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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

Bertini 2 (b2) is a C++17 numerical algebraic geometry library with Python bindings. It implements homotopy continuation for solving polynomial systems, including path tracking, endgames (power series, Cauchy), and start systems (total degree, multihomogeneous). The Python package is published to PyPI as bertini.

Build Commands

C++ Core Library (CMake + Ninja)

# Configure (from repo root)
cmake -DENABLE_UNIT_TESTING=ON -G Ninja -B build -S .

# Build
cmake --build build --target all --config Release

# Run all C++ tests
ctest --test-dir build/core

Python Wheel (scikit-build-core)

python3 -m build --wheel

The build system uses scikit-build-core (configured in pyproject.toml). The wheel build invokes CMake internally.

macOS Dependencies (Homebrew)

brew install gmp mpfr libmpc eigen@3 eigenpy boost boost-python3

Linux/CI Dependencies (conda)

Use environment.yml (Ubuntu) or environment-win.yml (Windows) with conda/mamba/micromamba.

Running Tests

C++ Tests (Boost.Test)

Tests are defined in core/CMakeLists.txt. Each test suite is a separate executable:

# All tests
ctest --test-dir build/core

# Individual test executables (after build)
./build/core/test_classes
./build/core/test_blackbox
./build/core/test_classic
./build/core/test_endgames
./build/core/test_generating
./build/core/test_nag_algorithms
./build/core/test_nag_datatypes
./build/core/test_tracking_basics
./build/core/test_settings

Python Tests

pytest python/test/

Architecture

The project has three layers, built in order:

  1. core/ -- C++ shared library (libbertini2). Header-only-heavy design under core/include/bertini2/. Key subsystems:

    • function_tree/ -- Expression tree (nodes, operators, symbols) for representing polynomial systems
    • system/ -- Polynomial system construction, start systems (start/total_degree.hpp, start/mhom.hpp), patches, slices
    • trackers/ -- Path tracking (fixed-precision and adaptive-precision trackers, predictors, Newton correctors)
    • endgames/ -- Power series and Cauchy endgames for singular endpoint handling
    • nag_algorithms/ -- Higher-level algorithms (zero-dim solve, numerical irreducible decomposition)
    • io/parsing/ -- Boost.Spirit Qi parsers for classic Bertini input format
    • blackbox/ -- CLI executable entry point (bertini2_exe)

  2. python_bindings/ -- Boost.Python + eigenpy bindings producing _pybertini native module. Each *_export.cpp wraps the corresponding C++ subsystem. Depends on eigenpy for NumPy/Eigen interop.

  3. python/bertini/ -- Pure Python package that wraps _pybertini into a user-friendly API. Submodules mirror the C++ structure: function_tree, system, tracking, endgame, parse, nag_algorithm, multiprec, etc.

Key Dependencies

  • GMP/MPFR/MPC -- Arbitrary-precision arithmetic (found via custom CMake modules in cmake/)
  • Eigen 3.3 -- Linear algebra (pinned to v3.3)
  • Boost (serialization, filesystem, log, graph, regex, timer, chrono, thread, unit_test_framework, python) -- Boost >= 1.82 required; boost_system is conditionally linked for Boost < 1.89
  • eigenpy -- Eigen/NumPy bridge for Python bindings
  • jrl-cmakemodules -- CMake helper macros (auto-fetched via FetchContent if not found)

Build System Notes

  • The root CMakeLists.txt uses jrl-cmakemodules (fetched automatically). It currently only adds core/ as a subdirectory; python_bindings/ and python/ subdirectory calls are commented out (the wheel build via scikit-build-core handles them).
  • pyproject.toml configures scikit-build-core: wheel packages from python/bertini/, build dir is bld/.
  • Cross-platform: Linux uses manylinux Docker + auditwheel; macOS uses Homebrew; Windows uses conda + clang-cl (MSVC has template compilation issues).
  • -Werror is disabled globally. -pedantic is stripped from flags.

CI/CD

  • .github/workflows/build-and-publish-to-pypi.yml -- Builds wheels on Ubuntu/macOS/Windows, publishes to TestPyPI on develop push, PyPI on version tags (v*.*.*).
  • Pushes to develop trigger TestPyPI publish; tagged releases go to PyPI with Sigstore signing and GitHub Releases.

Conventions

  • C++ standard: C++17. Headers use .hpp extension.
  • License: GPL v3 with additional terms (see licenses/, core/ADDITIONAL_GPL_TERMS).
  • Version is tracked in python/bertini/_version.py and pyproject.toml.