Installation

  1. You’ll need a Fortran compiler and Fortran-compiled fastell4py, which you can get on a debian system by running
$sudo apt-get install gfortran
$git clone https://github.com/sibirrer/fastell4py.git <desired location>
$cd <desired location>
$python setup.py install --user
  1. Virtual environments are strongly recommended, to prevent dependencies with conflicting versions. Create a conda virtual environment and activate it:
$conda create -n baobab python=3.6 -y
$conda activate baobab
  1. Now do one of the following.

Option 2(a): clone the repo (please do this if you’d like to contribute to the development).

$git clone https://github.com/jiwoncpark/baobab.git
$cd baobab
$pip install -e . -r requirements.txt

Option 2(b): pip install the release version (only recommended if you’re a user).

$pip install pybaobab
  1. (Optional) To run the notebooks, add the Jupyter kernel.
$python -m ipykernel install --user --name baobab --display-name "Python (baobab)"
  1. (Optional) To enable online data augmentation for machine learning, install the relevant dependencies.
$pip install torch torchvision
$pip install tensorflow-gpu