Updating CaImAn

If you have you not used the pip installation before (established in May 2018) follow the instructions in the README file.

If you already have CaImAn installed with the pip installer, but want to upgrade, please follow the procedure below. If you reinstall CaImAn frequently, you can try skip deleting and recreating your Conda environment. In this case you can do only steps 1, 5, and 7 below to update the code. However, if the environment file has changed since your last update this may lead to you not the latest version.

From the conda environment you used to install CaImAn:

1. pip uninstall caiman
2. remove or rename your ~/caiman_data directory
3. Remove your conda environment: conda env remove -n NAME_OF_YOUR_ENVIRONMENT
4. Close and reopen your shell (to clear out the old conda environment)
5. Do a git pull from inside your CaImAn folder.
6. Recreate and reenter your conda environment as you did in the README
7. Do a pip install . inside that code checkout
8. Run caimanmanager.py install to reinstall the data directory (use --inplace if you used the pip install -e . during your initial installation).

• If you used the pip install -e . option, then you can try updating by simply doing a git pull. Again, this might not lead to the latest version of the code if the environment variables have changed.