[Mne_analysis] python-MNE installation

[raij at nmr.mgh.harvard.edu]

Hi Alex,

I think this is a path error at multiple levels - installations go one way
and the expected paths in another. I tried to follow your suggestions
(uninstall yum pip > install canopy pip > re-install MNE python) but keep
getting similar/same errors as before. Some observations and questions
(details of terminal commands and feedback at the end):

1. Do I need to cd to a specific directory when I do "easy_install pip" and
"pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev?"
This seems to determine where the "src" dir and paths are set (I did not
see this mentioned in the "getting started" web page - and now after
several installation attempts I see I have a few "src" dirs in different
locations).

2. For cleaning up extra copies (see above), how do I remove spurious mne
python installations? Attempt to "pip uninstall mne-python" at the dirs
where they were installed gives the error:
Cannot uninstall requirement mne-python, not installed
Storing debug log for failure in /root/.pip/pip.log

3. Post installation, where should the user level ~/.cshrc path point? I
now have it at
setenv PATH /usr/pubsw/packages/python/System/bin:${PATH}

4. As one might reasonable expect given the above mess, the good old
errors remain: given from a csh window either as root or as a user, the
command "ipython --pylab qt", and ipython followed by ">>>import mne"
result in the same errors as before.

Cheers,

Tommi


DETAILS:

su root + pw
csh
whoami: root

- uninstall yum-pip <yum remove python-pip> as root. Result: OK

- install Canopy pip <easy_install pip> as root. Result: OK. Details:
[raij at tmsh raij]# easy_install pip
Searching for pip
Reading http://pypi.python.org/simple/pip/
Best match: pip 1.5.6
Downloading
https://pypi.python.org/packages/source/p/pip/pip-1.5.6.tar.gz#md5=01026f87978932060cc86c1dc527903e
Processing pip-1.5.6.tar.gz
Running pip-1.5.6/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-HjVeBr/pip-1.5.6/egg-dist-tmp-HRsylX
warning: no files found matching 'pip/cacert.pem'
warning: no files found matching '*.html' under directory 'docs'
warning: no previously-included files matching '*.rst' found under
directory 'docs/_build'
no previously-included directories found matching 'docs/_build/_sources'
Adding pip 1.5.6 to easy-install.pth file
Installing pip script to /usr/bin
Installing pip2.6 script to /usr/bin
Installing pip2 script to /usr/bin
Installed /usr/lib/python2.6/site-packages/pip-1.5.6-py2.6.egg
Processing dependencies for pip
Finished processing dependencies for pip

- re-install MNE-python <pip install -e
git+https://github.com/mne-tools/mne-python#egg=mne-dev> as root. Result
looks OK but for some reason setup.py path points to my home dir even
though I am here as root:

[raij at tmsh raij]# pip install -e
git+https://github.com/mne-tools/mne-python#egg=mne-dev
Obtaining mne from git+https://github.com/mne-tools/mne-python#egg=mne-dev
  Cloning https://github.com/mne-tools/mne-python to ./src/mne
  Running setup.py (path:/home/raij/src/mne/setup.py) egg_info for package
mne
    build_src
    warning: no previously-included files matching '*' found under
directory 'examples/MNE-sample-data'
  Installing extra requirements: 'egg'
Installing collected packages: mne
  Running setup.py develop for mne
    changing mode of build/scripts.linux-x86_64-2.6/mne from 644 to 755
    build_src
    warning: no previously-included files matching '*' found under
directory 'examples/MNE-sample-data'
    Creating /usr/lib/python2.6/site-packages/mne.egg-link (link to .)
    Removing mne 0.9.git from easy-install.pth file
    Adding mne 0.9.git to easy-install.pth file
    Installing mne script to /usr/bin

    Installed /home/raij/src/mne
Successfully installed mne
Cleaning up...


> hi Tommi,
>
>> Then, I checked that both "which python" and "which pip" already point
>> to
>> Canopy (I did not do anything to the system yet). Specifically:
>> which python
>> /usr/pubsw/packages/python/System/bin/python
>> which pip
>> /usr/pubsw/packages/python/System/bin/pip
>
> good
>
>> Next, I re-installed (as root) the python mne package just to make sure
>> it
>> is there:
>> pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
>
> what did it say? did it complete successfully?
>
> if pip is from canopy and you see no error then typing in (i)python
>
> import mne
>
> should really work.
>
>> However, the errors for
>> ipython --pylab gt
>> and
>> ipython -> import mne
>>
>> remain exactly the same as before.
>>
>> If you still believe I need to uninstall the pip I installed with yum, I
>> would greatly appreciate if you could let me know which command I should
>> use for uninstallation (I found a ton of different ways, and some of
>> these
>> will likely mess up the system in more than one way).
>
> yum uninstall python-pip
>
> ?
>
> don't hesitate to paste error messages.
>
> Alex
>
> PS : we're going to improve the getting started doc...
> PS2 : if you really struggle get rid of canopy and give a try to
> anaconda installing it in your home folder without root access.
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