harmonypy Files

Fixed

• Fixed a memory-corruption bug when correcting for more than one covariate (e.g. lab and processing day). covariate_bounds was allocated one element too small, so std::partial_sum wrote one entry past the end of the buffer — undefined behavior that could silently corrupt memory or crash. The correction results are unchanged. Thanks to @jkhales for finding and fixing this (#53).

Development

• Added an AddressSanitizer + UndefinedBehaviorSanitizer CI job that builds the extension with -fsanitize=address,undefined and runs the test suite under the sanitizer runtime, so memory errors like the one above fail CI. Build it locally with pip install -e . -C cmake.define.HARMONYPY_SANITIZE=ON.
• Linux wheels are now built on manylinux_2_28 (glibc 2.28+, e.g. RHEL/ AlmaLinux 8, Ubuntu 18.10+) instead of manylinux2014. Recent NumPy releases no longer ship manylinux2014 wheels and require GCC >= 10.3, which the old build image did not provide; manylinux_2_28 matches NumPy's own wheels.