
Updating pangolin
Updating pangolin
New feature: streamlined updating thanks to Finlay Maguire!
Note: This flag will update versions of pangolin and pangoLEARN to the latest tagged releases. Major releases that involve any changes to dependencies (like v2.3) will need to also update the pangolin environment using the instructions below.
Run:
pangolin --update
Alternatively:
conda activate pangolin
git pull
pulls the latest changes from githubpython setup.py install
re-installs pangolin.conda env update -f environment.yml
updates the conda environment (you’re unlikely to need to do this, but just in case!)pip install git+https://github.com/cov-lineages/pangoLEARN.git --upgrade
updates if there is a new data releasepip install git+https://github.com/cov-lineages/lineages.git --upgrade
updates if there is a new data release, this is the legacy data repo and is unlikely to have tagged releases in the future
Troubleshooting update
- If you have previously installed pangolin using
pip
, you will need to update pangolin in the same way (pip install .
) - Try
pip uninstall pangolin
and then re-install withpython setup.py install