Editing Reproducible computational experiments using SCons (section)

===Tools for reproducible research===
The reproducible research system developed at Stanford is based on
"make" (Stallman et al., 2004<ref>Stallman, R. M., R. McGrath, and P. D. Smith,  2004, GNU make: A program for directing recompilation: GNU Press.</ref>), a Unix software construction utility.
Initially, SEP used "cake," a dialect of "make"
(Nichols and Cole, 1989<ref>Nichols, D. and S. Cole,  1989, Device independent software installation with  CAKE, ''in'' SEP-61,  341--344. Stanford Exploration Project.</ref>;Claerbout and Nichols, 1990<ref>Claerbout, J. F. and D. Nichols,  1990, Why active documents need cake, ''in'' SEP-67,  145--148. Stanford Exploration Project.</ref>;Claerbout, 1992b<ref>-------- 1992b, How to use Cake with interactive documents, ''in'' SEP-73,  451--460. Stanford Exploration Project.</ref>;Claerbout and Karrenbach, 1993<ref>Claerbout, J. F. and M. Karrenbach,  1993, How to use cake with interactive  documents, ''in'' SEP-77,  427--444. Stanford Exploration Project.</ref>).
The system was converted to "GNU make," a more standard dialect, by
Schwab and Schroeder (1995<ref>Schwab, M. and J. Schroeder,  1995, Reproducible research documents using  GNUmake, ''in'' SEP-89,  217--226. Stanford Exploration Project.</ref>). The "make" program keeps track of dependencies between different
components of the system and the software construction targets, which,
in the case of a reproducible research system, turn into figures and
manuscripts. The author specifies the targets and commands for their construction in "makefiles," which serve as databases for
defining source and target dependencies. A dependency-based system
leads to rapid development because when one of the sources changes,
only parts that depend on this source get recomputed. Buckheit and Donoho (1995<ref>Buckheit, J. and D. L. Donoho,  1995, Wavelab and reproducible research, ''in'' Wavelets and Statistics, volume '''103''',  55--81. Springer-Verlag.</ref>)
based their system on MATLAB, a popular integrated development
environment produced by MathWorks (Sigmon and Davis, 2001<ref>Sigmon, K. and T. A. Davis,  2001, MATLAB primer, sixth edition: Chapman &  Hall.</ref>). While MATLAB is an adequate tool for prototyping numerical algorithms, it may not be
sufficient for large-scale computations typical for many applications
in computational geophysics.
"Make" is a handy utility employed by thousands of
software development projects. Unfortunately, it is not
well designed from the perspective of user experience. "Make" employs
an obscure and limited special language (a mixture of Unix shell
and special-purpose commands), which often appears confusing
to inexperienced users. According to Peter van der Linden, a software
expert from Sun Microsystems (van der Linden, 1994<ref>van der Linden, P.,  1994, Expert C programming: Prentice Hall.</ref>),
<blockquote>
"Sendmail" and "make" are two well-known programs that are
pretty widely regarded as originally being debugged into existence.
That's why their command languages are so poorly thought out and
difficult to learn. It's not just you -- everyone finds them
troublesome.
</blockquote>
The inconvenience of the "make" command language is also in its limited
capabilities. The reproducible research system developed by
Schwab et al. (2000<ref>Schwab, M., M. Karrenbach, and J. Claerbout,  2000, Making scientific computations reproducible: Computing in Science & Engineering, '''2''',  61--67.</ref>) includes not only custom "make" rules but also an obscure and hardly portable agglomeration of shell and Perl scripts that extend "make" (Fomel et al., 1997<ref>Fomel, S., M. Schwab, and J. Schroeder,  1997, Empowering SEP's documents,  ''in'' SEP-94,  339--361. Stanford Exploration Project.</ref>).
Several alternative systems for dependency-checking software
construction have been developed in recent years. One of the most
promising new tools is SCons, enthusiastically endorsed by
Dubois (2003<ref>Dubois, P. F.,  2003, Why Johnny can't build: Computing in Science &  Engineering, '''5''', 83--88.</ref>). The SCons initial design won the Software Carpentry competition sponsored by Los Alamos National Laboratory in 2000 in the category of "a dependency management tool to replace make." Some of the main advantages of SCons are:
  
*SCons configuration files are Python scripts. Python is a modern programming language praised for its readability, elegance, simplicity, and power (Rossum, 2000a<ref>Rossum, G. V.,  2000a, Python reference manual: Iuniverse Inc.</ref>;Rossum, 2000b<ref>-------- 2000b, Python tutorial: Iuniverse Inc.</ref>). Scales and Ecke (2002<ref>Scales, J. A. and H. Ecke,  2002, What programming languages should we teach our undergraduates?: The Leading Edge, '''21''', 260--267.</ref>) recommend Python as the first programming language for geophysics students. 
*SCons offers reliable, automatic, and extensible dependency analysis and creates a global view of all dependencies—no more "make depend," "make clean," or multiple build passes of touching and reordering targets to get all the dependencies. 
*SCons has built-in support for many programming languages and systems, including C, C++, Fortran, Java, and LaTeX. 
*While "make" relies on timestamps to detect file changes (creating numerous problems on platforms with different system clocks), SCons uses a more reliable detection mechanism, employing MD5 signatures by default. It can detect changes not only in files but also in commands used to build them. 
*SCons provides integrated support for parallel builds. 
*SCons provides configuration support analogous to the "autoconf" utility for testing the environment on different platforms. 
*SCons is designed from the ground up as a cross-platform tool. It works equally well on POSIX systems (Linux, Mac OS X, Solaris, etc.) and Windows. 
*The stability of SCons is assured by an incremental development methodology utilizing comprehensive regression tests. 
*SCons is publicly released under a liberal open-source license<ref>As of this writing, SCons is in a beta version of 0.96, approaching the 1.0 official release. See http://www.scons.org/.</ref>.
In this paper, we propose to adopt SCons as a new platform for
reproducible research in scientific computing.