Updated 2/21/2025.
| This information is outdated. |
I now recommend using uv to manage your environments. If you do, much of the complexity below dissapears.
Hopefully, this repositoy can be archived soon.
- Install miniforge
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh
- Clone all the repositories you will need:
mkdir ~/projects/ece/
cd ~/projects/ece/
git clone https://github.com/grahamfindlay/ece-env.git
git clone https://github.com/CSC-UW/spikeinterface.git # Be mindful of branch. wisc/sorting for running sorting, wisc/dev for everything else. Unfortunate we cannot use upstream spikeinterface[full] without significant refactoring of `ecephys`. See that README for more.
git clone https://github.com/CSC-UW/ephyviewer.git # You may be able to get away with just the PyPI version of this.
git clone https://github.com/CSC-UW/kCSD-python.git # Can hopefully just use PyPI version once scipy.integrate.simpson is used
git clone https://github.com/CSC-UW/ecephys.git
git clone https://github.com/CSC-UW/wisc_ecephys_tools.git
# These following repositories are really not essential, but you might choose to install one (or both) of them.
git clone https://github.com/grahamfindlay/seahorse.git
git clone https://github.com/CSC-UW/discoflow.git
- Install
cd ~/projects/ece/ece-env
mamba create -n ece python=3.13.2 # Confirmed to work.
mamba env update -n ece -f environment.yml
mamba activate ece