Technology Spotlight/
Python Scripting: The Return to Programming
Mark Bakker1
More than 30 years ago, before the first public version
of MODFLOW, programming was an essential skill for
groundwater modelers. With the advent of graphical user
interfaces, models could be built by clicking a series
of buttons. This allowed modelers to spend more time
on simulation without the need for programming skills.
Unfortunately, models created with a user interface are
not easily reproduced, archived, or independently verified.
Modeling errors are easily made, yet difficult to find and
correct.
In recent years, computer programming is making a
comeback in the form of scripting. A script is a piece of
computer code designed to perform one or more specific
tasks. A script can be written, for example, to read
GIS files, build a model, run it, analyze the output, and
create graphical output. Scripts are also well-suited to
perform data analysis from the original measurements
to the final result. As scripts are readable files, it is
much easier to catch and correct errors. A script is a
record of the entire modeling or data analysis process.
By simply running the script you reprocess the entire
model or analysis. How about that for reproducible
results?
The advantage of using scripts to document modeling
and data analysis is recognized in many fields. For
example, Baggerly and Coombes (2009) recommend the
use of scripts in response to the well-published cancer
research scandal at Duke University, where patients
were put at risk as a consequence of errors in data
analysis.
The free and open-source computer language Python
is ideal for writing scripts. Python has a simple yet
powerful syntax and is becoming increasingly popular
among hydrogeologists. There are many packages for
Python to perform advanced tasks from statistical analysis
of large datasets to parameter optimization and the
1
Water Resources Section, Civil Engineering and Geosciences,
Delft University of Technology, Delft, The Netherlands; mark.bakker
@tudelft.nl
2014, National Ground Water Association.
doi: 10.1111/gwat.12269
NGWA.org
Yu-Feng Forrest Lin, Technology Editor
creation of publication-ready graphics. Conveniently,
Python is the scripting language adopted by GIS software
such as ArcGIS and QGIS.
Python scripts can run MODFLOW and friends by
using the FloPy (pronounce: Flow Pie) package (FloPy
2014). The FloPy package consists of a set of scripts to run
MODFLOW, MT3DMS, SEAWAT, SWI, PHT3D, and
other MODFLOW-related groundwater programs. FloPy
is functional for most MODFLOW packages. It is a
community project and is actively being developed by
volunteers to add new capabilities.
There are several analytic element computer pro-
grams written in Python, such as the TTim code for
simulating transient multi-layer flow (e.g., Bakker 2013).
TTim makes use of Pythons capabilities to seamlessly
interface with FORTRAN and C code by including small
pieces of FORTRAN code to boost performance. TTim
can be run interactively from the Python prompt or
from a Python script. You can even write your own
basic analytic element program in Python as was out-
lined in Ground Water a few years ago (Bakker and
Kelson 2009).
There is one more important capability that needs
to be mentioned here: the IPython Notebook (IPython
2014). An IPython Notebook combines Python scripts
with text, mathematics, and graphical output into a single
document. The amazing part is that a Notebook can
actually be executed, which means that all Python code
in the Notebook is run and all output is regenerated.
A Notebook is a full executable report of the entire
modeling endeavor. Notebooks can be sent directly to
clients, or can be converted to static pdf or html files.
Entire books are written as IPython Notebooks. It is
not inconceivable that scientific journals will accept (or
require?) modeling papers as IPython Notebooks in the
future.
Excited about a return to programming? There are
many free tutorials on the web to get you started
with Python scripting. A good introduction is the free
book Python in Hydrology which provides a practical
introduction into the language including many examples
related to hydrology (Tomer 2011).
Groundwater 1
References
Baggerly, K.A., and K.R. Coombes. 2009. Deriving chemosen-
sitivity from cell lines: Forensic bioinformatics and repro-
ducible research in high-throughput biology. Annals of
Applied Statistics 3, no. 4: 13091334.
Bakker, M. 2013. Semi-analytic modeling of transient multi-
layer flow with TTim. Hydrogeology Journal 21, no. 4:
935943.
2 Groundwater
Bakker, M., and V.A. Kelson. 2009. Writing analytic element
programs in Python. Ground Water 47, no. 6: 828834.
FloPy. 2014. http://code.google.com/p/flopy/
IPython. 2014. http://ipython.org/notebook.html
Tomer, S.K. 2011. Python in Hydrology. http://www.green
teapress.com/pythonhydro/pythonhydro.html
NGWA.org