[Mne_analysis] python-MNE installation

Thu Oct 2 16:08:17 EDT 2014

Hi Alex,

Thank you. Before switching to Anaconda I need to clean up Canopy and the
multiple mne-python installations that got created. However, this appears
to be easier said than done.

First, I do not quite understand why it would not matter in which dir I am
when I do

pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev

Every installation attempt has created a new "src" dir in the specific
directory where I give the command. The contents of the dir "src" are:
 - mne (which is a dir containing a MNE-Python installation)
 - pip-delete-this-directory.txt

My system now has (at least) 3 copies of the "src" dir in different
locations, corresponding to (at least) 3 installation attempts while being
cd:d in the specific dir (these have different time staps so they were
clearly not created at once):

/home/raij/
/usr/pubsw/packages/
/usr/pubsw/packages/python/System/

There is only one location that has a file called "mne" related to one of
the installation attempts. This is at /home/raij/

Then, to the more relevant business of removing these installations. The
command you suggested

pip uninstall mne

returns the error:

Cannot uninstall requirement mne, not installed
Storing debug log for failure in /root/.pip/pip.log

I also tried to remove "mne-dev" instead of "mne", and tried doing this at
all 3 paths listed above. Same error regardless. Any suggestion why this
might be the case?

Bests,

Tommi

> 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.
>>> _______________________________________________
>>> 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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