Introduction

See BEST-PRACTICES.md for repository layout and coding best practices. Particularly, this repository has been setup to use Poetry for Python dependency management and renv for R dependency management. Additionally, a Conda-compatible tool (such as micromamba, mamba or conda) can be used to set up compatible versions of R, Python and Poetry if these are not already available on the system.

Thus, to get the project running, do the following:

1. Ensure you have compatible versions of R, Python and Poetry available on the system. If you have a conda-compatible tool, you can also use that to install these in an isolated environment, e.g. through [micromamba/mamba/conda] create -f environment.yml -p ./.venv. If you have Micromamba, you can also get the exact versions of the packages stored in conda-lock.yml through micromamba create -n ./.venv -f conda-lock.yml (If you want to do this using the other conda tools, you can install Conda lock and run conda-lock install -p ./.venv conda-lock.yml).
2. Install R dependencies with Rscript -e 'renv::restore()'
3. Install Python dependencies with poetry install

For quick-start introductions on how to use the data in practice from code, look at src/example_user/example_analysis.Rmd andsrc/example_user/parquet_example.ipynb.