Installation
============

Conda environment
"""""""""""""""""

Create and activate a conda environment:

  .. code:: bash

    conda create --name pensa python=3.9 numpy==1.22 scipy==1.9 pandas==1.4 matplotlib==3.5 MDAnalysis==2.2 cython biotite -c conda-forge -c conda-forge
    conda activate pensa

If you want to use PENSA with Jupyter notebooks:

  .. code:: bash

    conda install jupyter

Option 1: Install the PENSA library from PyPI
"""""""""""""""""""""""""""""""""""""""""""""

This installs the latest released version.

Within the environment created above, execute:

  .. code:: bash

    pip install pensa

To use the example scripts or tutorial folder, you'll have to download them from the repository.

Option 2: Create editable installation from source
""""""""""""""""""""""""""""""""""""""""""""""""""

This installs the latest version from the repository, which might not yet be officially released.

Within the environment created above, execute:

  .. code:: bash

    git clone https://github.com/drorlab/pensa.git  
    cd pensa
    pip install -e .