[Mne_analysis] python-MNE installation
Mainak Jas
mainakjas at gmail.com
Wed Oct 1 06:00:51 EDT 2014
Hi Tommi,
On Wed, Oct 1, 2014 at 5:11 AM, <raij at nmr.mgh.harvard.edu> wrote:
>
> Hi Mainak,
>
> Thank you for the suggestion. I am using csh and am able to launch ipython
> (that I believe is what I installed with Canopy) from the csh terminal.
I think what you have is the system default ipython, not the one installed
with Canopy.
> To
> make this happen, I just added the following line to my .cshrc:
> setenv PATH /usr/pubsw/packages/python/System/bin:${PATH}
>
shouldn't it be something like: ~/Enthought/Canopy_64bit/User/bin ? (see
here:
https://support.enthought.com/entries/23646538-Make-Canopy-User-Python-be-your-default-Python-i-e-on-the-PATH-
)
I have very little experience in using bash (yes I am a horrible person
> :D). In my system I have not been able to launch ipython at all from bash
> (perhaps there is something wrong with my ~/.bash_profile ? though I did
> try to add a path to the canopy installation). Anyway based on the
> following page canopy would appear to ok with both bash and tcsh:
> http://wiki.nmr-relax.com/Epd_canopy
>
Yes, but are you actually using the tcsh activation script? I suspect that
the default activation script that comes with canopy is bash. You need to
run the activation script to have your canopy virtual environment set up.
Usually, this is added in the .bashrc or something and it gets executed
every time you start the bash terminal.
The reason I suspect this is the problem is because in your error messages
(from the first email), I don't see the canopy virtual environment which is
strange. Maybe you have disabled the virtual environment prompt? If you
enable it, you should see something like this:
http://docs.enthought.com/canopy/_images/canopy_terminal.png as your prompt
in terminal.
(Canopy 64-bit) ~ tommi$
> Let me know if you still think this might the root of the problem...
>
> I also wonder that since many seem to be using Anaconda instead of Canopy,
> if I should move my camp there instead.
>
Yes, I agree. It might be easier. I switched to Anaconda earlier this year
and I found it much easier to use than Canopy.
Mainak
> Best regards,
>
> Tommi
>
>
> > 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]:
> >> >
> >> >
> >> > _______________________________________________
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> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >
> >> >
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