[Mne_analysis] python-MNE installation

Mon Oct 6 18:28:42 EDT 2014

Hi Alex,

Mainly a success! Anaconda installed ok, basic version of mne also
installed ok. However, the developmental mne version does not seem to
install/work properly.  Details:

I succesfully installed anaconda as root to all users (one copy at
/usr/pubws/packages/python/anaconda/. After this,
ipython --pylab qt
seemed to work and did not return any errors.

Attempts to install the developmental version of mne continue to be
unsuccesful. The command
pip install -e git+https://github.com/mne-tools/mne-python#egg=mne-dev
suggested that mne was installed at /usr/pubsw/packages/python/src/mne
However,
ipython --pylab qt
>>> import mne
returned an error package not found (both for root and individual users).

In contrast,
pip install mne --upgrade
installed /usr/pubsw/packages/python/anaconda/bin/mne
ipython --pylab qt
>>> import mne
works (both for root and individual users).

Any suggestions what I am doing wrong with installation of the dev package?

Cheers,

Tommi

> 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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