bioLEC is a pure Python package and can be installed via pip as well as Docker.


You will need Python 2.7 or 3.5+ and the following packages are required: numpy, scipy, pandas, mpi4py, scikit-image, pyevtk.


The mpi4py module has to be installed as a wrapper around an existing installation of MPI. The easiest way to install it is to use anaconda, which will install a compatible version of MPI and configure mpi4py to use it: conda install -c conda-forge mpi4py

The complete list of Dependencies is available in the src/requirements.txt file and looks like:


Optionally, lavavu is needed to support interactive visualisation in Jupyter environment (as shown in the notebook examples available from binder).

Installing using pip

PyPI version

You can install bioLEC package using the latest stable release available via pip!

pip install bioLEC

If you need to install it for different python versions:

$ python2 -m pip install bioLEC
$ python3 -m pip install bioLEC

To install the development version: Clone the repository using

git clone

Navigate into the bioLEC directory and run

$ cd src/
$ pip install -r requirements.txt
$ pip install .

Installing using Docker

Another straightforward installation which does not depend on specific compilers relies on docker virtualisation system.

To install the docker image and test it is working:

$ docker pull geodels/biolec:latest
$ docker run --rm geodels/biolec:latest help

On Linux, to build the dockerfile locally, we provide a script. First ensure you have checked out the source code from github and then run the script in the Docker directory. If you modify the dockerfile and want to push the image to make it publicly available, it will need to be retagged to upload somewhere other than the GEodels repository.

$ git checkout
$ cd bioLEC
$ source Docker/


For non-Linux platforms, the use of Docker Desktop for Mac or Docker Desktop for Windows is recommended. The docker container to look for is named geodels/biolec!

Testing installation

A test is provided to check the correct installation of the bioLEC package.If you’ve cloned the source into a directory bioLEC, you may verify it as follows:

Navigate the the directory src/tests and run the tests.

$ python2
$ python3

You will need to have all dependencies installed.

The following result indicates success.

$ Test bioLEC installation:: [####################] 100.0% DONE
$ All tests were successful...