Simphony-common

The native implementation of the SimPhoNy cuds objects and io code (http://www.simphony-project.eu/).

Repository

Simphony-common is hosted on github: https://github.com/simphony/simphony-common

Requirements

• enum34 >= 1.0.4
• stevedore >= 1.2.0
• numpy >= 1.11.1

Optional requirements

To support the HDF5 based native IO:

• PyTables >= 3.1.1

To support the documentation built you need the following packages:

• sphinx >= 1.3.1
• mock

Note

Packages that depend on the optional features and use setuptools should append the H5IO and/or CUBAGen identifier next to simphony in their setup_requires configuration option. For example:

install_requires = ["simphony[H5IO, CUBAGen]"]

Will make sure that the requirements of H5IO and CUBAGen support are installed. (see setuptools extras for more information)

Installation

The package requires python 2.7.x, installation is based on setuptools:

# build and install
python setup.py install

or:

# build for in-place development
python setup.py develop

Testing

To run the full test-suite run:

python -m unittest discover -p test*

Documentation

To build the documentation in the doc/build directory run:

python setup.py build_sphinx

If you recreate the uml diagrams you need to have java and xdot installed:

sudo apt-get install default-jre xdot

A copy of the plantuml.jar needs also to be available in the :file:`doc/` folder. Running make uml inside the :file:`doc/` directory will recreate all the UML diagrams.

Note

• One can use the --help option with a setup.py command to see all available options.
• The documentation will be saved in the :file:`./build` directory.
• Not all the png files of the UML diagrams are used.

Directory structure

There are four subpackages:

• core -- used for common low level classes and utility code
• cuds -- to hold all the native cuds implementations
• io -- to hold the io specific code
• bench -- holds basic benchmarking code
• examples -- holds SimPhoNy example code
• doc -- Documentation related files
  • source -- Sphinx rst source files
  • build -- Documentation build directory, if documentation has been generated using the make script in the doc directory.

SimPhoNy Framework

The simphony library is the core component of the SimPhoNy Framework; information on setting up the framework is provided on a separate repository https://github.com/simphony/simphony-framework.

For Developers

The data structures used in this project are based on the metadata which is defined in a separate repository called simphony-metadata located at: https://github.com/simphony/simphony-metadata.

In order to reflect latest changes to the metadata repository, one should regenerate these entities. The generator is hosted in the repository simphony-metatools located at: https://github.com/simphony/simphony-metatools . The generator is used to recreate the python classes in simphony/cuds/meta.

Guide to generating metadata classes

After installing the dev_requirements, rebuild the meta classes by issuing the following command:

$ python setup.py build_meta

The command will rebuild the classes against the simphony-metadata repository tag as written in setup.cfg build_meta/repotag entry.