2018-04-07 23:18

3 files changed, 53 insertions, 26 deletions

diff --git a/bibliography.bib b/bibliography.bib
index 0859f66..b633eae 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -843,7 +843,6 @@ year = {1998}
   publisher =    {{AIP} Publishing},

 }

 

-

 @article{HammPeter1999a,

   author =       {Hamm, Peter and Lim, Manho and DeGrado, W. F. and Hochstrasser, Robin M},

   title =        {{The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in

@@ -858,6 +857,7 @@ year = {1998}
   month =        {mar},

 }

 

+

 @article{HammPeter2000a,

   author =       {Hamm, Peter and Lim, Manho and DeGrado, William F. and Hochstrasser, Robin M},

   title =        {{Pump/probe self heterodyned 2D spectroscopy of vibrational transitions of a

@@ -1003,6 +1003,20 @@ year = {1998}
 }

 

 @article{JoppaLucasN2013a,

+  author =       {L. N. Joppa and G. McInerny and R. Harper and L. Salido and K. Takeda and K.

+                  O{\textquotesingle}Hara and D. Gavaghan and S. Emmott},

+  title =        {Troubling Trends in Scientific Software Use},

+  journal =      {Science},

+  volume =       340,

+  number =       6134,

+  pages =        {814--815},

+  year =         2013,

+  doi =          {10.1126/science.1231535},

+  month =        {may},

+  publisher =    {American Association for the Advancement of Science ({AAAS})},

+}

+

+@article{JoppaLucasN2013a,

   author =       {Joppa, Lucas N. and McInerny, Greg and Harper, Richard and Salido, Lara and

                   Takeda, Kenji and O{\textquoteright}Hara, Kenton and Gavaghan, David and Emmott,

                   Stephen},

diff --git a/dissertation.tex b/dissertation.tex
index 29d1821..b2aa572 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -68,16 +68,16 @@ This dissertation is approved by the following members of the Final Oral Committ
 \include{software/chapter}

 

 \part{Development} \label{prt:development}

-%\include{processing/chapter}

-%\include{acquisition/chapter}

-%\include{active_correction/chapter}

-%\include{opa/chapter}

-%\include{mixed_domain/chapter}

+\include{processing/chapter}

+\include{acquisition/chapter}

+\include{active_correction/chapter}

+\include{opa/chapter}

+\include{mixed_domain/chapter}

 

 \part{Applications} \label{prt:applications}

-%\include{PbSe/chapter}

-%\include{MX2/chapter}

-%\include{PEDOT_PSS/chapter}

+\include{PbSe/chapter}

+\include{MX2/chapter}

+\include{PEDOT_PSS/chapter}

 

 % appendix -----------------------------------------------------------------------------------------

 

@@ -85,15 +85,15 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 \part{Appendix} \label{prt:appendix}

 \begin{appendix}

-%\include{public/chapter}

-%\include{procedures/chapter}

-%\include{hardware/chapter}

+\include{public/chapter}

+\include{procedures/chapter}

+\include{hardware/chapter}

 % TODO: consider inserting WrightTools documentation as PDF

-%\include{irf/chapter}

-%\include{quantitative_ta/chapter}

-%\include{tg/chapter}

-%\include{errata/chapter}

-%\include{colophon/chapter}

+\include{irf/chapter}

+\include{quantitative_ta/chapter}

+\include{tg/chapter}

+\include{errata/chapter}

+\include{colophon/chapter}

 \end{appendix}

 

 % post --------------------------------------------------------------------------------------------

diff --git a/software/chapter.tex b/software/chapter.tex
index 26636f1..14693ee 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -158,17 +158,30 @@ written by generation upon generation of student.  %
 Worse, software is sometimes abandoned or left untouched to become a crucial but arcane component

 of a scientific research project.  %

 

-\textbf{Testing.} \cite{SandersRebecca2008a, PrabhuPrakash2011a}

+\textbf{Lack of testing.} \cite{SandersRebecca2008a, PrabhuPrakash2011a, JoppaLucasN2013a}

 Testing is a huge part of software development practices, but many researchers do not engage in

-sufficient testing of their software...  %

-The issue of testing is also consistent with the system of peer review...

-Software is not typically peer reviewed...

+sufficient testing of their software.  %

+Without testing, even small software projects can rapidly ``get out of hand''---they can become

+unsustainable and unmaintainable.  %

 Especially for domain-specific computational software, determining the ``correct outcome'' to test

 against is often infeasible.  %

-

-\textbf{Optimization.} \cite{PrabhuPrakash2011a}

-Scientists do not optimize for the common case.  %

-Scientists are unaware of parallelization paradigms.  %

+Software is not typically peer reviewed, so a lack of software testing is often a weak link in the

+loop of critical self assessment that science depends upon.  %

+On the positive side, testing can be an easy-to-add development practice with huge rewards.  %

+Well written tests can be a programmers best friend: helping her to ensure that her code has met

+all of the given requirements.  %

+Well written tests allow programmers to optimize without worrying about breaking crucial components

+of their software.  %

+

+\textbf{Struggles with optimization.} \cite{PrabhuPrakash2011a}

+Sometimes, a scientific application requires performant code.  %

+Scientists typically struggle to write such code.  %

+They may struggle with parallelization paradigms, or they may not understand what is limiting the

+speed of their software.  %

+They may not have good intuitions about how long certain operations should take, or what patterns

+could be used to speed up execution.  %

+Scientists typically do not use profiling tools which help them see which parts of their program

+would benefit most from optimization.  %

 

 \section{Good-enough practices}  % ================================================================

 

@@ -274,7 +287,7 @@ Don't be afraid to be verbose, most programming environments have tab completion
 not all that hard to type.  %

 Try to follow the recommended style for your language, but don't obsess about it.  %

 

-\textbf{Avoid premature optimization.} \cite{WilsonGreg2017a}

+\textbf{Avoid premature optimization.} \cite{WilsonGreg2014a, WilsonGreg2017a}

 Don't get pulled into the trap of trying to make things perfect the first time.  %

 Software design is typically a very iterative process, and for good reason.  %

 Write for correctness first, and if it works, consider optimization.  %