Installation issues on x86_64 Ubuntu 20.04.4See original GitHub issue
I’m trying to use brainrender to visualize Neuropixel probe tracks, but ran into several issues during installation.
I began by trying a basic installation per the documentation:
conda create -n brainrender python=3.7 conda activate brainrender pip install brainrender python >> from brainrender import Scene; s = Scene()
This leads to issue #197, which is fixed by pinning
vedo==2021.0.5. However, this leads to a new issue, which is an unrecognized keyword argument
print_authors passed to the
Atlas constructor on line 26 of
atlas.py. The latest source shows that this should be handled by commit ae92a40c2769f249d8ae7a040a64d43fad949ba0, so I tried installing from source using
pip install git+https://github.com/brainglobe/brainrender.git. This leads to a situation where I can
import brainrender, but
from brainrender import Scene fails because Python can’t find the
brainrender module. Even though the wheel reports building successfully and
pip show brainrender shows the correct path. This issue persists also using
pip install https://github.com/brainglobe/brainrender/tarball/master and
pip install https://github.com/brainglobe/brainrender.git#egg=brainrender. It also occurs if I clone from source and install using
pip install .
FYI, the documentation linked to above references a different, deprecated repository:
https://github.com/BrancoLab/BrainRender.git. I wonder if it is also not necessary to use python 3.7 as the documentation suggests, since 3.8 is listed as valid target in both
Also, It looks like the default PyPI release is version
18.104.22.168, although for some reason this is timestamped January 19, 2022, while version
22.214.171.124 actually has a later release date.
Anyways, I eventually discovered with
pip show -f and
pip install -vvv that dist-info and tests are added to the wheel, but the actual brainrender package is not! I suspect the issue lies in line 90 of
packages=find_packages(include=("tests",)),, which should probably include
In the end, if I clone from source and do an editable install with
pip install -e ., this works and I can finally create a
Scene object. Actually, I’m having new issues with some of the provided examples clearly not rendering properly, but that may be a separate issue, and I haven’t had time to look into it yet.
- Created a year ago
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Thanks @noisysky . I actually got the most recent version working using an editable pip install from source (
pip install -e) before opening the issue 😄. Just wanted to make sure someone was aware of the problem.
I’ve been trying to figure out what is going on here.
With the version that is currently on github I can install and use brainrender on windows. I can install it on Mac, and it all looks fine but when I try to use it it fails to find
loguru or any other package used. So it finds
brainrender, it’s not the same as what you had @grahamfindlay but it doesn’t find other package used within brainrender even though they were install correctly and are in the environment.
I have no idea why this is happening now or how to fix it!
pip install -e . also doesn’t seem to work for me