The instructions here are for the cellfinder repository, but the process is similar for all the others (e.g. brainreg).
To set up a development install, please fork the cellfinder repository and then:
Clone your fork
git clone https://github.com/YOUR_USERNAME/cellfindercd cellfinder
Add the cellfinder repository as the upstream
git remote add upstream https://github.com/SainsburyWellcomeCentre/cellfinder
Install an editable, development version of cellfinder
pip install -e .[dev]
Finally, when working on cellfinder, keep your fork up to date
git fetch upstreamgit merge upstream/master