[Mne_analysis] python-MNE installation

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Tue Oct 7 03:21:18 EDT 2014
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hi Tommi,

glad to hear you made progress !

can you paste the output of:

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

out of curiosity why do you want the development version of the code?
we release every 5 to 6 months and make sure we stay backward
compatible for at least one release. The stable version is also
what is documented on the website.

Alex


On Tue, Oct 7, 2014 at 12:28 AM,  <raij at nmr.mgh.harvard.edu> wrote:
>
> 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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