1 files changed, 25 insertions, 24 deletions
diff --git a/software/chapter.tex b/software/chapter.tex
index 0027c5f..b52764b 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -1,5 +1,4 @@
 % TODO: add StoddenVictoria2016a (Enhancing reproducibility for computational methods)
-% TODO: http://pubs.acs.org/doi/10.1021/cen-09535-scitech2
 
 \chapter{Software}
 
@@ -146,11 +145,11 @@ parallelization paradigms''
 \section{Good-enough practices}  % ================================================================
 
 In their [...] perspective, ``Good enough practices in scientific computing'', (from which this
-section gets its name) [WILSON ET AL] describe a set of techniques that, in their words, ``every
-researcher can and should consider adopting''.  %
+section gets its name) \textcite{WilsonGreg2017a} describe a set of techniques that, in their
+words, ``every researcher can and should consider adopting''.  %
 In this section, I attempt to very quickly summarize my personal perspective on what makes good
 software development good---with citations to literature that supports each idea.  %
-These practices are not, generally, ``extra work''.  %
+These practices are not, generally, \emph{extra work}.  %
 In fact, many of them save massive amounts of time and effort in the long \emph{and} short run,
 when properly applied.  %
 
@@ -158,8 +157,8 @@ when properly applied.  %
 Before you sit down and implement a piece of software, stop!  %
 First you should try hard to find a library that already has what you need.  %
 You'll often surprise yourself with what you can find.  %
-Search the package repository for your language, such as PyPI [CITE], MATLAB File Exchange [CITE]
-or CRAN [CITE].  %
+Search the package repository for your language, such as PyPI \cite{PyPI}, MATLAB File Exchange
+\cite{FileExchange} or CRAN \cite{CRAN}.  %
 Even if there is not a full solution to your problem out there, there is almost certainly a
 solution to some part of it.  %
 Much better to have a dependency than a custom implementation.  %
@@ -177,8 +176,8 @@ As a general rule, once you have two classes you need multiple files.  %
 Choose a non-proprietary format if at all possible---remember: you yourself might not have access
 to the proprietary software in 10 years.  %
 Choose plain text if you can.  %
-Consider conforming to specifications, such as Tidy Data. [CITE]  %
-If you must, use open binary formats such as HDF5.  %
+Consider conforming to specifications, such as Tidy Data \cite{WickhamHadley2014a}.  %
+If you must, use open binary formats such as HDF5 \cite{FolkMike2011a}.  %
 Put as much metadata as you can into the file.  %
 Any piece of metadata that can automatically be added by the computer is essentially free---you
 might as well do it.  %
@@ -196,12 +195,13 @@ This is indispensable when trying to diagnose software problems.  %
 In order to use version control as effectively as possible, try to save the package after every
 change (feature addition, bugfix, etc).  %
 Typically version control is coupled with uploading to a remote server, for example using git with
-GitHub [CITE] or git.chem.wisc.edu [CITE], but version control need not be synonymous with
-uploading and distribution.  %
+GitHub \cite{GitHub} or git.chem.wisc.edu \cite{git.chem.wisc.edu}, but version control need not be
+synonymous with uploading and distribution.  %
 Tools like git have a lot of fantastic features beyond simply saving [CITE], but those are beyond the
 scope of these ``good enough'' recommendations.  %
 Also consider defining a version for the software package as a whole.  %
-Use semantic versioning [CITE], unless there is a strong reason not to.  %
+Use semantic versioning (MAJOR.MINOR.PATCH) \cite{SemanticVersioning}, unless there is a strong
+reason not to.  %
 If the language you are using has a convention for representing the version programmatically, such
 as a \python{__version__} attribute in Python, comply with that convention.  %
 
@@ -220,7 +220,7 @@ unless your project becomes very important.  %
 Distribute test datasets, when appropriate.  %
 Remember, your tests can serve double duty as simple minimal examples.  %
 
-\textbf{Collaborate and share.} \cite{WilsonGreg2017a}  %
+\textbf{Collaborate and share.} \cite{WilsonGreg2017a, BarnesNick2010a}  %
 If you are part of a team, consider sharing software and collaborating to create it.  %
 Try using practices like code review and issue tracking, but don't feel obligated to use them if it
 doesn't make sense for your project.  %
@@ -228,7 +228,7 @@ When working as part of a team, making incremental changes and using version con
 more important.  %
 Earlier we mentioned ``do not reinvent''.  %
 The other side of that coin is ``if you make something, consider sharing it''.  %
-Put your software on an open platform, like GitHub, and mint a DOI.  %
+Put your software on an open platform, like GitHub \cite{GitHub}, and mint a DOI.  %
 Cite your software, and ask other people who are using your software to do the same.  %
 Choose a license early, and choose permissive and commercially compatible unless you 1. know what
 you are doing and 2. plan to enforce.  %
@@ -245,9 +245,11 @@ Try to follow the recommended style for your language, but don't obsess about it
 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 first, and if it works, consider optimization.  %
-If you do need to make your software faster, use profiling tools like cProfile [CITE] and SnakeVis
-[CITE] to empirically determine what operations are taking the longest, rather than trying to guess
-or use intuition.  %
+If you do need to make your software faster, use profiling tools like cProfile
+\cite{PythonProfilers} and SnakeViz \cite{SnakeViz} to empirically determine what operations are
+taking the longest, rather than trying to guess or use intuition.  %
+Only optimize speed-limiting operations, and stop optimizing once the code runs as quickly as
+needed.  %
 
 \section{Object oriented programming}  % ----------------------------------------------------------
 
@@ -364,17 +366,15 @@ Certain metadata conventions were also introduced, including named dimensions.
 NetCDF remains popular in the aerospace and 
 
 The Flexable Image Transform System (FITS) is a similar format with a focus on visualization and
-backwards compatibility. \cite{WellsDC1981a}  %
-% CITE https://fits.gsfc.nasa.gov/
-% CONSIDER CITING https://fits.gsfc.nasa.gov/rfc4047.txt
+backwards compatibility. \cite{FITS, WellsDC1981a}  %
 Fits is still popular in the astronomy community.  %
 
 Today, these hierarchical data formats have gathered under the umbrella of the HDF5 format, built
-and maintained by the HDF Group. [CITE]  %
+and maintained by the HDF Group. \cite{FolkMike2011a}  %
 This format has all of the advantages of FITS, CDF, and NetCDF.  %
 It can support arbitrary datatypes and is optimized to quickly process large and complex
 datasets.  %
-In Python, HDF5 is supported primarily through the h5py package. [CITE]  %
+In Python, HDF5 is supported primarily through the h5py package. \cite{h5py}  %
 
 \section{Scientific Python}  % --------------------------------------------------------------------
 
@@ -383,7 +383,8 @@ SciPy is a collection of ``open-source software for mathematics, science, and eg
 SciPy was an absolute essential component of this dissertation and the work it describes.  %
 There are packages under the SciPy umbrella.  %
 NumPy is a very powerful and fast package for working with multidimensional arrays.
-\cite{vanderWaltStefan2011a}  %
+\cite{OliphantTravisE2006a}  %
 The SciPy library contains a vast number of scientific computing tools, including many mathematical
-operations that this work depends on. [CITE]  %
-Matplotlib is a beautiful visualization package for 1, 2, and 3D plotting. [CITE]  %
+operations that this work depends on. \cite{SciPy}  %
+Matplotlib is a beautiful visualization package for 1, 2, and 3D plotting.
+\cite{HunterJohnD2007a}  %