Fix build system and CI issues#18
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Updates outdated GitHub Actions to their latest versions: - actions/checkout v3 → v4 - pypa/cibuildwheel v2.11.1 → v2.21.3 - actions/upload-artifact v3 → v4 - actions/download-artifact v3 → v4 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Fixes multiple CI issues:
- Fix artifact upload conflicts by giving each job a unique artifact name
(dist-{os}-py{version}) to avoid conflicts with actions/upload-artifact@v3
- Update download step to collect all artifacts into dist folder
- Replace deprecated macOS-11 runner with macOS-13
These changes address the artifact conflicts that were causing build failures
and the macOS runner timeout issues.
Note: C++ test failures and Python example test failures still need investigation
as logs are not available from previous runs.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Remove Python 3.6 and 3.7 from the build matrix as they are no longer supported (3.6 EOL: Dec 2021, 3.7 EOL: June 2023). Current supported versions: 3.8, 3.9, 3.10, 3.11 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Update Makefile to auto-detect GSL and Boost paths using gsl-config and common installation directories (macOS Homebrew/MacPorts, Ubuntu) - Update setup.py to include GSL and Boost paths for Python extension - Fix numpy.i SWIG typemaps for compatibility with SWIG 4.3.1 (update SWIG_Python_AppendOutput calls to use 3-argument signature) - Add test_ffpopsim.py demo showing population evolution with selection These changes enable successful compilation on macOS and Ubuntu without hardcoded paths. All targets now build: C++ library, tests, and Python bindings. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add swig to CI dependencies (both Linux and macOS) - Drop Python 3.8 and 3.9 from CI matrix (EOL versions) - Keep only Python 3.10 and 3.11 for wheel builds The previous CI failures were due to missing swig in the cibuildwheel environment. SWIG is required to generate Python bindings. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add -std=c++11 to Makefile CXXFLAGS for C++ library compilation - Add -std=c++11 to setup.py extra_compile_args for Python extension - Fix run-tests target to run all tests in single shell context Boost 1.89.0 requires C++11 or later. Without specifying the C++ standard, the compiler defaulted to C++98/C++03, causing compilation errors with C++11 features like auto, rvalue references, and variadic templates. The run-tests target was failing because each cd command ran in a separate shell, causing "tests: No such file or directory" errors. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Add pre-generated SWIG wrapper (SWIG 4.3.1) to repository - Add generated FFPopSim.py module - Update .gitignore to allow SWIG-generated files - Remove `make swig` step from cibuildwheel.toml - Remove swig from CI dependencies The manylinux container has SWIG 3.x which generates incompatible SWIG_Python_AppendOutput signatures. By committing the wrapper generated with SWIG 4.3.1, we ensure consistent builds across all platforms. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
The GSL libraries installed via Homebrew on macOS-13 have a minimum deployment target of macOS 13.0. Set MACOSX_DEPLOYMENT_TARGET=13.0 to match the GSL library requirements and fix delocate-wheel errors. Error was: libgsl.28.dylib has a minimum target of 13.0 libgslcblas.0.dylib has a minimum target of 13.0 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- Pin numpy<2 in test dependencies to avoid numpy 2.0 compatibility issues - Make macOS run full test suite (./run-examples --skip-slow) for consistency with Linux The numpy 2.0 changes to array creation are stricter and cause test failures in examples like genetic_drift.py. Pinning to numpy v1 allows tests to pass while we address numpy v2 compatibility in a future PR. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Change is_void parameter from 0 to 1 in SWIG_Python_AppendOutput calls in numpy.i. For void functions that output arrays via ARGOUT parameters, is_void=1 ensures the array is returned directly instead of as a tuple. The bug caused functions like get_allele_frequencies() to return (None, array) tuples instead of just the array, leading to numpy errors when examples tried to create arrays from these results. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Replace macOS-13 with latest runners: - macos-15 (ARM64/Apple Silicon) - macos-15-intel (Intel x86_64) This provides better architecture coverage and future-proofs the CI as Apple discontinues Intel support. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Update MACOSX_DEPLOYMENT_TARGET from 13.0 to 14.0 to fix build failures on macOS 15 runners (both Intel and ARM64). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
On macos-15 (ARM): skip x86_64 wheel tests (prevents brew/Rosetta issues) On macos-15-intel: skip arm64 wheel tests (not runnable on Intel) Each runner now only tests wheels for its native architecture. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Configuration: - macos-14: ARM64 runner with GSL 14.0 - macos-15-intel: Intel runner - MACOSX_DEPLOYMENT_TARGET: 14.0 across all macOS runners This avoids the GSL minimum target mismatch that occurred with macos-15 ARM runners where GSL requires 15.0. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
The free_mem() function was not releasing several allocated arrays, causing significant memory leaks during evolution simulations with CROSSOVERS recombination model. Fixed by adding deletion of: - genome array (auxiliary array for crossover points) - crossovers array (crossover points storage) - trait_stat array (trait statistics) - trait_covariance matrix (2D array) - trait_weights array - gsl_rng generator (via gsl_rng_free) This reduces memory growth during evolution, though further investigation is needed for remaining accumulation during evolve(). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
When available_clones.size() > n, the subtraction (n - available_clones.size()) caused unsigned arithmetic underflow, wrapping to INT_MAX (2^31-1). This made the code try to allocate 2 billion clones, causing catastrophic memory growth. The fix checks if we already have enough available clones before performing the arithmetic. This prevents the underflow and keeps memory usage reasonable. Before: decay_of_LD_highd.py would hit 12GB after 5 generations After: Completes all 250 generations with <1GB memory 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
- speed_highd.py: Cast float to int for evolve() argument - genealogies_with_selection.py: Use integer division (//) instead of float division (/) for locus index In Python 3, `/` always returns float, while `//` returns int. Functions expecting integer arguments now get the correct type. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Remove parallel dependency and run examples in a simple bash loop instead. This ensures truly serial execution to avoid any potential memory pressure in CI environments. Changes: - Removed parallel from before-test dependencies - Replaced ./run-examples script call with direct bash loop - Still skip slow examples for CI efficiency - Use MPLBACKEND=Agg to avoid interactive matplotlib 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Previously cibuildwheel was configured to build both x86_64 and arm64 wheels on BOTH runners, causing unnecessary cross-compilation: - macos-14 (ARM) was cross-compiling x86_64 via Rosetta - macos-15-intel (x86) was cross-compiling arm64 This was slower, less reliable, and produced duplicate wheels. Changes: - Set CIBW_ARCHS_MACOS per-runner: arm64 on macos-14, x86_64 on macos-15-intel - Removed macos.archs from cibuildwheel.toml (now set in workflow) - Removed test-skip config (no longer needed without cross-arch builds) - Each runner now builds only its native architecture Benefits: - Faster builds (no cross-compilation overhead) - More reliable (no Rosetta issues) - Cleaner artifact naming (no duplicates) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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Summary
This PR resolves build system failures and updates CI infrastructure:
Changes
Build System
gsl-configfor GSL detectionCI/CD
Testing
Test Plan
Notes
The build system changes are backward compatible and will work on systems with standard GSL/Boost installations via package managers.
🤖 Generated with Claude Code