Bento requires Python version 3.8 or 3.9.
Setup a virtual environment#
We highly recommend using a virtual environment to install Bento to avoid conflicting dependencies with other packages. If you are unfamiliar with virtual environments, we recommend using Miniconda.
To setup a virtual environment with
Miniconda, run the following. This will create and activate a new environment called
bento with Python 3.8.
VERSION=3.8 # or 3.9 conda create -n bento python=$VERSION # set channel priorities conda config --env --add channels defaults conda config --env --add channels bioconda conda config --env --add channels conda-forge conda activate bento
Bento makes use of several packages for spatial analyses that require addtional non-Python dependencies.
conda install -c conda-forge gdal cmake
For developing docs, you will also need pandoc:
conda install -c conda-forge pandoc
3. Install Bento#
All that’s left is the package itself. Install with pip:
pip install bento-tools
The package and its dependencies are built using Poetry.
Use poetry to manage dependencies and pip to install the package in editable mode.
cd bento-tools poetry install pip install -e .
For updating documentation locally, install extra dependencies and launch a live server to preview doc builds:
First install pandoc (see dependencies section for more details).
poetry install --extras "docs" pip install -e .\[docs\] cd docs make livehtml # See output for URL
GPU Support (Optional)#
Bento currently only uses GPUs to accelerate tensor decomposition (via Tensorly) GPU support can be enabled by installing PyTorch. We recommend the PyTorch installation instructions for more details as installation varies by platform.