README.template

# Kompressor

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|:-:|:-:|:-:|
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A neural compression framework built on top of JAX.

## Install

`setup.py` assumes a compatible version of JAX and JAXLib are already installed. Automated build is tested for a `cuda:11.1-cudnn8-runtime-ubuntu20.04` environment with `jaxlib==0.1.76+cuda11.cudnn82`.

```
git clone https://github.com/rosalindfranklininstitute/kompressor.git
cd kompressor
pip install -e .

# Run tests
python -m pytest --cov=src/kompressor tests/
```

## Install & Run through Docker environment

Docker image for the Kompressor dependencies are provided in the `quay.io/rosalindfranklininstitute/kompressor:main` Quay.io image.

```
# Run the container for the Kompressor environment
docker run --rm quay.io/rosalindfranklininstitute/kompressor:main \
    python -m pytest --cov=/usr/local/kompressor/src/kompressor /usr/local/kompressor/tests
```

## Install & Run through Singularity environment

Singularity image for the Kompressor dependencies are provided in the `rosalindfranklininstitute/kompressor/kompressor:main` cloud.sylabs.io image.

```
singularity pull library://rosalindfranklininstitute/kompressor/kompressor:main
singularity run kompressor_main.sif \
    python -m pytest --cov=/usr/local/kompressor/src/kompressor /usr/local/kompressor/tests
```