[Mne_analysis] python-MNE installation

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Fri Oct 3 07:14:15 EDT 2014
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hi Tommi,

> Removing Canopy python should be easy (fingers crossed), but the question
> is how I remove mne-python (dev version) - without breaking my system.
> Since removing mne with "pip uninstall mne" is not working, can I just
> delete all "src" folders and "mne" files I can find?

just remove the folder that are called mne* something.

> Should I delete
> something else as well? Are there any dependencies that should be taken
> into account, and if so, how?

mne does not automatically install any dependency.

Alex

> Thanks,
>
> Tommi
>
>> 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.
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>>>>>>
>>>>>>
>>>>>
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