Installation

Requirements

Biotite requires at least Python version 3.6. If you are still using Python 2.7, you should hurry up with upgrading to Python 3.

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, it is recommended to install numpy and matplotlib via Conda, or alternatively Anaconda which already contains the aforementioned packages.

Some functions require some extra packages:

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

  • matplotlib - Required for plotting purposes.

Install via Conda

For Conda users, for example Windows users who use the Anaconda Python distribution, the simplest way for installing Biotite is

$ conda install -c conda-forge biotite

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 from doing 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 Biotite from the project repository, navigate to the top-level directory of your local Biotite repository 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. For convenience this Conda environment, contains all runtime and build dependencies for Biotite.

Having the Biotite package always pointing to your directory containing the repository 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 created wheel and the source distribution in the dist directory.

Common issues and solutions

Compiler error when building Biotite

There is a known problem with GCC compiler errors in some Linux distributions (e.g. Arch Linux) when building Biotite from source. Among other error lines the central error is the following:

unable to initialize decompress status for section .debug_info

While the exact reason for this error is still unknown, this can be fixed by using a GCC installed via Conda:

$ conda install -c conda-forge c-compiler

ValueError when importing Biotite

When importing one of Biotite’s subpackages the following error might occur:

ValueError: numpy.ufunc size changed, may indicate binary incompatibility.

The reason for this error is, that Biotite was built against a NumPy version other than the one installed. This happens for example when NumPy is updated, but Biotite is already installed. Simply reinstall Biotite to solve this issue.