RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject

Description

When trying to import astropy.stats I get the above AttributeError. Making the code unusable. Downgrading numpy has not worked at all.

Expected behavior

astropy.stats to be imported.

Actual behavior

Crashed with the above error. Note that if I just import astropy.stats then I get a different error

Steps to Reproduce

# Put your Python code snippet here.
from astropy.stats import sigma_clipped_stats

Traceback (most recent call last):
  File "apply_correction.py", line 52, in <module>
    from astropy.stats import sigma_clipped_stats
  File "/home/trystan/.local/lib/python3.6/site-packages/astropy/stats/__init__.py", line 14, in <module>
    from . import funcs
  File "/home/trystan/.local/lib/python3.6/site-packages/astropy/stats/funcs.py", line 17, in <module>
    from . import _stats
  File "__init__.pxd", line 918, in init astropy.stats._stats
RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
Error in sys.excepthook:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/apport_python_hook.py", line 72, in apport_excepthook
    from apport.fileutils import likely_packaged, get_recent_crashes
  File "/usr/lib/python3/dist-packages/apport/__init__.py", line 5, in <module>
    from apport.report import Report
  File "/usr/lib/python3/dist-packages/apport/report.py", line 13, in <module>
    import fnmatch, glob, traceback, errno, sys, atexit, locale, imp, stat
  File "/usr/lib/python3.6/imp.py", line 33, in <module>
    DeprecationWarning, stacklevel=2)
DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses

Original exception was:
Traceback (most recent call last):
  File "apply_correction.py", line 52, in <module>
    from astropy.stats import sigma_clipped_stats
  File "/home/trystan/.local/lib/python3.6/site-packages/astropy/stats/__init__.py", line 14, in <module>
    from . import funcs
  File "/home/trystan/.local/lib/python3.6/site-packages/astropy/stats/funcs.py", line 17, in <module>
    from . import _stats
  File "__init__.pxd", line 918, in init astropy.stats._stats
RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject

System Details

[GCC 8.4.0] Numpy 1.19.5 astropy 4.1 Scipy 1.5.4 Matplotlib 3.3.3

[embray]

I get this sometimes; it’s a Python environment error when you’re using some extension modules that were compiled against a different version of Numpy than the one you’re using.

[taldcroft]

BTW, if you are wondering about that warning there is useful info at:

• https://stackoverflow.com/questions/40845304/runtimewarning-numpy-dtype-size-changed-may-indicate-binary-incompatibility
• https://github.com/numpy/numpy/issues/11788

tl;dr it should be benign. I’ve seen this and occasionally had to ignore it in pytest.ini to get warning-free test runs.