Installation issues on x86_64 Ubuntu 20.04.4

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 setup.py and pyproject.toml.

Also, It looks like the default PyPI release is version 2.0.5.0, although for some reason this is timestamped January 19, 2022, while version 2.0.4.7 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 setup.py: packages=find_packages(include=("tests",)),, which should probably include brainrender.

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.

[grahamfindlay]

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.

[FedeClaudi]

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