Codebase for the Koo Lab at Cold Spring Harbor Laboratory.
This is a work in progress.
One can install the master branch (the bleeding edge) with pip
. One must also install
TensorFlow.
pip install https://github.com/p-koo/libre/tarball/master tensorflow
Clone and install the package as below. This also creates a virtual environment, so the dependencies of this package are contained within this directory.
Note regarding TensorFlow: the installation of TensorFlow depends on the environment.
For example, if there is no GPU, one can install tensorflow-cpu
. If there is a GPU,
then one must take care to install the proper TensorFlow version for the given CUDA
and cuDNN versions.
git clone https://github.com/p-koo/libre.git
cd libre
python -m venv venv
source ./venv/bin/activate
python -m pip install --no-cache-dir --upgrade pip setuptools wheel
python -m pip install --no-cache-dir --editable .[dev] tensorflow
It is also useful to use pre-commit
to run the styler (black
) and lint the code on
every commit.
pre-commit
Run tests with pytest
:
pytest libre