Editing Package overview (section)

===Reproducibility and Project Management===

Madagascar uses and extends [http://www.scons.org/ SCons], an open-source 
software construction package to document and maintain data processing flows. Documented projects become 
computational recipes that can be easily exchanged among Madagascar users. 

SCons is a rule-based package in Python typically used as a build system analogous to <tt>make</tt>. Familiarity with any build system will
help understand SCons. SCons statements, as Python statements, are invoked in the sequence in which they are 
written, but as such, they only define rules. The rules are invoked by a dependency graph, which
SCons builds based on those rules. Components regarded as "up-to-date" are not rebuilt. 

SCons allows for user-contributed Builders (meta-rule categories), and Madagascar uses this capability extensively. 
The idea is that building an output file based on a workflow chain is analogous to building a 
software package based on a software toolchain. The calculation is seen simply as a build with dependencies. 
This setup greatly benefits developing alternative workflows using a given dataset. The system 
maintains an awareness of already completed calculations. Without user intervention, redundant calculations 
are avoided.

Madagascar calculations are thus expressed as SCons scripts (<tt>SConstruct</tt> files). SCons extensions follow SCons conventions, beginning 
with an uppercase letter. The most common Madagascar extensions are <tt>Flow()</tt>, <tt>Result()</tt>, and <tt>End()</tt>. A <tt>Flow()</tt> invocation wraps Madagascar computational components. <tt>Result()</tt> is a version of <tt>Flow()</tt> with a graphical output. Finally an
End() invokes the default rules for multiple results. 

Finally, Madagascar enables a collection of reproducible documents to be organized into living books. Each 
reproducible book contains a collection of Madagascar recipes (<tt>SConstruct</tt> files) used to generate book figures. The recipes 
cover a variety of data processing and imaging tasks described in the books. Figures and recipes serve 
a dual purpose concerning Madagascar maintenance. They provide demos to introduce new users to the 
functionality of the package and, at the same time, [[Automatic Testing|regression tests]] to assure the system's stability 
under change.