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When installing SciPy 1.7.1 from source on Linux using

python setup.py build
python setup.py install

(along with environment and site.cfg hacking as needed) I end up with a broken build. My particular build recipe works for SciPy <= 1.6

Once SciPy 1.7.1 is built, importing e.g. scipy.optimize or scipy.special results in errors

AttributeError: module 'scipy.special._ufuncs_cxx' has no attribute 'pyx_capi'

ImportError: cannot import name 'levinson' from 'scipy.linalg._solve_toeplitz'

ImportError: cannot import name 'csgraph_to_dense' from 'scipy.sparse.csgraph._tools'

What has changed, and how do I solve this?

jmd_dk
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1 Answers1

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Looking at the site-packages directory I see that SciPy 1.7 installs itself as a zipped Python egg, whereas previous versions used to install as directories (though still Python eggs). This behaviour can be chosen by specifying the zip_safe argument to setuptools.setup(), called from within setup.py. In SciPy 1.7 this is called as

setup(**metadata)

with metadata not including 'zip_safe', meaning that whether zipped eggs are safe to use are automatically determined. This might also be the case for older SciPy versions, but for whatever reason the process ends up declaring zipped eggs to be safe for 1.7 on my system, which does not seem to be the case.

Manually adding

metadata['zip_safe'] = False

above setup(**metadata) prior to executing setup.py results in the egg being a directory (as opposed to a zipped archive), and the build works.

To do the patching of setup.py programatically, use e.g. (GNU sed)

sed -i "s/\(^ *\)\(setup *(.*\)$/\1metadata['zip_safe'] = False; \2/" setup.py
jmd_dk
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  • Out of curiosity, what does a command like `git submodule update --init && git clean -xdf && python3.9 -m pip install --user --upgrade --use-feature=in-tree-build .` result in? – Patol75 Aug 18 '21 at 01:11