Fix build system and CI issues

.github/workflows/build_and_publish.yml

@@ -26,7 +26,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
@@ -53,27 +53,36 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-24.04, macOS-11 ]
-        python-version: [ 36, 37, 38, 39, 310, 311 ]
+        os: [ ubuntu-24.04, macos-14, macos-15-intel ]
+        python-version: [ 310, 311 ]
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
 
       - name: "Build wheel (${{ matrix.os }}, py${{ matrix.python-version }})"
-        uses: pypa/cibuildwheel@v2.11.1
+        uses: pypa/cibuildwheel@v2.21.3
         with:
           config-file: cibuildwheel.toml
         env:
           CIBW_BUILD: "cp${{ matrix.python-version}}-*"
+          # Override deployment target to 14.0 for all macOS runners
+          MACOSX_DEPLOYMENT_TARGET: "14.0"
+          # Build only native architecture on each runner (no cross-compilation)
+          CIBW_ARCHS_MACOS: >-
+            ${{
+              matrix.os == 'macos-14' && 'arm64' ||
+              matrix.os == 'macos-15-intel' && 'x86_64' ||
+              'auto'
+            }}
 
       - name: "Upload build artifacts (${{ matrix.os }}, py${{ matrix.python-version }})"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: dist
+          name: dist-${{ matrix.os }}-py${{ matrix.python-version }}
           path: ./wheelhouse/*.whl
 
   make_sdist:
@@ -83,7 +92,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
           submodules: true
@@ -94,9 +103,9 @@ jobs:
           pipx run build --sdist
 
       - name: "Upload build artifacts"
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: "dist"
+          name: "dist-sdist"
           path: "dist/*.tar.gz"
 
   publish_to_pypi:
@@ -113,10 +122,14 @@ jobs:
 
     steps:
       - name: "Download build artifacts"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: "dist"
-          path: "dist"
+          path: "artifacts"
+
+      - name: "Collect all artifacts into dist folder"
+        run: |
+          mkdir -p dist
+          find artifacts -type f \( -name '*.whl' -o -name '*.tar.gz' \) -exec cp {} dist/ \;
 
       - name: "Publish to PyPI"
         if: startsWith(github.ref, 'refs/tags')

.gitignore

@@ -28,9 +28,8 @@ tests/FFPopSim.py
 tests/FFPopSim.pyc
 tests/_FFPopSim.so
 
-# SWIG generated files (they are kept in the static-gsl branch)
-src/python/FFPopSim.py
-src/python/FFPopSim_wrap.cpp
+# SWIG generated Python module (FFPopSim.py is kept in repo)
+# Wrapper is now committed to ensure consistent SWIG 4.3.1 across platforms
 
 # Compiled Object files
 *.slo

Makefile

@@ -55,7 +55,7 @@
 # Please set your Python 3 executable if you want to build the Python
 # bindings. If you are only interested in the C++ part of the library,
 # comment out the following line
-PYTHON := python3
+PYTHON := micromamba run -n ffpopsim11 python
 
 # Note: please look in 'setup.py' if you are building the Python extension!
 #       You can call distutils with 'setup.py' directly if you prefer. The
@@ -73,11 +73,19 @@ OPTIMIZATION_LEVEL := O2
 
 # Please use the following variable for additional flags to the C++ compiler,
 # such as include folders (e.g. -I/opt/local/include)
-CXXFLAGS = -c -Wall -$(OPTIMIZATION_LEVEL) -fPIC
+GSL_CFLAGS := $(shell gsl-config --cflags 2>/dev/null)
+# Try to find Boost in common locations (macOS Homebrew, MacPorts, or standard Linux paths)
+BOOST_INCLUDE := $(shell \
+	if [ -d /opt/homebrew/opt/boost/include ]; then echo "-I/opt/homebrew/opt/boost/include"; \
+	elif [ -d /usr/local/opt/boost/include ]; then echo "-I/usr/local/opt/boost/include"; \
+	elif [ -d /opt/local/include/boost ]; then echo "-I/opt/local/include"; \
+	fi)
+CXXFLAGS = -c -Wall -$(OPTIMIZATION_LEVEL) -fPIC -std=c++11 $(GSL_CFLAGS) $(BOOST_INCLUDE)
 
 # Please use the following variable for additional flags to the linker, such
 # as library folders for GSL (e.g. -L/opt/local/lib)
-LDFLAGS = -$(OPTIMIZATION_LEVEL)
+GSL_LDFLAGS := $(shell gsl-config --libs 2>/dev/null | sed 's/-lgsl -lgslcblas//')
+LDFLAGS = -$(OPTIMIZATION_LEVEL) $(GSL_LDFLAGS)
 
 # Additional options used to regenerate the SWIG files or to rebuild the docs.
 
@@ -263,11 +271,7 @@ $(TESTSDIR)/$(TESTS_OBJECT_GENEALOGY): $(TESTSDIR)/$(TESTS_SOURCE_GENEALOGY)
 	$(CXX) $(TESTS_CXXFLAGS) -c $(@:.o=.cpp) -o $@
 
 run-tests:
-	cd "tests" && ./highd
-	cd "tests" && ./hivpopulation
-	cd "tests" && ./lowd
-	cd "tests" && ./recombination_lowd
-	cd "tests" && ./test_genealogy
+	cd tests && ./highd && ./hivpopulation && ./lowd && ./recombination_lowd && ./test_genealogy
 
 clean-tests:
 	cd $(TESTSDIR); rm -rf *.o $(TESTS_LOWD) $(TESTS_HIGHD) $(TESTS_GENEALOGY) $(TESTS_LOWD_REC) $(TESTS_HIVPOP)

cibuildwheel.toml

@@ -11,46 +11,57 @@ skip = [
   "pp*",
 ]
 
-macos.archs = ["x86_64", "arm64"]
+# Architecture is set per-runner in the workflow file to avoid cross-compilation
+# GSL libraries from Homebrew require macOS 14.0 minimum
+macos.environment = {MACOSX_DEPLOYMENT_TARGET = "14.0"}
 
 build-verbosity = 1
 
 linux.before-build = [
   "yum makecache fast",
   "yum install -y boost-devel gsl-devel >/dev/null",
-  "make swig",
 ]
 
 macos.before-build = [
   "brew install boost gsl",
-  "make swig",
-]
-
-
-test-skip = [
-  "*aarch64*",
-  "*arm64*",
-  "*ppc64*",
-  "*s390x*",
 ]
 
 
 linux.before-test = [
-  "yum install -y parallel >/dev/null",
-  "pip install biopython matplotlib numpy pandas pygments scipy"
+  "pip install 'biopython' 'matplotlib' 'numpy<2' 'pandas' 'pygments' 'scipy'"
 ]
 
+# Run examples serially (one at a time) without parallel to avoid memory issues in CI
 linux.test-command = [
-  "cd {project} && bash ./run-examples --skip-slow"
+  """cd {project}/examples && for f in *.py; do
+    case "$f" in
+      benefits_of_sex.py|genealogies_with_selection.py|measuring_fixation_probabilities.py|multi_sample_adaptive.py|mutation_selection_balance_highd.py|neutral_LD_highd.py|speed_highd.py|speed_lowd.py)
+        echo "Skipping slow example: $f"
+        ;;
+      *)
+        echo "Testing $f..."
+        MPLBACKEND=Agg python3 "$f" || exit 1
+        ;;
+    esac
+  done"""
 ]
 
 
 macos.before-test = [
-  "brew install parallel >/dev/null",
-  "pip install biopython matplotlib numpy pandas pygments scipy"
+  "pip install 'biopython' 'matplotlib' 'numpy<2' 'pandas' 'pygments' 'scipy'"
 ]
 
-# Tests are very slow on mac, so only do basics
+# Run same tests as Linux for consistency - serially without parallel
 macos.test-command = [
-  "cd {project} && python examples/example.py"
+  """cd {project}/examples && for f in *.py; do
+    case "$f" in
+      benefits_of_sex.py|genealogies_with_selection.py|measuring_fixation_probabilities.py|multi_sample_adaptive.py|mutation_selection_balance_highd.py|neutral_LD_highd.py|speed_highd.py|speed_lowd.py)
+        echo "Skipping slow example: $f"
+        ;;
+      *)
+        echo "Testing $f..."
+        MPLBACKEND=Agg python3 "$f" || exit 1
+        ;;
+    esac
+  done"""
 ]

examples/genealogies_with_selection.py

@@ -38,8 +38,8 @@
 #set the effect sizes of the mutations that are injected (the same at each site in this case)
 pop.set_fitness_additive(np.ones(L)*s)
 
-#track the genealogy at a central locus L/2 (which one doesn't matter in the asexual case)
-pop.track_locus_genealogy([L/2])
+#track the genealogy at a central locus L//2 (which one doesn't matter in the asexual case)
+pop.track_locus_genealogy([L//2])
 
 #initialize the populations
 pop.set_wildtype(pop.carrying_capacity)

examples/speed_highd.py

@@ -41,7 +41,7 @@
 
         pop.set_wildtype(N)                     # set a wildtype population of size N
 
-        pop.evolve(1.0 / (L * (mu + r)))        # evolve until equilibrium
+        pop.evolve(int(1.0 / (L * (mu + r))))   # evolve until equilibrium
 
         # run for G generations to measure execution time
         t1=time.time()

setup.py

@@ -2,6 +2,8 @@
 # vim: fdm=indent
 
 import sys
+import subprocess
+import os
 
 # Python 3.6 compatibility: Python 3.6 has no compatible version of setuptools that supports
 # PEP-517 (the `pyproject.toml`-based config), so we use a shim package `ppsetuptools` instead.
@@ -12,6 +14,31 @@
 
 import numpy as np
 
+# Get GSL include paths
+def get_gsl_include():
+    try:
+        output = subprocess.check_output(['gsl-config', '--cflags'], stderr=subprocess.DEVNULL)
+        cflags = output.decode().strip().split()
+        return [flag[2:] for flag in cflags if flag.startswith('-I')]
+    except:
+        return []
+
+# Get Boost include paths
+def get_boost_include():
+    for path in ['/opt/homebrew/opt/boost/include', '/usr/local/opt/boost/include', '/opt/local/include']:
+        if os.path.isdir(path):
+            return [path]
+    return []
+
+# Get GSL library paths
+def get_gsl_lib_dirs():
+    try:
+        output = subprocess.check_output(['gsl-config', '--libs'], stderr=subprocess.DEVNULL)
+        ldflags = output.decode().strip().split()
+        return [flag[2:] for flag in ldflags if flag.startswith('-L')]
+    except:
+        return []
+
 setup_args = dict(
   py_modules=["FFPopSim"],
   package_dir={ '': 'src/python' },
@@ -29,8 +56,10 @@
         'src/hypercube_lowd.cpp',
         'src/hypercube_highd.cpp',
       ],
-      include_dirs=[np.get_include()],
+      include_dirs=[np.get_include()] + get_gsl_include() + get_boost_include(),
+      library_dirs=get_gsl_lib_dirs(),
       libraries=['gsl', 'gslcblas'],
+      extra_compile_args=['-std=c++11'],
       py_limited_api = True
     )
   ]

src/haploid_highd.cpp

@@ -187,9 +187,18 @@ int haploid_highd::free_mem() {
 		cerr <<"haploid_highd::free_mem(): No memory allocated!\n";
 		return HP_BADARG;
 	} else {
+		delete [] genome;
+		delete [] crossovers;
 		delete [] allele_frequencies;
 		delete [] gamete_allele_frequencies;
 		delete [] trait;
+		delete [] trait_stat;
+		for (int t = 0; t < number_of_traits; t++){
+			delete [] trait_covariance[t];
+		}
+		delete [] trait_covariance;
+		delete [] trait_weights;
+		gsl_rng_free(evo_generator);
 		mem = false;
 		return 0;
 	}
@@ -203,6 +212,10 @@ int haploid_highd::free_mem() {
 int haploid_highd::provide_at_least(int n) {
 	//calculate the number of clones that need to be newly allocated. Allow for some slack
 	//to avoid calling this too often
+	// BUG FIX: Check if we already have enough clones to avoid unsigned arithmetic underflow
+	if (available_clones.size() >= n) {
+		return 0;  // We already have enough clones available
+	}
 	int needed_gts = n - available_clones.size() + 100 + 0.1 * population.size();
 
 	//allocate at the necessary memory