[Biopython] [Numpy-discussion] setuptools/distutils merger & numpy.distutils

[Peter Cock]

This might explain a pypy3 TravisCI failure, but that seems to have sorted
itself out on a later commit / rerun, e.g.

https://travis-ci.org/github/biopython/biopython/jobs/722740797

1.69s$ tox -c .travis-tox.ini -e $TOXENV --notest
278pypy3-nocov create: /home/travis/build/biopython/biopython/.tox/pypy3-nocov
279ERROR: invocation failed (exit code 1), logfile:
/home/travis/build/biopython/biopython/.tox/pypy3-nocov/log/pypy3-nocov-0.log
280================================== log start
===================================
281Traceback (most recent call last):
282  File "/opt/python/pypy3.6-7.1.1/lib-python/3/runpy.py", line 193,
in _run_module_as_main
283    "__main__", mod_spec)
284  File "/opt/python/pypy3.6-7.1.1/lib-python/3/runpy.py", line 85,
in _run_code
285    exec(code, run_globals)
286  File "/home/travis/virtualenv/pypy3.6-7.1.1/site-packages/virtualenv.py",
line 22, in <module>
287    import distutils.spawn
288  File "/home/travis/virtualenv/pypy3.6-7.1.1/site-packages/_distutils_hack/__init__.py",
line 82, in create_module
289    return importlib.import_module('._distutils', 'setuptools')
290  File "/home/travis/virtualenv/pypy3.6-7.1.1/lib-python/3/importlib/__init__.py",
line 126, in import_module
291    return _bootstrap._gcd_import(name[level:], package, level)
292  File "<frozen importlib._bootstrap>", line 974, in _gcd_import
293  File "<frozen importlib._bootstrap>", line 924, in _sanity_check
294SystemError: Parent module 'setuptools' not loaded, cannot perform
relative import


Peter

Peter

On Wed, Sep 2, 2020 at 1:07 PM Peter Cock <p.j.a.cock at googlemail.com> wrote:

>
> FYI, I’ve seen some recent continuous integration failures likely linked
> to setuptools v50.0.0 - might affect Biopython too?
>
> ---------- Forwarded message ---------
> From: Ralf Gommers <ralf.gommers at gmail.com>
> Date: Wed, 2 Sep 2020 at 11:34
> Subject: [Numpy-discussion] setuptools/distutils merger & numpy.distutils
> To: Discussion of Numerical Python <numpy-discussion at python.org>
>
>
> Hi all,
>
> I spent some time looking at the fallout of the setuptools 50.0 release.
> There's quite a few small issues, those can/should all be worked around by
> pinning setuptools to a lower version.
>
> The root cause and main longer-term issue is that numpy.distutils extends
> and monkeypatches distutils, which mostly was fine because distutils moved
> super slowly and had a decent QA process. Now with setuptools, any patch
> goes into master and gets released to the whole wide world without any
> testing. The summary of that and how to deal with it I posted on
> https://github.com/pypa/setuptools/issues/2372 for discussion.
>
> Cheers,
> Ralf
>
>
>
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>
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>
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>
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