Updating the pipeline

Fast explanation¶

For convenience, I created a script that will do all operations explained in the second section. To update the pipeline:

1. Deactivate the environment and close scripts, notebooks, terminals, where it’s activated

2. Run the update script

cd ~/towbintools_pipeline #(or where you installed the pipeline)
bash update_pipeline.sh

Optionally, you can run

bash update_pipeline.sh --pipeline-only

To update only the pipeline scripts and not the underlying packages

Longer explanation¶

Updating the pipeline is done in two parts. First, update the repository using the source on github. This can be done different ways:

1. using git pull

2. by resetting the repository based on the upstream content, using

git fetch origin
git checkout main
git reset --hard origin/main

If what you want is to reset the repository to how it is on github, use option 2.

Then, you need to update the packages. For consistency’s sake, the pipeline uses conda lock files. They ensure that the package versions you end up having is exactly the same as what was tested during development. To update your environment according to a lock file, run

cd ~/towbintools_pipeline
micromamba run -n towbintools conda-lock install --name towbintools ./requirements/conda-lock.yml