Updating Pangolin
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.
- cd pangolin
- conda activate pangolin
- git pull pulls the latest changes from github
- conda env update -f environment.yml updates the conda environment
- 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
- If there are issues with updating pangolin, first port of call is to uninstall and re-install.
- If you have previously installed pangolin using pip you will need to update pangolin in the same way, ie pip install .
- Try pip uninstall pangolin and then re-install with python setup.py install
- Try removing and re-creating the pangolin environment in conda (or mamba).
- If all else fails, post an issue on the GitHub, or check previously solved GitHub issues which may offer some insight!