Mne-python: problem installing dependencies and MNE

[yonlev]

i am attempting to install dependencies and MNE, but when i type pip install mayavi i get the following error message (see attached).
any help is welcome,
thanks
Yoni

[agramfort]

hi,

did you read:

http://martinos.org/mne/stable/install_mne_python.html

you recommend to install mayavi with conda and for python 3.6 use our
envrionment.yml file.

HTH

[yonlev]

hi
yes of course, that is exactly what i followed though it recommends version 2.7.
I currently have conda 4.3.30, and python 2.7.14.
but installing mayavi on conda prompt gives me that error i mentioned

[agramfort]

did you try to "pip install mayavi" or "conda install mayavi"

[mmagnuski]

Judging from the first post and the screenshot - this is definitelly a result of pip install, conda should be fine.

[yonlev]

thank you, yet even running conda install mayavi gives the following

[mmagnuski]

This means that the requirements of these packages are in conflict (and conda is unable to solve that conflict). Your best solution might be creating a separate environment for mne+mayavi. You could try using the environment file mentioned in the mne-python install docs.

[dafrose]

Hi and thanks a lot for this amazing package!

I just wanted to drop a note on installing mne on python 3.6, relating to what you wrote above:

did you read:
http://martinos.org/mne/stable/install_mne_python.html
you recommend to install mayavi with conda and for python 3.6 use our environment.yml file.

We tried to install mne on python 3.6 using the above mentioned environment.yml. We exactly followed the recommendation in the (above mentioned) docs, saying:

$ curl -O https://raw.githubusercontent.com/mne-tools/mne-python/master/environment.yml
$ conda env create -f environment.yml
$ source activate mne

but pip did something wrong and the install aborted, even leaving behind a broken pip. Instead we succeeded, by installing everything but mne using conda and the conda-forge channel and then installed mne using pip:

conda config --append channels conda-forge
conda create -n mne python=3.6 pysurfer scipy matplotlib scikit-learn mayavi jupyter spyder
pip install mne

We then verified the install using an example in the docs.

Best,
DR

[larsoner]

Maybe it's time to update the config file. If conda-forge has VTK for Python 3.6, then we don't need to use the clinicalgraphics repo anymore. @dafrose feel free to open a PR to update the environment.yml file and we can see if the CIs pass.

[dafrose]

I've tried to move as much as possible in the environment.yml from pip to conda. Some issues that I encountered:

• pysurfer and mayavi conflict with pyqt=5 → left them in pip section
• when trying to build mayavi with pip, I encounter the following error: ModuleNotFoundError: No module named 'vtkIOParallelPython' . I thought, this might be related to VTK 8.1, but fixing the version to vtk=7 didn't help either

I forked at https://github.com/dafrose/mne-python

[larsoner]

Can you open a PR to facilitate looking at the diff?

[dafrose]

done! (PR #4885)

I had to remove the pyqt version requirement to be able to install mayavi and pysurfer with conda, since they require pyqt 4. Installing (and building) mayavi and pysurfer via pip failed on both a windows and a linux machine with vtk from conda-forge and pyqt v5.

I noticed that mne is already available on conda-forge for python 2.7 and 3.5 (in contrast to what the docs suggest). Wouldn't it be simpler and more reliable to suggest conda install mne as default installer?

[agramfort]

I personally don't maintain the conda packages of mne or pysurfer (just pip)

if you can help us with this it's great

[dafrose]

I don't have any experience with deployment (be it conda or pip) yet - but if you don't maintain the conda packages, then who does?

thx for maintaining on PyPi, though!

[agramfort]

>

then who does?

good people :) honestly I am not sure.

[larsoner]

had to remove the pyqt version requirement

This is bad because it forces matplotlib to version 1.5 (as 2+ requires
qt5). This is why we have pinned versions of pyface and so forth -- those
support qt5.

Thus maybe all we should change is where we get VTK (and maybe also how we
install MNE).

[dafrose]

Thus maybe all we should change is where we get VTK (and maybe also how we install MNE).

Seems so. I noticed that many of the pip-installed packages are available on conda-forge, so I moved them. Also building mayavi from pip failed on my (Windows) machine and I can't try my (Linux) office machine right now.

I've just run a few test installs with python 3.5 and 3.6 . As it seems, mayavi installs alright from conda under python 3.5 with pyqt5 present but throws a conflict error (UnsatisfiableError) under python 3.6 (with pyqt5 present). Installing mayavi with pip under python 3.6 fails on my machine, so I can't get mayavi to run under python 3.6 and Qt5. The official docs and PyPI don't state any (!) python version dependency, so I don't quite understand the difference between 3.5 and 3.6 although Qt5 was present in both cases. Be it as it is. This is not an MNE but a mayavi problem.

[larsoner]

For what it's worth the current environment file should build on your
system on windows, it runs on AppVeyor for every PR

[jjnurminen]

FWIW, I just tried to install according to the docs (Python 2.7, conda 4.4.10), resulting in:

root@jupiter:/home/jussi# /opt/anaconda2/bin/conda install scipy matplotlib scikit-learn mayavi jupyter spyder
Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:
  - anaconda-navigator
  - astropy
  - mayavi

[larsoner]

Can you try environment.yml from #5012?

[larsoner]

Closing as this should be fixed with the master install instructions

[ayoubbenaissa]

Check this out
http://martinos.org/mne/stable/install_mne_python.html

it is very efficient