ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

I'm in Python 3.8.5. It sounds too simple to be real, but I had this same issue and all I did was reinstall numpy. Gone.

pip uninstall numpypip install numpy

try with numpy==1.20.0 this worked here, even though other circumstances are different (python3.8 on alpine 3.12).

Indeed, (building and) installing with numpy>=1.20.0 should work, as pointed out e.g. by this answer below. However, I thought some background might be interesting -- and provide also alternative solutions.

There was a change in the C API in numpy 1.20.0. In some cases, pip seems to download the latest version of numpy for the build stage, but then the program is run with the installed version of numpy. If the build version used in <1.20, but the installed version is =>1.20, this will lead to an error.

(The other way around it should not matter, because of backwards compatibility. But if one uses an installed version numpy<1.20, they did not anticipate the upcoming change.)

This leads to several possible ways to solve the problem:

• upgrade to numpy>=1.20.0
• use minmum supported numpy version in pyproject.toml (oldest-supported-numpy)
• install with --no-binary
• install with --no-build-isolation

For a more detailed discussion of potential solutions, seehttps://github.com/scikit-learn-contrib/hdbscan/issues/457#issuecomment-773671043.