bioLEC is a pure Python package and can be installed via pip as well as Docker.
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:
numpy>=1.15 six>=1.11.0 setuptools>=38.4.0 mpi4py>=3.0.0 pandas>=0.24 scipy>=1.2 scikit-image>=0.15 pyevtk>=1.1.1 matplotlib>=3.0 rasterio>=1.0.23
Installing using pip¶
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 https://github.com/Geodels/bioLEC.git
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 https://github.com/Geodels/bioLEC.git $ cd bioLEC $ source Docker/build-dockerfile.sh
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 testInstall.py $ python3 testInstall.py
You will need to have all dependencies installed.
The following result indicates success.
$ Test bioLEC installation:: [####################] 100.0% DONE $ All tests were successful...