From aff7629182048ea264a024fd32ceac70006a9caa Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Wed, 4 Apr 2018 14:18:43 -0500
Subject: 2018-04-04 14:18

---
 software/chapter.tex | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

(limited to 'software/chapter.tex')

diff --git a/software/chapter.tex b/software/chapter.tex
index 0027c5f..7fb9e6c 100644
--- a/software/chapter.tex
+++ b/software/chapter.tex
@@ -158,8 +158,8 @@ 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 +177,8 @@ 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].  %
 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 +196,13 @@ 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.  %
 
@@ -245,9 +246,11 @@ 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}  % ----------------------------------------------------------
 
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