[Mne_analysis] python-MNE installation

Eric Larson larson.eric.d at gmail.com
Tue Sep 30 10:13:58 EDT 2014
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I personally have found Anaconda easier to work with than Canopy, too, if
you want to try that.

Eric


On Tue, Sep 30, 2014 at 4:11 AM, Mainak Jas <mainakjas at gmail.com> wrote:

> Hi Tommi,
>
> Can you verify that you are actually on bash and not on tcsh or some other
> shell when you try the pip command? I think canopy works only on bash.
>
> Mainak
>
> On Tue, Sep 30, 2014 at 2:02 PM, Tommi Raij <raij at nmr.mgh.harvard.edu>
> wrote:
>
>> Hi Alex,
>>
>> Thank you, will try. However, as far as I could tell, Canopy does not
>> include pip (following full Canopy installation, attempts to give pip
>> commands just resulted in "command not found" errors until I used the yum
>> command below). Then, the question becomes, how to properly install pip for
>> Canopy?
>>
>> Best regards,
>>
>> Tommi
>> ------------------------------
>> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
>> Sent: ‎9/‎30/‎2014 2:13 AM
>> To: Discussion and support forum for the users of MNE Software
>> <mne_analysis at nmr.mgh.harvard.edu>
>> Subject: Re: [Mne_analysis] python-MNE installation
>>
>> hi Tommi,
>>
>> the problem is that you have 2 python systems installed:
>> - the system one that uses yum for installs + updates
>> - canopy
>>
>> when you did "yum install -y python-pip" you installed pip
>> for the system and not for canopy. I suspect canopy already
>> comes with pip installed.
>>
>> I recommend you uninstall pip with yum and any other python
>> packages you installed with yum and then make sure you use canopy.
>>
>> to check this use:
>>
>> which python
>>
>> it should point to the canopy folder. If it's the case do the same with
>> pip
>>
>> which pip
>>
>> if it points to canopy then you can safely do:
>>
>> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>>
>> let us know how it goes.
>>
>> Alex
>>
>>
>>
>>
>> On Mon, Sep 29, 2014 at 11:50 PM,  <raij at nmr.mgh.harvard.edu> wrote:
>> >
>> > Hi,
>> >
>> > New python (and longtime MNE) user here, hello to all.
>> >
>> > I am having trouble installing MNE-python on a linux box outside
>> Martinos
>> > Center. The machine (Dell Precision T7500)) runs CentOS 6.5 and has
>> > Freesurfer (5.3), MNE suite (developmental), and MATLAB installed -
>> these
>> > are running no prob.
>> >
>> > I am doing installation as root on a csh terminal.
>> >
>> > I have tried to follow the instructions at
>> > http://martinos.org/mne/stable/getting_started.html as follows:
>> >
>> > 1. Install Canopy python. When launcing for the first time, I set up the
>> > environment to point to /usr/pubsw/packages/python/, then make Canopy as
>> > the default python. Version: canopy-1.4.1-full-rh5-64.sh
>> >
>> > 2. Install pip (this did not exist on my system):
>> > yum install -y python-pip
>> >
>> > 3. Install developmental MNE-python suite
>> > pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>> >
>> > Then I open a new csh terminal as a regular user, and
>> > 4. Add the following line to my user-level ~/.cshrc:
>> > setenv PATH /usr/pubsw/packages/python/User/bin:${PATH}
>> >
>> > Next, I launch a fresh csh terminal, and launch ipython. This appears
>> (?)
>> > to work OK:
>> >
>> > tmsh:raij[55] ipython
>> >
>> > Python 2.7.6 | 64-bit | (default, Jun  4 2014, 16:32:15)
>> > Type "copyright", "credits" or "license" for more information.
>> >
>> > IPython 2.1.0 -- An enhanced Interactive Python.
>> > ?         -> Introduction and overview of IPython's features.
>> > %quickref -> Quick reference.
>> > help      -> Python's own help system.
>> > object?   -> Details about 'object', use 'object??' for extra details.
>> >
>> > In [1]:
>> >
>> >
>> >
>> >
>> > However, trying to follow the instructions:
>> >
>> > ipython --pylab qt
>> >
>> > produces a long list of errors suggesting that matplotlib (that I did
>> not
>> > see mentioned in the MNE-python guide - is it needed and how is it best
>> > installed to avoid breaking dependencies?) may not be installed.
>> >
>> > Moreover, regardless of if I launch ipython alone or with --pylab qt,
>> > trying to "import mne" gives the error "No module named mne". See the
>> end
>> > of message for the full error list.
>> >
>> > Any suggestions would be much appreciated!
>> >
>> > Best regards,
>> >
>> > Tommi
>> >
>> >
>> > ---
>> > Tommi Raij, MD, PhD
>> > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
>> > Bldg 149, 13th St
>> > Charlestown, MA 02129
>> > U.S.A.
>> >
>> >
>> > ERROR OUTPUT FOR
>> >
>> > ipython --pylab qt (from a csh terminal)
>> >
>> > Python 2.7.6 | 64-bit | (default, Jun  4 2014, 16:32:15)
>> > Type "copyright", "credits" or "license" for more information.
>> >
>> > IPython 2.1.0 -- An enhanced Interactive Python.
>> > ?         -> Introduction and overview of IPython's features.
>> > %quickref -> Quick reference.
>> > help      -> Python's own help system.
>> > object?   -> Details about 'object', use 'object??' for extra details.
>> > [TerminalIPythonApp] WARNING | Eventloop or matplotlib integration
>> failed.
>> > Is matplotlib installed?
>> >
>> ---------------------------------------------------------------------------
>> > ImportError                               Traceback (most recent call
>> last)
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/shellapp.pyc
>> > in <lambda>(key)
>> >     231         shell = self.shell
>> >     232         if self.pylab:
>> > --> 233             enable = lambda key: shell.enable_pylab(key,
>> > import_all=self.pylab_import_all)
>> >     234             key = self.pylab
>> >     235         elif self.matplotlib:
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
>> > in enable_pylab(self, gui, import_all, welcome_message)
>> >    2980         from IPython.core.pylabtools import import_pylab
>> >    2981
>> > -> 2982         gui, backend = self.enable_matplotlib(gui)
>> >    2983
>> >    2984         # We want to prevent the loading of pylab to pollute the
>> > user's
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc
>> > in enable_matplotlib(self, gui)
>> >    2941                 gui, backend =
>> > pt.find_gui_and_backend(self.pylab_gui_select)
>> >    2942
>> > -> 2943         pt.activate_matplotlib(backend)
>> >    2944         pt.configure_inline_support(self, backend)
>> >    2945
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/IPython/core/pylabtools.pyc
>> > in activate_matplotlib(backend)
>> >     285     matplotlib.rcParams['backend'] = backend
>> >     286
>> > --> 287     import matplotlib.pyplot
>> >     288     matplotlib.pyplot.switch_backend(backend)
>> >     289
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/pyplot.py
>> > in <module>()
>> >      22
>> >      23 import matplotlib
>> > ---> 24 import matplotlib.colorbar
>> >      25 from matplotlib import _pylab_helpers, interactive
>> >      26 from matplotlib.cbook import dedent, silent_list,
>> is_string_like,
>> > is_numlike
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/colorbar.py
>> > in <module>()
>> >      27 import matplotlib.artist as martist
>> >      28 import matplotlib.cbook as cbook
>> > ---> 29 import matplotlib.collections as collections
>> >      30 import matplotlib.colors as colors
>> >      31 import matplotlib.contour as contour
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/collections.py
>> > in <module>()
>> >      21 import matplotlib.artist as artist
>> >      22 from matplotlib.artist import allow_rasterization
>> > ---> 23 import matplotlib.backend_bases as backend_bases
>> >      24 import matplotlib.path as mpath
>> >      25 from matplotlib import _path
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/backend_bases.py
>> > in <module>()
>> >      48
>> >      49 import matplotlib.tight_bbox as tight_bbox
>> > ---> 50 import matplotlib.textpath as textpath
>> >      51 from matplotlib.path import Path
>> >      52 from matplotlib.cbook import mplDeprecation
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/textpath.py
>> > in <module>()
>> >       9 from matplotlib.path import Path
>> >      10 from matplotlib import rcParams
>> > ---> 11 import matplotlib.font_manager as font_manager
>> >      12 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT,
>> > LOAD_NO_HINTING
>> >      13 from matplotlib.ft2font import LOAD_TARGET_LIGHT
>> >
>> >
>> /usr/pubsw/packages/python/User/lib/python2.7/site-packages/matplotlib/font_manager.py
>> > in <module>()
>> >      51 import matplotlib
>> >      52 from matplotlib import afm
>> > ---> 53 from matplotlib import ft2font
>> >      54 from matplotlib import rcParams, get_cachedir
>> >      55 from matplotlib.cbook import is_string_like
>> >
>> > ImportError: libpng16.so.16: cannot open shared object file: No such
>> file
>> > or directory
>> >
>> >
>> >
>> > Inside python, the attempt to import MNE gives this error:
>> >
>> > In [1]: import mne
>> >
>> ---------------------------------------------------------------------------
>> > ImportError                               Traceback (most recent call
>> last)
>> > <ipython-input-1-39fc8b1a8697> in <module>()
>> > ----> 1 import mne
>> >
>> > ImportError: No module named mne
>> >
>> > In [2]:
>> >
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >
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