Installation

Requirements

PoreMind requires Python 3.10 or later. Download the ZIP archive from the PoreMind GitHub repository, extract it, and open a terminal in the extracted project root—the directory containing pyproject.toml and src/.

Install the package

conda create -n poremind python=3.10 -y
conda activate poremind
pip install -e .

Optional dependencies

Install only the packages needed for the planned analysis:

pip install pyabf        # ABF input
pip install torch        # waveform deep learning
pip install captum tqdm  # DL attribution
pip install umap-learn   # UMAP
pip install xgboost      # XGBoost models

Verify the installation

from poremind import __version__, create_analysis_object

print(__version__)

To build or preview this documentation locally, install its separate requirements with pip install -r docs/requirements-docs.txt, then run python scripts/prepare_docs.py and mkdocs serve from the project root.