[Mne_analysis] python-MNE installation

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Tue Sep 30 03:12:56 EDT 2014
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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]:
>
>
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