OpenMS Development

Build Gotchas

Boost on macOS: Use -DBOOST_USE_STATIC_LIBS=OFF (upstream Boost issue with transitive deps)
CMAKE_PREFIX_PATH: Use ; separator with -D flag, : with env var on Unix
delocate-wheel -L: Destination subdir inside wheel, NOT library search path. Use delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}

When CI tests fail, always investigate the root cause first before patching reference files or test expectations. Never bulk-replace expected values or regenerate test outputs as a first approach.
Never dismiss a test failure as "acceptable behavior" or "pre-existing/unrelated" without explicit user confirmation. Always investigate fully before concluding a failure is not actionable.
When asked to fix something, prefer using existing APIs/utilities in the codebase over heuristic approaches. Search for existing helper functions, conversion utilities, or detection APIs before implementing custom logic.
Before implementing non-trivial changes, first explore the codebase for existing patterns and utilities, then explain the planned approach before writing code.
For multi-file changes or unfamiliar areas, use plan mode or explore the relevant code first. Do not dive into implementation without understanding the existing architecture.

See src/pyOpenMS/CLAUDE.md for Python binding development.

Quick commands:

Build: cmake --build OpenMS-build --target pyopenms -j$(nproc)
Test: PYTHONPATH=OpenMS-build/pyOpenMS python3 -m pytest src/pyOpenMS/tests/ -v
Force rebuild after addon changes: rm OpenMS-build/pyOpenMS/.cpp_extension_generated