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How to structure a GNU scientific project

From: Luke
Subject: How to structure a GNU scientific project
Date: Mon, 8 Nov 2010 10:36:13 -0800

I'm trying to organize the directory and file structure of my project
and figure out how everything should be installed in a way that
complies with the GCS and FHS.  Currently, my project provides several
command line binary executables that do some numerical number
crunching using GNU GSL.  The inputs to these binaries are a few human
readable text files which specify some simulation parameters and
settings.  The outputs of the executables are a couple of data files
(time histories, level curves, etc.) and a couple of text files that
show the simulation settings that were actually used and specify the
format of the output data.  On top of this, I have some Python scripts
which generate plots from the data files, and save them as pdfs.  The
python scripts call os.system to specify the simulation inputs, run
the simulation, and process output data to make some plots.  It also
takes all inputs and outputs (input text files + output data + plots)
and bundles them into a time-stamped tar.gz file so that multiple
simulation runs don't overwrite each other, and to provide a way to go
back and look at simulation results and know exactly what conditions
created them.

I have several sets of example input text files that allow a user to
run the simulations with some default parameters.  I'm not clear on
where these files should be placed in the source distribution and
where they should be installed during 'make install'.  I would like a
user to be able to easily find and open these text files so they can
use them as templates for running simulations with different

My questions are:
1)  Where should I put these text simulation configuration files
within my source distribution, and where should they be installed to
by default?
2)  How should I make my application and/or user aware of where they
are installed?  The way these files are used is by specifying a
command line flag that directs the executable to parse a particular
input file, so in order for this to be useful, the directory they are
installed into must be known.
3)  Should the python scripts go in site-packages, or would it make
more sense for them to be installed alongside the binary executables?
4)  I use the python scripts to save everything in a results/ folder
(and I'm often working with my source directory, so this is
src/results).  It seems like this folder ought to be in the users home
directory somewhere, but maybe there are other places it would make
sense to put this type of output data?

It seems like the text input files should go in a subdirectory of
/usr/local/share, or maybe the whole project should go into a
subdirectory of /opt.  The way I'm using the tools is by having
everything within a folder in my home directory, but this is probably
not a good way to distribute.

The basic source layout is:
top-level -- has the standard GCS files and Autotools files
    src -- sources files which compile to executables, also has some
python scripts for postprocessing the data
    src/common -- convenience libraries that are used by executables
    src/intialconditions -- text files for controlling initial
simulation conditions
    src/parameters -- text files for specify different numerical
values for simulation parameters
    src/integrationsettings -- text files for choosing different
numerical integration settings

There are anywhere from 5-20 text files in each of the
src/initialconditions, src/parameters, src/integrationsettings folders
that I want to distribute in some logical fashion.

Any thoughts?  Also, I'm using Autotools (Autoconf and Automake), so
if there are good ways to do this automagically with these tools, that
would be ideal.


Dale L. Peterson
Sports Biomechanics Lab, UC Davis
Office:  +01 530-752-2163
Mobile: +01 805-698-6157

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