2018-04-04 21:38

1 files changed, 12 insertions, 12 deletions

diff --git a/software/chapter.tex b/software/chapter.tex
index 36e2949..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.  %

 

@@ -178,7 +177,7 @@ Choose a non-proprietary format if at all possible---remember: you yourself migh
 to the proprietary software in 10 years.  %

 Choose plain text if you can.  %

 Consider conforming to specifications, such as Tidy Data \cite{WickhamHadley2014a}.  %

-If you must, use open binary formats such as HDF5 [CITE].  %

+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.  %

@@ -221,7 +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.  %

@@ -229,7 +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.  %

@@ -371,11 +370,11 @@ 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}  % --------------------------------------------------------------------

 

@@ -384,7 +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}  %