Installation

Installation

FleXgeo2 requires Python >=3.10.

Editable install

From the repository root:

python -m venv .venv
source .venv/bin/activate
pip install -e .

This installs the flexgeo2 command-line entry point and makes the package importable from Python.

Main dependencies

FleXgeo2 uses:

• melodia-py for differential-geometry descriptors
• pandas and numpy for tables and numeric operations
• matplotlib for plots
• hdbscan for conformation clustering
• nglview and numba through the analysis stack

Verify the install

Run:

flexgeo2 --help

You should see the command-line options for input files, output directories, chain filtering, plotting, reference-state comparison and clustering.

Development extras

For local testing and linting:

pip install -e ".[dev]"

The development extras include pytest, ruff, and pre-commit.