[Matplotlib-users] Import error: Cannot import pylab modules

Thomas Caswell tcaswell at gmail.com
Mon Apr 25 22:50:00 EDT 2016


We have reported the name collision to both the individual who upload
'pylab' to pip (no response) and pypi told us that they would not get
involved in name disputes.

I have put PRs into both of those projects to remove pylab from their code
bases


https://github.com/biocore/qiime/pull/2143
https://github.com/Ecogenomics/GroopM/pull/20

Tom

On Mon, Apr 25, 2016 at 5:44 PM Benjamin Root <ben.v.root at gmail.com> wrote:

> Yup, I think that is your problem. You will want to do a "sudo pip
> uninstall pylab". By the way, it is really a bad idea to do any pip
> installs with sudo. Pip installs execute arbitrary code, and you don't want
> to give arbitrary code sudo access. Furthermore, it is probably best to
> maintain a distinction between the "user's python" and the "system's
> python". This is why virtual environments or anaconda has been so valuable
> because it helps with maintaining that distinction.
>
> I hope that helps!
> Ben Root
>
>
> On Mon, Apr 25, 2016 at 5:28 PM, blavergar <blancaverag at gmail.com> wrote:
>
>> Thank you for the answer!
>>
>> This is the output:
>>
>> /usr/local/lib/python2.7/site-packages/pylab/__init__.pyc
>>
>> 2016-04-25 21:31 GMT+02:00 Benjamin Root [via matplotlib] <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=47021&i=0>>:
>>
>>> Can you do the following (from the python interpreter)
>>>
>>> import pylab
>>> print pylab.__file__
>>>
>>> There has been a rogue package on pypi called "pylab" that we have been
>>> trying to get taken off of the listing, since it conflicts with our
>>> long-standing package and trademark. Nothing nefarious, just some person's
>>> collection of dependencies that he decided to call pylab and uploaded to
>>> pypi for his personal use.
>>>
>>> Ben Root
>>>
>>>
>>> On Mon, Apr 25, 2016 at 5:00 AM, blavergar <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=47019&i=0>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I want to use two programs (GroopM and QIIME) requiring matplotlib
>>>> >=1.1.0
>>>> and python 2.7, which I have installed. My OS is Centos 6.
>>>>
>>>> They both give similar errors:
>>>>
>>>> 1.
>>>> (...)
>>>> *** ERROR RAISED DURING STEP: Plot Taxonomy Summary
>>>> Command run was:
>>>>  plot_taxa_summary.py -i
>>>>
>>>> taxa_summary2/OTU_L2.txt,taxa_summary2/OTU_L3.txt,taxa_summary2/OTU_L4.txt,taxa_summary2/OTU_L5.txt,taxa_summary2/OTU_L6.txt
>>>> -o taxa_summary2/taxa_summary_plots/
>>>> Command returned exit status: 1
>>>> Stdout:
>>>>
>>>> Stderr
>>>> Traceback (most recent call last):
>>>>   File "/usr/local/bin/plot_taxa_summary.py", line 20, in <module>
>>>>     from qiime.plot_taxa_summary import make_all_charts
>>>>   File
>>>> "/usr/local/lib/python2.7/site-packages/qiime/plot_taxa_summary.py",
>>>> line 24, in <module>
>>>>     from pylab import rc, axis, title, axes, pie, figlegend, clf,
>>>> savefig,
>>>> figure\
>>>> *ImportError: cannot import name rc*
>>>>
>>>>
>>>>
>>>> Pylab is imported in plot_taxa_summary.py as follows:
>>>>
>>>> (...)
>>>>
>>>> import matplotlib
>>>> import re
>>>> matplotlib.use('Agg', warn=False)
>>>> from matplotlib.font_manager import FontProperties
>>>> from pylab import rc, axis, title, axes, pie, figlegend, clf, savefig,
>>>> figure\
>>>>     , close
>>>>
>>>> (...)
>>>>
>>>>
>>>> 2.
>>>> (...)
>>>> File "/usr/local/lib/python2.7/site-packages/groopm/cluster.py", line
>>>> 54, in
>>>> <module>
>>>> from pylab import show
>>>>
>>>> *ImportError: cannot import name show*
>>>>
>>>>
>>>>
>>>> And the content of cluster.py involving the importing of pylab is:
>>>> (...)
>>>> from sys import stdout, exit
>>>>
>>>> from colorsys import hsv_to_rgb as htr
>>>> import matplotlib.pyplot as plt
>>>> from pylab import show
>>>> from numpy import (abs as np_abs,
>>>>  (...)
>>>>
>>>>
>>>>
>>>> As I read that pylab is installed directly with matplotlib I have
>>>> already
>>>> tried different versions and installations (conda, pip, yum...) but
>>>> none of
>>>> them got those programs working.
>>>>
>>>>
>>>> Could someone help with this, please?
>>>>
>>>> Thank you!
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://matplotlib.1069221.n5.nabble.com/Import-error-Cannot-import-pylab-modules-tp47010.html
>>>> Sent from the matplotlib - users mailing list archive at Nabble.com.
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>>>>
>>>
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>> modules
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