Installation

CIRCE requires Python 3.8+ and can be installed via pip or from source. It is recommended to use a virtual environment or a conda environment to manage dependencies.

The package can be installed using pip:

pip install circe-py

and from github

pip install "git+https://github.com/cantinilab/circe.git"

Essential dependencies

Since CIRCE depends on lapack and blas to compute the graphical lasso, you may need to install these libraries first.

It means that you might not be able to use CIRCE in a standard Windows environment without WSL or similar. For that, you can use a singularity or docker container, such as provided here (singularity).

If you are working in a conda environment and are encountering any issue with the installation of circe-py, you can try installing first these dependencies via:

conda install conda-forge::lapack
conda install conda-forge::libfortran=3
conda install -c conda-forge cmake llvmlite=0.46
conda install gxx_linux-64

If you are not working with conda, on Ubuntu, you can do this via:

sudo apt-get install libblas-dev liblapack-dev

On macOS, you can use Homebrew:

brew install openblas