[Mne_analysis] python-MNE installation

Fri Oct 3 06:55:25 EDT 2014

Hi Alex,

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

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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>>>>> Mne_analysis at nmr.mgh.harvard.edu
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
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