Incompatible install in Python3 (Setuptools warns about Python 2 incompatibility)

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The reason to submit this is because this warning came up when building a package for a program (HTSeq: https://github.com/htseq/htseq ) via python3 setup.py install: The program compiled fine, but -as said- I get this in the output:

… htseq-release_0.11.4/todo.txt symlinking folders for python3 running install running build running build_py running preprocess cythonizing /usr/lib64/python2.7/site-packages/pkg_resources/py2_warn.py:22: UserWarning: Setuptools will stop working on Python 2 ************************************************************ You are running Setuptools on Python 2, which is no longer supported and >>> SETUPTOOLS WILL STOP WORKING <<< in a subsequent release (no sooner than 2020-04-20). .. .. SWIGging correcting SWIG for python3

I do not understand why this popped up, not calling python at all, nor using pip or pip3 for creating the HTSeq package.

Environment Details

• Operating System and version: Slackware64-current
• Python versions on the system: 2.7.17 and 3.8.2
• Python installed how: via packages build by ‘setup.py install’ route https://packages.slackware.com/?r=slackware64-current&p=python-2.7.17-x86_64-2.txz https://packages.slackware.com/?r=slackware64-current&p=python3-3.8.2-x86_64-1.txz https://packages.slackware.com/?r=slackware64-current&p=python-pip-20.0.2-x86_64-1.txz https://packages.slackware.com/?r=slackware64-current&p=python-setuptools-45.3.0-x86_64-1.txz

Output of pip --version from commandline: bash-5.0$ pip --version /usr/lib64/python2.7/site-packages/pkg_resources/py2_warn.py:22: UserWarning: Setuptools will stop working on Python 2 ************************************************************ You are running Setuptools on Python 2, which is no longer supported and >>> SETUPTOOLS WILL STOP WORKING <<< in a subsequent release (no sooner than 2020-04-20). Please ensure you are installing Setuptools using pip 9.x or later or pin to setuptools<45 in your environment. If you have done those things and are still encountering this message, please comment in https://github.com/pypa/setuptools/issues/1458 about the steps that led to this unsupported combination. ************************************************************ sys.version_info < (3,) and warnings.warn(pre + “" * 60 + msg + "” * 60) pip 20.0.2 from /usr/lib64/python2.7/site-packages/pip (python 2.7) bash-5.0$ pip3 --version pip 20.0.2 from /usr/lib64/python3.8/site-packages/pip (python 3.8) bash-5.0$

[brobr]

Thanks, I’ve pointed the developers of HTSeq to this post again; maybe they can take this on board.

[McSinyx]

So, isn’t it a python bug due to the mixed usage of p/cython vs p/cython3 etc.?

AFAIK the more canonical way to do it is to call Cython with sys.executable (that’s how Cython performs functional tests), however I think it might be a better idea to avoid calling the shell command and use the Python function cythonize.