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

blavergar blancaverag at gmail.com
Tue Apr 26 03:05:07 EDT 2016


Thank you very much! I got it working now!

2016-04-26 4:50 GMT+02:00 tcaswell [via matplotlib] <
ml-node+s1069221n47027h81 at n5.nabble.com>:

> 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 <[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=47027&i=0>> 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 <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=47027&i=1>> 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!
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
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