INSTALL

Installation:
-------------

cbcbeat can be installed as any other Python module using
distutils:

For system-wise install do:

  sudo python setup.py install

Or specify a local path:

  python setup.py install --prefix=/home/me/favorite-path

Tests and demos can be run without installation by adding the top
level directory to your PYTHONPATH:

  export PYTHONPATH=`pwd`:$PYTHONPATH

Verifying the installation:
---------------------------

The tests are based on pytest (pytest.org).

The installation can be verified by running the collection of tests
located under test/:

  cd test
  py.test -m "not slow" -v

Dependencies:
-------------

cbcbeat depends in particular on the following software components

* The FEniCS Project software: www.fenicsproject.org (v. 2016.1.0 or later)

  The FEniCS Project is a collection of software for automated
  solution of partial differential equations using finite element
  methods. 

* dolfin-adjoint: www.dolfin-adjoint.org (compatible with FEniCS)

  dolfin-adjoint provides tools for automatically deriving the
  discrete adjoint and tangent linear models from a DOLFIN forward
  model.

* [Optional] gotran: https://bitbucket.org/johanhake/gotran 

  Gotran is a general ODE translator

* [Optional] Sphinx: sphinx-doc.org

  Sphinx is a tool for generating documentation for Python module

* [Optional] Model Parameters: https://bitbucket.org/johanhake/modelparameters

  Model Parameters is a Python library for easy use of parameters in
  Python models, written by Johan Hake. Obtain by

    bzr branch lp:modelparameters

  This module is only required for running some of the tests (and this
  dependency will be removed).

* [Optional] py.test (pytest.org)

  This testing tools is used for, well: the tests

Installation with docker
------------------------
1. Install docker: https://docs.docker.com/engine/installation/
2. Build docker container with
       `docker build -t cbcbeat .`
3. Start docker container with
       `docker run -i -t cbcbeat`