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.


pangolin --update


  1. conda activate pangolin
  2. git pull
    pulls the latest changes from github
  3. python setup.py install
    re-installs pangolin.
  4. conda env update -f environment.yml
    updates the conda environment (you’re unlikely to need to do this, but just in case!)
  5. pip install git+https://github.com/cov-lineages/pangoLEARN.git --upgrade
    updates if there is a new data release
  6. pip 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 with python setup.py install

Next: Usage