Installation

Requirements

ANTIPASTI is developed using Python 3.8, 3.9, 3.10 and 3.11 and might be fine with older versions.

It requires adabelief-pytorch, biopython, matplotlib, numpy, opencv-python, optuna, pandas, scikit-learn, scipy, torch, and torchmetrics to work properly.

Through PyPI

ANTIPASTI releases are distributed through the Python Package Index (PyPI). To install the latest version use pip:

pip install antipasti

Through Anaconda

We provide an Anaconda environment that satisfies all the dependencies in antipasti-env.yml.

git clone https://github.com/kevinmicha/ANTIPASTI
cd ANTIPASTI
conda env create -f antipasti-env.yml
conda activate antipasti-env
pip install .

Next, you can run the tests to make sure your installation is working correctly.

# While still in the ANTIPASTI directory:
pytest .

Manually handling the dependencies

If you want to use an existing environment, just omit the Anaconda commands above:

git clone https://github.com/kevinmicha/ANTIPASTI
cd ANTIPASTI
pip install .

or if you need to install it for your user only:

python setup.py install --user