[Mne_analysis] python-MNE installation

[Alexandre Gramfort]

hi Tommi,

> 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).

no you can be anywhere

> 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

use "pip uninstall mne"

"mne" is the name on pypi.

> 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}

yes I think.

> DETAILS:
>
> su root + pw
> csh
> whoami: root
>
> - uninstall yum-pip <yum remove python-pip> as root. Result: OK

good

> - 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

if you see /usr/lib and not /usr/pubsw/packages/python/System/...
you install on the linux tree and not canopy. That's the problem.
easy_install and canopy seem to install stuff in the wrong place.
You should have everything in the canopy folder.

same thing happens below with pip install mne

if you did not do anywrong and easy_install is the one from canopy
then canopy is buggy and you should give a try to anaconda.

Alex

> - 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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>>
>>
>>
>
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