Updating the Libraries

PaleoPAL’s knowledge base libraries are updated regularly to include new notebooks, code, and documentation. To keep your local installation up to date, you can follow these steps:

1. Pull the latest changes from the PaleoPAL repository

Make sure you are in the PaleoPAL directory and run:

git pull origin main

2. Activate the PaleoPAL conda environment

Make sure that you are in the conda environment you created for PaleoPAL (if you followed the Docker installation instructions). If not, activate your environment:

conda activate paleopal

If you did not keep this environment, follow the instructions in the Docker installation guide to create a new environment and install the required Python packages.

3. Run PaleoPAL using Docker

docker compose up -d

and Navigate to the Qdrant Dashboard: http://localhost:6333/dashboard.

4. Remove existing collections in Qdrant

There is no way to update the libraries in place, so you will need to remove the existing collections in Qdrant before re-indexing the libraries. You can do this by clicking on the “Delete” button (garbage can) for each collection in the Qdrant Dashboard. If you only want/need to update specific libraries, you can delete only the collections for those libraries.

5. Re-index the libraries

If you have removed all collections, you can re-index all libraries by running the following command:

cd backend/libraries
bash index_everything.sh

If you only need to update specific libraries, you can run the commands in the index_everything.sh script for those libraries. For example, to only index the spaqrl library, you can run the following command:

python sparql_library/index_queries.py --queries-dir sparql_library/queries