README

/*
 * README
 * 
 * Copyright 2012 Chaitanya Talnikar <chaitukca@gmail.com>
 * 
 */
 
Welcome to the biographer simulator.

The simulator uses a Makefile to manage the project. make by default
executes the directive 'all' which consists of 'lint', 'doc', 'test' and
'pkg'. 
The simulator source code does not consist of any external libraries
by default and they have to be fetched and installed.

Build libs:
1. If you are using Ubuntu, install necessary dependences to test and 
build the software by typing in the terminal:
    make deps
Otherwise please refer below for a list of dependencies:
    #required to build bui
    nodejs
    npm
    node-uglify
    #required to build libSBGN.js
    ant
    git-core(git)
    #required for creating documentation
    jsdoc-toolkit(jsdoc)
    #required for the offline app
    libqtwebkit4
    python-qt4
    #required for lint code check
    jshint
    #required for unit testing
    selenium python api
    chromedriver(selenium webdriver)
    
2. Fetch and build the libs by executing the command:
    make libs
The above commands adds the following libs:
    biographer-ui
    d3.js
    libSBGN.js
    
3. To support SBML files in the simulator the biographer server needs to 
be setup. Please read the README in the server folder. 
    
4. For testing purposes if you are using Chrome you need to download the
Chrome WebDriver available at the following url:
    http://code.google.com/p/chromedriver/downloads/list
Download the linux zip depending on your architechture and install it using 
the commands:
    tar -xvf chromedriver*.zip
    sudo cp chromedriver /usr/bin


Now once you have the necessary libs you are ready to test the simulator or
create a deployable package.

Offline App(browse):
To test the application offline(no SBML support) using the qt webkit engine. Run:
    make browse
    
Testing(test):
To run all the tests for the simulator, run:
    make test
This executes all the tests including the file import/export, SBML server
tests and the Simulate, Analyse and Plot features using the selenium
browser testing framework along with python's unittest.
To run specific tests take a look at the main.py file in the tests directory.
The default browser is Chrome and the default URL is the localhost web2py
server. To change these settings modify the simulator.py file.

Packaging(pkg):
To create a package which can be easily deployed on a server execute:
    make pkg
A zip file simulator.zip will be created in the root directory. 

The following tasks don't really require the libs.
Code checking(lint):
To perform jshint on the js files execute:
    make lint

Documentation(doc):
To generate documentation using jsdoc execute:
    make doc
The docs will reside in the jsdoc directory.