Bump iqtree2 from f04b6f2 to 18fa5a3

.github/workflows/ci.yml

@@ -48,6 +48,12 @@ jobs:
           python-version: ${{ matrix.python-version }}
           cache-key: libiqtree-${{ matrix.os }}-${{ needs.build-iqtree.outputs.iqtree2-sha }}
 
+      - name: Update Homebrew
+        if: matrix.os != 'ubuntu-latest'
+        run: |
+          brew update
+          brew install llvm
+
       - name: Run Nox Testing
         run: |
           pip install nox

build_tools/before_all_mac.sh

@@ -3,6 +3,10 @@ if [ "$GITHUB_ACTIONS" = "true" ]; then
     brew update
 fi
 
-brew install eigen boost
+brew install llvm eigen boost libomp make
+
+export LDFLAGS="-L$(brew --prefix libomp)/lib"
+export CPPFLAGS="-I$(brew --prefix libomp)/include"
+export CXXFLAGS="-I$(brew --prefix libomp)/include"
 
 bash build_tools/build_iqtree.sh

build_tools/build_iqtree.sh

@@ -1,7 +1,19 @@
 cd iqtree2
 rm -rf build
 mkdir build && cd build
-cmake -DIQTREE_FLAGS="single" -DBUILD_LIB=ON ..
-make -j
+
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    echo "Building for macOS."
+    echo $LDFLAGS    
+    echo $CPPFLAGS
+    echo $CXXFLAGS    
+    cmake -DBUILD_LIB=ON -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ ..
+    gmake -j
+else
+    echo "Building for linux."
+    cmake -DBUILD_LIB=ON ..
+    make -j
+fi
+
 cd ../..
 mv iqtree2/build/libiqtree2.a src/piqtree2/_libiqtree/

pyproject.toml

@@ -100,7 +100,7 @@ target-version = "py310"
 # Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
 # McCabe complexity (`C901`) by default.
 select = ["ALL"]
-ignore = ["EXE002", "FA100", "E501", "PLR0913", "PLR2004", "D"]
+ignore = ["EXE002", "FA100", "E501", "PLR0913", "PLR2004", "S603", "S607", "D"]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]

setup.py

@@ -1,16 +1,58 @@
 """setup for piqtree2."""
 
+import os
+import platform
+import subprocess
+from pathlib import Path
+
 from pybind11.setup_helpers import Pybind11Extension, build_ext
 from setuptools import setup
 
 LIBRARY_DIR = "src/piqtree2/_libiqtree"
 
+
+def get_brew_prefix(package: str) -> Path:
+    """Get the prefix path for a specific Homebrew package."""
+    return Path(
+        subprocess.check_output(["brew", "--prefix", package]).strip().decode("utf-8"),
+    )
+
+
+if platform.system() == "Darwin":
+    brew_prefix_llvm = get_brew_prefix("llvm")
+    brew_prefix_libomp = get_brew_prefix("libomp")
+
+    # Use Homebrew's clang/clang++
+    os.environ["CC"] = str(brew_prefix_llvm / "bin" / "clang")
+    os.environ["CXX"] = str(brew_prefix_llvm / "bin" / "clang++")
+
+    # Define OpenMP flags and libraries for macOS
+    openmp_flags = ["-Xpreprocessor", "-fopenmp"]
+    openmp_libs = ["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 = []
+
 ext_modules = [
     Pybind11Extension(
         "_piqtree2",
         ["src/piqtree2/_libiqtree/_piqtree2.cpp"],
-        library_dirs=[LIBRARY_DIR],
-        libraries=["iqtree2", "z"],
+        library_dirs=[
+            *library_dirs,
+            LIBRARY_DIR,
+        ],
+        libraries=["iqtree2", "z", *openmp_libs],
+        extra_compile_args=openmp_flags,
+        include_dirs=[openmp_include] if openmp_include else [],
     ),
 ]