dgfreg

Regression models estimating standard condition Gibbs free energy changes of biological compounds

How to run the analysis

Install python >= 3.9. If this is not your default python3 then you should manually create the virtual environment with e.g. python3.10 -m venv .venv

To run the analysis, run the command make analysis from the project root. This will install a fresh virtual environment if one doesn't exist already, activate it and install python dependencies and cmdstan, then run the analysis with the following commands:

• python dgfreg/prepare_data.py
• python dgfreg/sample.py
• jupyter execute dgfreg/investigate.ipynb

How to create a pdf report

First make sure you have installed quarto.

Make sure to install librsvg2-bin for svg to pdf conversion

sudo apt install librsvg2-bin

Now run this command from the project root:

make docs

How to run tests

Run this command from the project root:

python -m pytest