
SEP's laboratory-wide standard rules 
for reproducible electronic documents

The SEP make rules fall into two groups:
The program compilation start with the Prefix <tt>Prg</tt>.
The document maintainance rules start with the Prefix <tt>Doc</tt>.
You can find more information about the document maintainance system 
at my reproducilbe research page.
(http://sepwww.stanford.edu/pub/sep/matt/join/redoc/web/index.html).

All these rules are adapted to SEP's compute environment.
You may have to adapt them to your specific computer setup.

To include the standard SEP rules in a makefile, 
you need include the files SEP.top at the top of the makefile and 
SEP.bottom at the bottom.
To make the shared rules available in any directory, we set an 
environment variable, e.g. SEPINC, to the root directory of the 
rule directory:

Makefile:

include ${SEPINC}/SEP.top

your_rules: ...

include  ${SEPINC}/SEP.bottom

                (matt@sep.stanford.edu)

  SUMMARY 

To organize computational scientific research 
and hence to conveniently transfer our technology,
we impose a simple filing discipline on the authors in our laboratory.
A document's makefile includes laboratory-wide standard rules
that offer readers these four standard commands:
   make burn  removes the document's result figures, 
   make build  recomputes them, 
   make view  displays the figures, and 
   make clean  removes any intermediate files.
Although we developed these standards to aid readers
we discovered that authors are often the principal beneficiaries.

Contents:

 o Doc files:   implements SEP's make rules and variable definitions 
                for SEP's electronic reproducible documents.

 o Prg files:   implements SEP's make rules and variable definitions for 
                compiling, linking, and installation of executables.

 o SEP files:   organizes the inclusion of the various make source code.


Other files serve special purposes and are not included into a makefile
routinely. 

