The purpose of this repository is to get a standard skeleton for documenting (also running, testing) models.

Then, you can run setup.py directly or use pip. In either case, run the commands from the top-level directory of the repository (directory with this file).

• Using "setup.py":

    python setup.py install
  

  • to install locally, so changes are immediately picked up:

      python setup.py develop
    

• Using "pip":

    pip install .   # note the "." at the end
  

  • to install locally, so changes are immediately picked up:

      pip install -e .    # note the "." at the end
    

Ipopt is a open-source solver that is often used. Prebuilt binaries for Ipopt are available from the link here.

The unittests and other tests are under the tests directory. To run,

     nose2

Note: the nose2 command, by default, runs all functions starting woth test in all the Python files starting in test that it can find below the current directory. It is part of the nose2 framework.

To get slightly more detailed output, add a verbose flag:

    nose2 -v

There are example Jupyter notebook(s) in the examples/ directory. To run them, you should invoke Jupyter on a Notebook file (these end in the extension .ipynb, which stands for "IPython Notebook").

jupyter notebook examples/run-mea-model.ipynb

This should start up a notebook server and then pop up a tab or window in your default web browser showing the Notebook. For more information on how to use Jupyter, see the "Help" menu in the Notebook window itself, and the extensive documentation on the Jupyter website.

Documentation is in the docs directory. It is generated with Sphinx, which uses a Makefile. To build documentation, use the "docs" subcommand of the setup.py script:

python setup.py docs

Alternatively you can run the Makefile yourself with:

cd docs
make html

The main page will be in _build/html/index.html.

See file LICENSE in this repository.