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Pypi and Cython

I'm trying to put together my first PyPi package and am growing confused about some basic aspects of it.

My package depends on SNPknock. When I try to install it on a fresh system (Ubuntu 18.04), I get:

pip install snpknock
Collecting snpknock
  Using cached https://files.pythonhosted.org/packages/68/a0/ceb6adc2b7f1a3009f2077c157a99640094021a66f881cb678ecf4
78887f/SNPknock-0.5.2.tar.gz
    Complete output from command python setup.py egg_info:
    You don't seem to have Cython installed. Please get a
    copy from www.cython.org and install it

I've extracted the setup.py from the tarball here, which includes that error message.

Here is my confusion. The setup.py file specifies Cython as a dependency:

DEPENDENCIES = ['Cython>='+CYTHON_MIN_VERSION,
                'numpy>='+NUMPY_MIN_VERSION]

However, it also imports Cython, but it seems that it needs to do that in order to cythonize some modules. It all seems a little circular, but I suspect that either I (or the author of this package) are missing something about this process.

Solution

  • The problem seems to be there are no wheels/eggs for you platform. In that case pip downloads sources and runs python setup.py install. If setup.py imports Cython it doesn't matter if said Cython is listed as a dependency. You must have Cython before running pip install because pip cannot get a list of dependencies from source code without running setup.py and setup.py requires Cython to be importable.

    If snpknock were ever release an egg or a wheel for your Python version pip would download it, get a list of dependencies and install them without consulting setup.py; after that it'd install the package. In that case pip would automatically download Cython or install compiled extensions right from the egg/wheel.