nel-lab/fiola

fiola's Issues

ProcessPoolExecutor crashes on Windows on machines with high core count

Running into this issue on an amd threadripper system: https://bugs.python.org/issue26903
This manifests as 'ValueError: need at most 63 handles, got a sequence of length 65'

It looks like this can be solved on my machine by setting n_processes=60 instead of n_processes=none (which then defaults to 64, causing the crash), e.g. in demo_initialize_ca.py. Since this seems to be caused by an external unfixed bug, might it make sense to default the N here to 60 generically?

NWB and permissive license?

This package looks great! If there is any interest in integrating this into NWB, I'd be happy to help either reading NWB data or writing the resulting ROIs and traces into NWB.

I noticed that you have a custom license that is non-permissive to commercial entities. Would you consider changing this to open-permissive like MIT, BSD, or Apache?

"Proprietary" license or GPL-2.0?

Hello!

i'd like to try this software, but there is conflicting package metadata re: the license -

There is a copy of the GPL-2.0 in LICENSE:
https://github.com/nel-lab/FIOLA/blob/ff41b86f0d3e494086f44bf01bc8b6739e1aae0a/LICENSE

but the python package metadata indicates that the license is "Proprietary":

FIOLA/setup.py

Line 19 in ff41b86

license="Proprietary",

With a "Proprietary" license (or without any license that has an explicit grant of permissions to use and redistribute it) the default is that it is illegal without permission from the author to run the software. Naturally this is pretty bad for the health of the scientific software community, so i would suggest the authors choose the GPL over "Proprietary" --- I'm presuming the authors want people to use their tool and that was unintentional.

Supporting python >= 3.7

According to https://github.com/nel-lab/FIOLA/blob/master/setup.py, the package supports Python >= 3.7, but it appears that https://github.com/nel-lab/FIOLA/blob/master/requirements.txt is set so strictly that only Python 3.8 is actually supported, and the setup instructions in the README also suggest this:

git clone https://github.com/nel-lab/FIOLA.git
git clone https://github.com/flatironinstitute/CaImAn.git -b v1.9.13
cd FIOLA
conda create --name fiola python==3.8
conda activate fiola
pip install -r requirements.txt 
pip install -e.
cd ../CaImAn
pip install -e . 

Lastly, there appears to be no CI/CD testing (e.g., via GitHub actions) of various python versions to show that Python >= 3.7 is actually supported.

Given that Python 3.8 is rather old and not supported by some platforms (e.g., Terra-Bio), it would be helpful to include more support for other Python versions.