Installation.md

Installation

Create the environment

make env                # create the conda env (conda env create -f environment.yml)
conda activate mbcausal
make install            # editable install (pip install -e .)

Verify

make check        # pytest + ruff + mypy

All three should pass.

Notes

• The env bundles the profiling tools (metaphlan, kraken2, bracken) and the Python stack.
• It pulls numpy 2 and pandas 3, so avoid idioms from pandas 1.
• In your editor, select the mbcausal interpreter so imports resolve.