<div dir="ltr">This might explain a pypy3 TravisCI failure, but that seems to have sorted itself out on a later commit / rerun, e.g.<div><br></div><div><a href="https://travis-ci.org/github/biopython/biopython/jobs/722740797">https://travis-ci.org/github/biopython/biopython/jobs/722740797</a><br></div><div><br></div><div><pre id="gmail-log" class="gmail-ansi gmail-log-body-content" style="box-sizing:border-box;min-height:42px;padding:15px 0px;color:rgb(241,241,241);font-family:Cousine,monospace;font-size:12px;line-height:19px;white-space:pre-wrap;background-color:rgb(34,34,34);margin-top:0px"><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><span id="gmail-0-522" class="gmail-duration" title="This command finished after 1.69 seconds." style="box-sizing:border-box;padding:4px 7px 2px;line-height:10px;font-size:10px;background-color:rgb(102,102,102);border-radius:6px;color:rgb(187,187,187);display:block">1.69s</span><span id="gmail-0-523" style="box-sizing:border-box">$ tox -c .travis-tox.ini -e $TOXENV --notest</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">278</a><span id="gmail-0-524" style="box-sizing:border-box">pypy3-nocov create: /home/travis/build/biopython/biopython/.tox/pypy3-nocov</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">279</a><span id="gmail-0-525" style="box-sizing:border-box">ERROR: invocation failed (exit code 1), logfile: /home/travis/build/biopython/biopython/.tox/pypy3-nocov/log/pypy3-nocov-0.log</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">280</a><span id="gmail-0-526" style="box-sizing:border-box">================================== log start ===================================</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">281</a><span id="gmail-0-527" style="box-sizing:border-box">Traceback (most recent call last):</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">282</a><span id="gmail-0-528" style="box-sizing:border-box">  File "/opt/python/pypy3.6-7.1.1/lib-python/3/runpy.py", line 193, in _run_module_as_main</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">283</a><span id="gmail-0-529" style="box-sizing:border-box">    "__main__", mod_spec)</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">284</a><span id="gmail-0-530" style="box-sizing:border-box">  File "/opt/python/pypy3.6-7.1.1/lib-python/3/runpy.py", line 85, in _run_code</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">285</a><span id="gmail-0-531" style="box-sizing:border-box">    exec(code, run_globals)</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">286</a><span id="gmail-0-532" style="box-sizing:border-box">  File "/home/travis/virtualenv/pypy3.6-7.1.1/site-packages/virtualenv.py", line 22, in <module></span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">287</a><span id="gmail-0-533" style="box-sizing:border-box">    import distutils.spawn</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">288</a><span id="gmail-0-534" style="box-sizing:border-box">  File "/home/travis/virtualenv/pypy3.6-7.1.1/site-packages/_distutils_hack/__init__.py", line 82, in create_module</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">289</a><span id="gmail-0-535" style="box-sizing:border-box">    return importlib.import_module('._distutils', 'setuptools')</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">290</a><span id="gmail-0-536" style="box-sizing:border-box">  File "/home/travis/virtualenv/pypy3.6-7.1.1/lib-python/3/importlib/__init__.py", line 126, in import_module</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">291</a><span id="gmail-0-537" style="box-sizing:border-box">    return _bootstrap._gcd_import(name[level:], package, level)</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">292</a><span id="gmail-0-538" style="box-sizing:border-box">  File "<frozen importlib._bootstrap>", line 974, in _gcd_import</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">293</a><span id="gmail-0-539" style="box-sizing:border-box">  File "<frozen importlib._bootstrap>", line 924, in _sanity_check</span></div><div class="gmail-log-line" style="box-sizing:border-box;padding:0px 15px 0px 62px;margin:0px;min-height:19px"><a style="box-sizing:border-box;color:rgb(102,102,102);display:inline-block;text-align:right;min-width:40px;padding-right:1em">294</a><span id="gmail-0-540" style="box-sizing:border-box">SystemError: Parent module 'setuptools' not loaded, cannot perform relative import</span></div></pre></div><div><br></div><div>Peter</div><div><br></div><div>Peter</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 2, 2020 at 1:07 PM Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com">p.j.a.cock@googlemail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><br></div><div><div dir="auto">FYI, I’ve seen some recent continuous integration failures likely linked to setuptools v50.0.0 - might affect Biopython too?</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">---------- Forwarded message ---------<br>From: <strong class="gmail_sendername" dir="auto">Ralf Gommers</strong> <span dir="auto"><<a href="mailto:ralf.gommers@gmail.com" target="_blank">ralf.gommers@gmail.com</a>></span><br>Date: Wed, 2 Sep 2020 at 11:34<br>Subject: [Numpy-discussion] setuptools/distutils merger & numpy.distutils<br>To: Discussion of Numerical Python <<a href="mailto:numpy-discussion@python.org" target="_blank">numpy-discussion@python.org</a>><br></div><br><br><div dir="ltr"><div>Hi all,</div><div><br></div><div>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. <br></div><div><br></div><div>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 <a href="https://github.com/pypa/setuptools/issues/2372" target="_blank">https://github.com/pypa/setuptools/issues/2372</a> for discussion.</div><div><br></div><div>Cheers,<br></div><div>Ralf</div><div><br></div></div><br><br>_______________________________________________<br><br>NumPy-Discussion mailing list<br><br><a href="mailto:NumPy-Discussion@python.org" target="_blank">NumPy-Discussion@python.org</a><br><br><a href="https://mail.python.org/mailman/listinfo/numpy-discussion" rel="noreferrer" target="_blank">https://mail.python.org/mailman/listinfo/numpy-discussion</a><br><br></div></div>
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