Installation¶

Use of the Python 9ML API requires that you have Python (version 2.7 or >=3.4) with the sympy package installed. To serialize NineML to XML, YAML and HDF5 formats the lxml, pyyaml and h5py packages are also required respectively.

Dependencies¶

macOS¶

If you are not already using another Python installation (e.g. Enthought, Python(x,y), etc…) it can be a good idea to install Python using the Homebrew package manager rather than using the system version as Apple has modified some package versions (e.g. six), which can cause difficulties down the track.

$ brew install python

While other Python installations should work fine, it is not recommended to use the system Python installation at /usr/bin/python for scientific computing as some of the standard pacakges (e.g. six) have been modified and this can cause problems with other packages down the track.

Before installing h5py you will also need to install a development version of HDF5. With Homebrew this can be done with:

$ brew install hdf5

Linux¶

On Linux, development packages for HDF5 (i.e. with headers). For Ubuntu/Debian the following packages can be used

libhdf5-serial-dev (serial)

libhdf5-openmpi-dev (parallel with Open MPI)

libhdf5-mpich-dev (parallel with MPICH)

Please consult the relevant documentation to find the appropriate package for other distributions.

Windows¶

On Windows, you can download the Python installer from http://www.python.org. To use HDF5 serialisation you will need to install HDF5 from source, see http://docs.h5py.org/en/latest/build.html.

Install Python packages¶

To install the Python package it is recommeded to install from PyPI using pip:

$ pip install nineml

Otherwise for the latest version you can clone the repository at http://github.com/INCF/nineml-python or install directly with:

$ pip install git+http://github.com/INCF/nineml-python