How to Ignore Cython, even if found

Currently, importing setuptools.command.build_ext pulls in a Cython dependency if it finds any Cython on a system.

That is not in all cases ideal, e.g. in a package manager (such as spack) or a virtual python environment that does not have a cython installed, while at the same time a system-wide Cython exists. In such a setup, nearly always binary incompatibilities with the system-wide python install will occur.

Is there any way to express “try not to import cython (even when found)” to setuptools?

[jaraco]

@ax3l: I don’t. I’d suggest starting with the mailing list or maybe file an issue with their tracker to explain the issue and get advice on how to proceed.

[jaraco]

Thanks @ax3l for the reproducer. I’ve uploaded it as this gist. I then made a couple of revisions. The first was to specify a base image, which I suspect was necessary because I’m testing on macOS. At that point, I was able to run the build and get the error you described.

But I noticed one thing - that you’re not in fact installing Cython system-wide; you’re installing it in the user site (pip install --user). And the way user-local works is it’s shared across different Python installs… which clarifies the answer to the question, how is import cython succeeding.

In the next revision, I installed Cython system-wide, and the issue goes away. Now that Cython is installed only to the system Python 2.7, it no longer appears in the miniconda install of Python 2.7, and all is well.

In rev 4, I took another tack and disabled that user-local environment before invoking the build. This also bypasses the issue. One could alternatively have set PYTHONNOUSERSITE=1.

I think this demonstrates that the issue originates from an incorrect usage of user-local environments and presents a couple of plausible workarounds.

I do sympathize with the issue and thinking about the presented workaround in Setuptools, I’m reluctant to go with that approach because of the complexity of behavior it adds on import. If on the other hand cython has or could add a call to check that it’s viable in this environment, like cython.assert_viable(), that is something I would be willing to add, something like:

try:
    # Attempt to use Cython for building extensions, if available
    from Cython.Distutils.build_ext import build_ext as _build_ext
    __import__('cython').assert_viable()
except (ImportError, AssertionError):
    _build_ext = _du_build_ext

In other words, if Cython is willing to support this use-case, then setuptools will support it as well.