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

Conda environment
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Create and activate a conda environment:

  .. code:: bash

    conda create --name pensa python==3.10 scipy numpy==1.26.4 pandas matplotlib MDAnalysis==2.8 deeptime biotite pip -c conda-forge
    conda activate pensa

If you want to use PENSA with Jupyter notebooks:

  .. code:: bash

    conda install jupyter
    python -m ipykernel install --user --name=pensa

Option 1: Install the PENSA library from PyPI
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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
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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 .