Updating Pangolin

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For Major Releases:

Updating a Bioconda or Mamba installation

If you used conda (or mamba) to install pangolin, conda activate the environment in which you installed pangolin if it's not already activated, and then update:

conda update pangolin

Updating a development installation

Navigate to your local directory where you cloned the pangolin repository on the command line.

  1. cd pangolin
  2. conda activate pangolin
  3. git pull pulls the latest changes from github
  4. conda env update -f environment.yml updates the conda environment
  5. pip install . re-installs pangolin.

For Minor Releases:

pangolin --update

To only update the data models:

pangolin --update-data

Note: The update flags will update versions of pangolin, pangolin-data, scorpio and constellations to the latest tagged releases. Major releases that involve any changes to dependencies (like updating to pangolin v4.0) will need to also update the pangolin environment using the instructions below.

Troubleshooting Update