(StringArray& names,
+                                 StringArray& seqs,
+                                 const char* model,
+                                 const char* intree,
+                                 int rand_seed = 0,
+                                 int num_thres = 1);
 
 /*
  * Perform phylogenetic analysis with ModelFinder
@@ -81,13 +98,13 @@ extern "C" char* fit_tree(StringArray& names,
  * of the optimal number of cpu threads output: modelfinder results in YAML
  * format
  */
-extern "C" char* modelfinder(StringArray& names,
-                             StringArray& seqs,
-                             int rand_seed = 0,
-                             const char* model_set = "",
-                             const char* freq_set = "",
-                             const char* rate_set = "",
-                             int num_thres = 1);
+extern "C" StringResult modelfinder(StringArray& names,
+                                    StringArray& seqs,
+                                    int rand_seed = 0,
+                                    const char* model_set = "",
+                                    const char* freq_set = "",
+                                    const char* rate_set = "",
+                                    int num_thres = 1);
 
 /*
  * Build pairwise JC distance matrix
@@ -97,19 +114,20 @@ extern "C" char* modelfinder(StringArray& names,
  * threads to be used, default: 1; 0 - use all available cpu threads on the
  * machine
  */
-extern "C" DoubleArray build_distmatrix(StringArray& names,
-                                        StringArray& seqs,
-                                        int num_thres = 1);
+extern "C" DoubleArrayResult build_distmatrix(StringArray& names,
+                                              StringArray& seqs,
+                                              int num_thres = 1);
 
 /*
  * Using Rapid-NJ to build tree from a distance matrix
  * output: a newick tree (in string format)
  */
-extern "C" char* build_njtree(StringArray& names, DoubleArray& distances);
+extern "C" StringResult build_njtree(StringArray& names,
+                                     DoubleArray& distances);
 
 /*
  * verion number
  */
-extern "C" char* version();
+extern "C" StringResult version();
 
 #endif /* LIBIQTREE2_FUN */

From bc80ae090dd71099912cfe5c6629fd4c37ffbaa9 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Mon, 24 Mar 2025 00:17:10 +1100
Subject: [PATCH 43/44] DEV: remove pytest skips on windows

---
 tests/test_app/test_app.py                   |  1 +
 tests/test_iqtree/test_build_tree.py         |  5 -----
 tests/test_iqtree/test_random_trees.py       |  6 ------
 tests/test_iqtree/test_segmentation_fault.py | 14 --------------
 4 files changed, 1 insertion(+), 25 deletions(-)

diff --git a/tests/test_app/test_app.py b/tests/test_app/test_app.py
index ce69516..7bd3aa2 100644
--- a/tests/test_app/test_app.py
+++ b/tests/test_app/test_app.py
@@ -111,6 +111,7 @@ def test_mfinder_result_roundtrip(five_otu: Alignment) -> None:
     assert isinstance(inflated, ModelFinderResult)
     assert str(got.best_aicc) == str(inflated.best_aicc)
 
+
 @pytest.mark.skipif(cogent3_vers < "2025.3.1", reason="requires cogent3 >= 2025.3.1")
 @pytest.mark.parametrize("use_hook", [None, "piqtree"])
 def test_quick_tree_hook(four_otu: Alignment, use_hook: str | None) -> None:
diff --git a/tests/test_iqtree/test_build_tree.py b/tests/test_iqtree/test_build_tree.py
index d8232d1..90cbf8a 100644
--- a/tests/test_iqtree/test_build_tree.py
+++ b/tests/test_iqtree/test_build_tree.py
@@ -1,4 +1,3 @@
-import platform
 import re
 
 import pytest
@@ -88,10 +87,6 @@ def test_rate_model_build_tree(
     )
 
 
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="IQ-TREE errors can't be caught yet on Windows",
-)
 def test_build_tree_inadequate_bootstrapping(four_otu: ArrayAlignment) -> None:
     with pytest.raises(IqTreeError, match=re.escape("#replicates must be >= 1000")):
         piqtree.build_tree(four_otu, Model(DnaModel.GTR), bootstrap_replicates=10)
diff --git a/tests/test_iqtree/test_random_trees.py b/tests/test_iqtree/test_random_trees.py
index 82ce8f4..60c09ce 100644
--- a/tests/test_iqtree/test_random_trees.py
+++ b/tests/test_iqtree/test_random_trees.py
@@ -1,5 +1,3 @@
-import platform
-
 import pytest
 
 import piqtree
@@ -47,10 +45,6 @@ def test_random_trees_no_seed(
 
 @pytest.mark.parametrize("num_taxa", [-1, 0, 1, 2])
 @pytest.mark.parametrize("tree_mode", list(piqtree.TreeGenMode))
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="IQ-TREE errors can't be caught yet on Windows",
-)
 def test_invalid_taxa(
     num_taxa: int,
     tree_mode: piqtree.TreeGenMode,
diff --git a/tests/test_iqtree/test_segmentation_fault.py b/tests/test_iqtree/test_segmentation_fault.py
index 1fb5857..701cc40 100644
--- a/tests/test_iqtree/test_segmentation_fault.py
+++ b/tests/test_iqtree/test_segmentation_fault.py
@@ -1,7 +1,5 @@
 """Test combinations of calls which under previous versions resulted in a segmentation fault."""
 
-import platform
-
 import pytest
 from cogent3 import make_aligned_seqs, make_tree
 
@@ -10,10 +8,6 @@
 from piqtree.model import DiscreteGammaModel, DnaModel, FreeRateModel, Model
 
 
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="IQ-TREE errors can't be caught yet on Windows",
-)
 def test_two_build_random_trees() -> None:
     """
     Calling build tree twice followed by random trees with a bad input
@@ -28,10 +22,6 @@ def test_two_build_random_trees() -> None:
         random_trees(3, 2, TreeGenMode.BALANCED, 1)
 
 
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="IQ-TREE errors can't be caught yet on Windows",
-)
 def test_two_fit_random_trees() -> None:
     """
     Calling fit tree twice followed by random trees with a bad input
@@ -49,10 +39,6 @@ def test_two_fit_random_trees() -> None:
 
 @pytest.mark.parametrize("rate_model_class", [DiscreteGammaModel, FreeRateModel])
 @pytest.mark.parametrize("categories", [0, -4])
-@pytest.mark.skipif(
-    platform.system() == "Windows",
-    reason="IQ-TREE errors can't be caught yet on Windows",
-)
 def test_two_invalid_models(
     rate_model_class: type[DiscreteGammaModel] | type[FreeRateModel],
     categories: int,

From 466e979d264ae43e46697621615b0ff7e9675542 Mon Sep 17 00:00:00 2001
From: Robert McArthur <robert.mcarthur@anu.edu.au>
Date: Mon, 12 May 2025 18:15:41 +1000
Subject: [PATCH 44/44] DEV: rebase windows-support on main  (#5)

* ENH: provide piqtree_nj and nj_tree option for positive branch lengths (#165)

* ENH: parameter to restrict negative value of branch length

* TST: allow_negative correctly control the behavior of branch length in nj_tree

* ENH: add parameter allow_negative in piqtree_nj app

* MAINT: fix double return error in merge

* MAINT: ruff formatting

* TST: Use full fasta file for checking `nj_tree` negative branch lengths

* MAINT: move from `ArrayAlignment` to `Alignment` in preparation for `new_type` default

* MAINT: simplify logic for negative branch lengths

* MAINT: Sort fixtures by number of taxa

* MAINT: Remove unused test data file

---------

Co-authored-by: Robert McArthur <robert.mcarthur@anu.edu.au>

* DEV: Update minimum required `cogent3` version (support cogent3 hooks)

* TST: Remove skip for `quick_tree` `cogent3` hook as `cogent3` min version has updated

* Bump ruff from 0.11.0 to 0.11.5

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.0 to 0.11.5.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.11.0...0.11.5)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/cibuildwheel from 2.23.1 to 2.23.2

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.1 to 2.23.2.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.23.1...v2.23.2)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump ruff from 0.11.5 to 0.11.8

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.5 to 0.11.8.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.11.5...0.11.8)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.8
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump pypa/cibuildwheel from 2.23.2 to 2.23.3

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23.2 to 2.23.3.
- [Release notes](https://github.com/pypa/cibuildwheel/releases)
- [Changelog](https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md)
- [Commits](https://github.com/pypa/cibuildwheel/compare/v2.23.2...v2.23.3)

---
updated-dependencies:
- dependency-name: pypa/cibuildwheel
  dependency-version: 2.23.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

* MAINT: upgrade min `cogent3` and use new `Table` API

* ENH: support use of `str` for model in `build_tree` and `fit_tree`

* TST: add tests for string represnetations of models

* API: simplify expression of model in apps (match that used by `build_tree` and `fit_tree`)

* DEV: add scriv fragment

* DEV: bump version to 0.5.0

* DEV: collate scriv fragment

* DOC: fix typo in release checklist

* DEV: update trove classifiers for supported python versions

* DEV: add minimum cmake version

* Bump ruff from 0.11.8 to 0.11.9

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.11.8 to 0.11.9.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.11.8...0.11.9)

---
updated-dependencies:
- dependency-name: ruff
  dependency-version: 0.11.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Yapeng Lang <u7181074@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/build_wheels.yml     |  2 +-
 .github/workflows/release.yml          |  2 +-
 build_tools/build_iqtree.sh            |  4 +--
 changelog.md                           | 20 +++++++++++
 docs/developers/release.md             |  2 +-
 pyproject.toml                         |  6 ++--
 src/piqtree/__init__.py                |  2 +-
 src/piqtree/_app/__init__.py           | 32 ++++++------------
 src/piqtree/iqtree/_tree.py            | 31 +++++++++++++----
 src/piqtree/model/_options.py          | 10 +++---
 tests/conftest.py                      | 14 +++++---
 tests/test_app/test_app.py             | 10 +++---
 tests/test_iqtree/test_build_tree.py   | 26 ++++++++++-----
 tests/test_iqtree/test_distance.py     |  4 +--
 tests/test_iqtree/test_fit_tree.py     | 46 +++++++++++++++++++++++---
 tests/test_iqtree/test_model_finder.py |  6 ++--
 tests/test_iqtree/test_nj_tree.py      | 17 ++++++++--
 17 files changed, 162 insertions(+), 72 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a6f62be..ebf7a97 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v2.23.3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index faca30e..fc4ff19 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -61,7 +61,7 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
     
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23.1
+        uses: pypa/cibuildwheel@v2.23.3
         env: # Can specify per os - e.g. CIBW_BEFORE_ALL_LINUX, CIBW_BEFORE_ALL_MACOS, CIBW_BEFORE_ALL_WINDOWS 
           CIBW_BEFORE_ALL_LINUX: ./build_tools/before_all_linux.sh
           CIBW_BEFORE_ALL_MACOS: ./build_tools/before_all_mac.sh
diff --git a/build_tools/build_iqtree.sh b/build_tools/build_iqtree.sh
index 5aedccd..cdc9526 100755
--- a/build_tools/build_iqtree.sh
+++ b/build_tools/build_iqtree.sh
@@ -30,8 +30,8 @@ elif [[ "$OSTYPE" == "msys"* || "$OSTYPE" == "cygwin"* ]]; then
         ..
     make -j
 else
-    echo "Building for Linux."
-    cmake -DBUILD_LIB=ON ..
+    echo "Building for linux."
+    cmake -DBUILD_LIB=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ..
     make -j
 fi
 
diff --git a/changelog.md b/changelog.md
index 5978672..818884e 100644
--- a/changelog.md
+++ b/changelog.md
@@ -1,4 +1,24 @@
 
+<a id='changelog-0.5.0'></a>
+# Changes in release "0.5.0"
+
+## Contributors
+
+- @GavinHuttley added `nj_tree` as a hook for `cogent3.Alignment.quick_tree`.
+- @YapengLang handled negative branch lengths from the rapidNJ tree.
+- @rmcar17, @thomaskf general maintanence on the piqtree/IQ-TREE sides including work on windows behind the scenes.
+
+## ENH
+
+- Add support for Python 3.13, remove support for 3.10
+- IQ-TREE's rapidNJ implementation can be used as a hook for `quick_tree` on `cogent3` alignment objects. Try `Alignment.quick_tree(use_hook="piqtree")`.
+- `nj_tree` now by default does not allow negative branch lengths. Set `allow_negative=True` if this behaviour is desired.
+- Allow `str` to be used for `model` in `build_tree` and `fit_tree`. The value is automatically coerced into the `Model` class.
+
+## API
+
+- Simplify API for `piqtree_phylo` and `piqtree_fit` apps. Both now take a single parameter for the model, matching the parameter for `model` in `build_tree` and `fit_tree`.
+
 <a id='changelog-0.4.0'></a>
 # Changes in release "0.4.0"
 
diff --git a/docs/developers/release.md b/docs/developers/release.md
index 974a38d..fae6fdd 100644
--- a/docs/developers/release.md
+++ b/docs/developers/release.md
@@ -8,7 +8,7 @@ The documentation is fetched by readthedocs from the "Build Docs" GitHub Action.
 
 - The `piqtree` version has been correctly bumped.
 - The testing, linting and type checking all pass on all supported platforms.
-- The code has been throuroughly tested (check what's been missed in the coverage report).
+- The code has been thoroughly tested (check what's been missed in the coverage report).
 - The documentation builds and appears correct.
 - The documentation has been updated on readthedocs (this must be triggered from readthedocs).
 - The "Release" GitHub Action has correctly uploaded to Test PyPI.
diff --git a/pyproject.toml b/pyproject.toml
index 9460368..f907df5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "piqtree"
-dependencies = ["cogent3>=2024.11.29a2", "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"}]
@@ -28,9 +28,9 @@ classifiers = [
 
     "Programming Language :: C++",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 
     "Typing :: Typed"
 ]
@@ -43,7 +43,7 @@ Documentation = "https://piqtree.readthedocs.io"
 [project.optional-dependencies]
 dev = ["cibuildwheel", "pybind11", "scriv", "piqtree[test]", "piqtree[lint]", "piqtree[typing]"]
 test = ["pytest", "pytest-cov", "nox"]
-lint = ["ruff==0.11.0"]
+lint = ["ruff==0.11.9"]
 typing = ["mypy==1.15.0", "piqtree[stubs]", "piqtree[test]"]
 stubs = ["types-PyYAML", "types-requests"]
 extra = ["cogent3[extra]"]
diff --git a/src/piqtree/__init__.py b/src/piqtree/__init__.py
index 5a91c95..5d7abd5 100644
--- a/src/piqtree/__init__.py
+++ b/src/piqtree/__init__.py
@@ -35,7 +35,7 @@ def _add_dll_path() -> None:
     make_model,
 )
 
-__version__ = "0.4.0"
+__version__ = "0.5.0"
 
 __all__ = [
     "Model",
diff --git a/src/piqtree/_app/__init__.py b/src/piqtree/_app/__init__.py
index e70c9de..32d6cfe 100644
--- a/src/piqtree/_app/__init__.py
+++ b/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
 
@@ -124,8 +108,12 @@ def main(
 
 @composable.define_app
 @extend_docstring_from(nj_tree)
-def piqtree_nj(dists: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
-    tree = nj_tree(dists)
+def piqtree_nj(
+    dists: c3_types.PairwiseDistanceType,
+    *,
+    allow_negative: bool = False,
+) -> cogent3.PhyloNode:
+    tree = nj_tree(dists, allow_negative=allow_negative)
     tree.params |= {"provenance": "piqtree"}
     return tree
 
diff --git a/src/piqtree/iqtree/_tree.py b/src/piqtree/iqtree/_tree.py
index 2485db0..a302e6e 100644
--- a/src/piqtree/iqtree/_tree.py
+++ b/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
 
@@ -312,7 +318,11 @@ def fit_tree(
     return tree
 
 
-def nj_tree(pairwise_distances: c3_types.PairwiseDistanceType) -> cogent3.PhyloNode:
+def nj_tree(
+    pairwise_distances: c3_types.PairwiseDistanceType,
+    *,
+    allow_negative: bool = False,
+) -> cogent3.PhyloNode:
     """Construct a neighbour joining tree from a pairwise distance matrix.
 
     Parameters
@@ -334,4 +344,11 @@ def nj_tree(pairwise_distances: c3_types.PairwiseDistanceType) -> cogent3.PhyloN
         pairwise_distances.keys(),
         np.array(pairwise_distances).flatten(),
     )
-    return make_tree(newick_tree)
+
+    tree = make_tree(newick_tree)
+
+    if not allow_negative:
+        for node in tree.traverse(include_self=False):
+            node.length = max(node.length, 0)
+
+    return tree
diff --git a/src/piqtree/model/_options.py b/src/piqtree/model/_options.py
index ebfa365..4229ad9 100644
--- a/src/piqtree/model/_options.py
+++ b/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": []}
 
diff --git a/tests/conftest.py b/tests/conftest.py
index 76778ad..7d4a1eb 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,7 +1,7 @@
 import pathlib
 
 import pytest
-from cogent3 import ArrayAlignment, load_aligned_seqs
+from cogent3 import Alignment, load_aligned_seqs
 
 
 @pytest.fixture(scope="session")
@@ -10,21 +10,27 @@ def DATA_DIR() -> pathlib.Path:
 
 
 @pytest.fixture
-def three_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def three_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
-def four_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def four_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Mouse"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
 
 
 @pytest.fixture
-def five_otu(DATA_DIR: pathlib.Path) -> ArrayAlignment:
+def five_otu(DATA_DIR: pathlib.Path) -> Alignment:
     aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
     aln = aln.take_seqs(["Human", "Chimpanzee", "Rhesus", "Manatee", "Dugong"])
     return aln.omit_gap_pos(allowed_gap_frac=0)
+
+
+@pytest.fixture
+def all_otu(DATA_DIR: pathlib.Path) -> Alignment:
+    aln = load_aligned_seqs(DATA_DIR / "example.fasta", moltype="dna", new_type=True)
+    return aln.omit_gap_pos(allowed_gap_frac=0)
diff --git a/tests/test_app/test_app.py b/tests/test_app/test_app.py
index 7bd3aa2..6470cb9 100644
--- a/tests/test_app/test_app.py
+++ b/tests/test_app/test_app.py
@@ -1,21 +1,20 @@
 import pytest
-from cogent3 import __version__ as cogent3_vers
 from cogent3 import get_app, make_tree
 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)
@@ -29,7 +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)
 
@@ -112,7 +111,6 @@ def test_mfinder_result_roundtrip(five_otu: Alignment) -> None:
     assert str(got.best_aicc) == str(inflated.best_aicc)
 
 
-@pytest.mark.skipif(cogent3_vers < "2025.3.1", reason="requires cogent3 >= 2025.3.1")
 @pytest.mark.parametrize("use_hook", [None, "piqtree"])
 def test_quick_tree_hook(four_otu: Alignment, use_hook: str | None) -> None:
     tree = four_otu.quick_tree(use_hook=use_hook)
diff --git a/tests/test_iqtree/test_build_tree.py b/tests/test_iqtree/test_build_tree.py
index 90cbf8a..250cba3 100644
--- a/tests/test_iqtree/test_build_tree.py
+++ b/tests/test_iqtree/test_build_tree.py
@@ -1,7 +1,7 @@
 import re
 
 import pytest
-from cogent3 import ArrayAlignment, make_tree
+from cogent3 import Alignment, make_tree
 
 import piqtree
 from piqtree.exceptions import IqTreeError
@@ -16,12 +16,13 @@
 
 
 def check_build_tree(
-    four_otu: ArrayAlignment,
+    four_otu: Alignment,
     dna_model: DnaModel,
     freq_type: FreqType | None = None,
     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())
@@ -49,7 +54,7 @@ def check_build_tree(
 @pytest.mark.parametrize("dna_model", list(DnaModel)[:22])
 @pytest.mark.parametrize("freq_type", list(FreqType))
 def test_non_lie_build_tree(
-    four_otu: ArrayAlignment,
+    four_otu: Alignment,
     dna_model: DnaModel,
     freq_type: FreqType,
 ) -> None:
@@ -57,10 +62,15 @@ def test_non_lie_build_tree(
 
 
 @pytest.mark.parametrize("dna_model", list(DnaModel)[22:])
-def test_lie_build_tree(four_otu: ArrayAlignment, dna_model: DnaModel) -> None:
+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(
@@ -74,7 +84,7 @@ def test_lie_build_tree(four_otu: ArrayAlignment, dna_model: DnaModel) -> None:
     ],
 )
 def test_rate_model_build_tree(
-    four_otu: ArrayAlignment,
+    four_otu: Alignment,
     dna_model: DnaModel,
     invariant_sites: bool,
     rate_model: RateModel,
@@ -87,12 +97,12 @@ def test_rate_model_build_tree(
     )
 
 
-def test_build_tree_inadequate_bootstrapping(four_otu: ArrayAlignment) -> None:
+def test_build_tree_inadequate_bootstrapping(four_otu: Alignment) -> None:
     with pytest.raises(IqTreeError, match=re.escape("#replicates must be >= 1000")):
         piqtree.build_tree(four_otu, Model(DnaModel.GTR), bootstrap_replicates=10)
 
 
-def test_build_tree_bootstrapping(four_otu: ArrayAlignment) -> None:
+def test_build_tree_bootstrapping(four_otu: Alignment) -> None:
     tree = piqtree.build_tree(four_otu, Model(DnaModel.GTR), bootstrap_replicates=1000)
 
     supported_node = max(tree.children, key=lambda x: len(x.children))
diff --git a/tests/test_iqtree/test_distance.py b/tests/test_iqtree/test_distance.py
index 38b694b..b3c1848 100644
--- a/tests/test_iqtree/test_distance.py
+++ b/tests/test_iqtree/test_distance.py
@@ -1,9 +1,9 @@
-from cogent3 import ArrayAlignment
+from cogent3 import Alignment
 
 from piqtree import jc_distances
 
 
-def test_jc_distance(five_otu: ArrayAlignment) -> None:
+def test_jc_distance(five_otu: Alignment) -> None:
     dists = jc_distances(five_otu)
 
     assert (
diff --git a/tests/test_iqtree/test_fit_tree.py b/tests/test_iqtree/test_fit_tree.py
index 91571a6..cf562ea 100644
--- a/tests/test_iqtree/test_fit_tree.py
+++ b/tests/test_iqtree/test_fit_tree.py
@@ -1,5 +1,5 @@
 import pytest
-from cogent3 import ArrayAlignment, get_app, make_tree
+from cogent3 import Alignment, get_app, make_tree
 from cogent3.app.result import model_result
 from cogent3.core.tree import PhyloNode
 
@@ -78,19 +78,57 @@ def check_branch_lengths(got: PhyloNode, expected: PhyloNode) -> None:
         (DnaModel.F81, "F81"),
     ],
 )
-def test_fit_tree(three_otu: ArrayAlignment, iq_model: DnaModel, c3_model: str) -> None:
+def test_fit_tree(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)
 
-    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)
diff --git a/tests/test_iqtree/test_model_finder.py b/tests/test_iqtree/test_model_finder.py
index fa98865..ce0af20 100644
--- a/tests/test_iqtree/test_model_finder.py
+++ b/tests/test_iqtree/test_model_finder.py
@@ -1,7 +1,7 @@
 import multiprocessing
 
 import pytest
-from cogent3 import ArrayAlignment
+from cogent3 import Alignment
 
 from piqtree.iqtree import ModelFinderResult, ModelResultValue, model_finder
 
@@ -47,7 +47,7 @@ def test_model_finder_result(model: str) -> None:
     assert result.model_stats[model].tree_length == 0.678
 
 
-def test_model_finder(five_otu: ArrayAlignment) -> None:
+def test_model_finder(five_otu: Alignment) -> None:
     result1 = model_finder(five_otu, rand_seed=1)
     result2 = model_finder(
         five_otu,
@@ -59,7 +59,7 @@ def test_model_finder(five_otu: ArrayAlignment) -> None:
     assert str(result1.best_bic) == str(result2.best_bic)
 
 
-def test_model_finder_restricted_submod(five_otu: ArrayAlignment) -> None:
+def test_model_finder_restricted_submod(five_otu: Alignment) -> None:
     result = model_finder(five_otu, rand_seed=1, model_set={"HKY", "TIM"})
     assert str(result.best_aic).startswith(("HKY", "TIM"))
     assert str(result.best_aicc).startswith(("HKY", "TIM"))
diff --git a/tests/test_iqtree/test_nj_tree.py b/tests/test_iqtree/test_nj_tree.py
index d3d1949..ae3c68c 100644
--- a/tests/test_iqtree/test_nj_tree.py
+++ b/tests/test_iqtree/test_nj_tree.py
@@ -1,12 +1,25 @@
-from cogent3 import ArrayAlignment, make_tree
+from cogent3 import Alignment, make_tree
 
 from piqtree import jc_distances, nj_tree
 
 
-def test_nj_tree(five_otu: ArrayAlignment) -> None:
+def test_nj_tree(five_otu: Alignment) -> None:
     expected = make_tree("(((Human, Chimpanzee), Rhesus), Manatee, Dugong);")
 
     dists = jc_distances(five_otu)
     actual = nj_tree(dists)
 
     assert expected.same_topology(actual)
+
+
+def test_nj_tree_allow_negative(all_otu: Alignment) -> None:
+    # a distance matrix can produce trees with negative branch lengths
+    dists = jc_distances(all_otu)
+
+    # check that all branch lengths are non-negative, by default
+    tree1 = nj_tree(dists)
+    assert all(node.length >= 0 for node in tree1.traverse(include_self=False))
+
+    # check that some branch lengths are negative when allow_negative=True
+    tree2 = nj_tree(dists, allow_negative=True)
+    assert any(node.length < 0 for node in tree2.traverse(include_self=False))