Installation

Pharmacon requires Python ≥ 3.12.

Option 1 — PyPI (recommended)

The simplest way to install Pharmacon. Downloads a pre-built wheel from the Python Package Index together with all required dependencies. Creating a virtual environment first is strongly recommended.

python3.12 -m venv venv
source venv/bin/activate      # Windows: venv\Scripts\activate

pip install pharmacon

Option 2 — Conda

Recommended if you manage binary dependencies (especially RDKit and MDAnalysis) through Conda. An environment.yml is provided in the repository.

conda env create -f environment.yml
conda activate pharmacon

pip install pharmacon

Option 3 — Source / development

Clone the repository and install in editable mode. Use this if you want to contribute or stay on the latest development version.

git clone https://github.com/k-georgiou/pharmacon.git
cd pharmacon
python -m venv venv && source venv/bin/activate
pip install -e ".[dev]"

The dev extra pulls in pytest. To run the full test suite:

python -m pytest

Optional: MPI-aware logging

Pharmacon’s parallel subcommands use Python multiprocessing and require no extra dependencies. The optional mpi extra only installs mpi4py, which Pharmacon uses — when present — to tag per-rank log files if you launch it under an MPI runner. Install it only in that case:

pip install "pharmacon[mpi]"

Optional: development tools only (no editable install)

If you already have Pharmacon installed and only need the test dependencies:

pip install "pharmacon[dev]"

Verifying the installation

pharmacon --help

You should see the Pharmacon banner followed by the top-level help listing all available commands.