Revisit refine.bio dependencies

### Context

In order to get fully reproducible builds all Python/R dependencies should be pinned to their latest known compatible versions.

### Problem or idea

- Get rid of unnecessary pip dependencies (if any) for Docker images.
- Inspect pip/renv requirements files for any entries with no specific version set.

### Solution or next step

Pin all packages to their latest known good versions.

Inspect the Docker image definitions and the pip/renv requirements files mentioned in the issue. Identify unnecessary dependencies and entries without specific versions, then verify that all remaining packages use the latest known compatible versions and that builds are reproducible.

Written by the indexing model from the issue text.