[Mne_analysis] Latest environment.yml again installing MNE in a dedicated 'mne' environment

Johan Wessberg johan.wessberg at gu.se
Fri Jul 10 08:43:35 EDT 2020
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Hi!

I just noted a discrepancy between the documentation for installation (‘Install’) on mne.tools, and the latest environment.yml file.


I did a clean install of MNE-Python under Conda on a Mac running OS X 10.15.5. I have been using MNE-Python on this specific machine for many years, but I do periodic upgrades to the latest MNE version.

I noted today that the latest environment.yml file has “name: mne” on the first line. This will create a dedicated Conda environment called ‘mne’. This was standard behavior going back a couple of years, but lately the documentation has instead suggested that MNE should be installed in the base environment.

So, PLEASE NOTE that the text on the ‘Install Python’ under ‘Install’ on mne.tools still refers to a “base environment file”. There is also an instruction on how to create the mne environment, if preferred. All this is now confusing since the current environment.yml does exactly that!
https://mne.tools/stable/install/mne_python.html


The problem I had with the dedicated mne environment that was created with the newly downloaded environment.yml was that spyder was not installed there. Trying to install spyder in the mne environment resulted in the previously described PyQt5 conflict problem (a mailing list discussion about a week ago). I tried the solution suggested by the devs of changing the Python interpreter in Spyder to point to the mne environment, but this was not accepted by Spyder, probably because the base environment Python interpreter was version 3.7.7, whereas the newly installed Python interpreter in the mne environment was 3.8.1? (According to the documentation, this should not be an issue, but I got an error message saying that the currently running and the pointed-to Python interpreters were incompatible.)
(Trying to upgrade the one in base does not work; and I gave up trying to downgrade the one in the mne environment.)


In the end, I changed the first line in environment.yml to “name: base” and reinstalled.

I then downgraded PyQt5 to 5.10 with the now usual
                pip install “PyQt5==5.10”
This will allow Spyder to run, and this is how we have done it for a long time now, on many installations on Mac OS X and Windows 10 computers.

Actually, after some unrelated tinkering (a Mayavi backend issue, topic for a later post), I ended up trying
pip install “PyQt==5.11.3”
This also allows Spyder to run.


All the best,
Johan Wessberg

Professor
Inst. of Neuroscience and Physiology
University of Gothenburg
Göteborg, Sweden

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