[Mne_analysis] python-MNE installation

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Fri Oct 3 05:24:31 EDT 2014
Search archives: 
hi Tommi,

remove everything you can (without breaking your system).

Just to give you an idea on my systems i have python related stuff in 2 places:
- anaconda folder that I have in my home : /Users/alex/anaconda
- my user installs (pip with --user param) in
~/.local/lib/python2.7/site-packages/

it means that to remove python from my system I just need to put these
2 folders to trash.

Alex


On Thu, Oct 2, 2014 at 10:08 PM,  <raij at nmr.mgh.harvard.edu> wrote:
>
> 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
>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>>
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

More information about the Mne_analysis mailing list