Install instructions

Requirements

Biotite requires at least Python version 3.4. If you are still using Python 2.7, you should hurry up with upgrading to Python 3.x.

Biotite also requires the following packages:

  • numpy
  • requests
  • msgpack

If you are a Linux user, you should be able to install these packages simply via pip (Tip: Use --only-binary :all: to ensure precompiled versions are installed). In case you are using Windows, I recommend installing numpy and matplotlib via Conda, or alternatively Anaconda which already contains the forementioned packages.

Some functions require some extra packages:

  • mdtraj - Required for trajetory file I/O operations.
  • matplotlib - Required for plotting purposes.

Install from PyPI

By default, Biotite uses wheels for its package distribution. Simply type

pip install biotite

If pip finds an appropriate wheel for your system configuration on PyPI, it will download and install it. Congratulations, you just installed Biotite! If no fitting wheel is found, pip will fall back to the source distribution. If you want to prevent pip to do that, use the following command:

pip install biotite --only-binary :all:

The source distribution can be used if there is no wheel available for you or you want to compile the package on your own for other reasons:

pip install biotite --no-binary :all:

Note that installing from source distribution requires a C-compiler (typically GCC).

Install from source

If you want to install your own Biotite build, navigate to the top-level directory of your local Biotite clone (the one setup.py is in) and type the following:

pip install .

Note that this requires a C-compiler (typically GCC) and the packages cython and wheel to be installed. Having the Biotite package always pointing to your development directory is also possible. Type the following in the top-level directory:

pip install -e .

To generate the wheels and source distribution for upload to PyPI (most probably you won’t need that, but just in case), simply type:

python setup.py bdist_wheel
python setup.py sdist

You can find the wheel and the source distribution in the dist directory (they should be the only files there, you can’t miss them).