2018-04-04 21:38

2 files changed, 67 insertions, 22 deletions

diff --git a/bibliography.bib b/bibliography.bib
index 2ddd43a..9e5921c 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -107,6 +107,19 @@
   month =        {feb},

 }

 

+@article{BarnesNick2010a,

+  author =       {Nick Barnes},

+  title =        {Publish your computer code: it is good enough},

+  journal =      {Nature},

+  volume =       467,

+  number =       7317,

+  pages =        {753--753},

+  year =         2010,

+  doi =          {10.1038/467753a},

+  month =        {oct},

+  publisher =    {Springer Nature},

+}

+

 @article{BesemannDanielM2004a,

   author =       {Besemann, Daniel M. and Meyer, Kent A. and Wright, John C.},

   title =        {{Spectroscopic Characteristics of Triply Vibrationally Enhanced Four-Wave Mixing

@@ -585,6 +598,12 @@ year = {1998}
   month =        {may},

 }

 

+@misc{FITS,

+  note =         {Accessed: 2018-03-27},

+  title =        {FITS: Flexable image transport},

+  url =          {https://fits.gsfc.nasa.gov/},

+}

+

 @article{FangHui2014a,

   author =       {H. Fang and C. Battaglia and C. Carraro and S. Nemsak and B.

                   Ozdol and J. S. Kang and H. A. Bechtel and S. B. Desai and F.

@@ -624,6 +643,17 @@ year = {1998}
   month =        {feb},

 }

 

+@inproceedings{FolkMike2011a,

+  author =       {Mike Folk and Gerd Heber and Quincey Koziol and Elena Pourmal and Dana Robinson},

+  title =        {An overview of the {HDF}5 technology suite and its applications},

+  booktitle =    {Proceedings of the {EDBT}/{ICDT} 2011 Workshop on Array Databases - {AD}

+                  {\textquotesingle}11},

+  year =         2011,

+  doi =          {10.1145/1966895.1966900},

+  publisher =    {{ACM} Press},

+}

+

+

 @article{FourkasJohnT1992a,

   author =       {Fourkas, John T. and Trebino, Rick and Fayer, M. D.},

   title =        {{The grating decomposition method: A new approach for understanding

@@ -639,7 +669,6 @@ year = {1998}
   month =        {jul},

 }

 

-

 @article{FourkasJohnT1992b,

   author =       {Fourkas, John T and Trebino, Rick and Fayer, M D},

   title =        {{The grating decomposition method: A new approach for understanding

@@ -857,7 +886,6 @@ year = {1998}
 	journal = {Science},

 	doi = {10.1126/science.37.955.610},

 }

-

 @article{HyblJohnD2001a,

   author =       {Hybl, John D. and {Albrecht Ferro}, Allison and Jonas, David M.},

   title =        {{Two-dimensional Fourier transform electronic spectroscopy}},

@@ -869,6 +897,7 @@ year = {1998}
   doi =          {10.1063/1.1398579},

   issn =         00219606,

 }

+

 @article{HyblJohnD2001b,

   author =       {Hybl, John D. and Christophe, Yannick and Jonas, David M.},

   title =        {{Peak shapes in femtosecond 2D correlation spectroscopy}},

@@ -1319,6 +1348,13 @@ year = {1998}
   month =        {dec},

 }

 

+@book{OliphantTravisE2006a,

+  author =       {Travis E Oliphant},

+  title =        {A guide to NumPy},

+  year =         2006,

+  publisher =    {Trelgol Publishing},

+}

+

 @article{OliphantTravisE2007a,

   author =       {Oliphant, Travis E.},

   title =        {{Python for Scientific Computing}},

@@ -1650,6 +1686,13 @@ year = {1998}
   month =        {mar},

 }

 

+@Misc{SciPy,

+  author =       {Eric Jones and Travis Oliphant and Pearu Peterson and others},

+  note =         {Accessed: 2018-04-04},

+  title =        {{SciPy}: Open source scientific tools for {Python}},

+  url =          {http://www.scipy.org/},

+}

+

 @inproceedings{SeamanCarolynB1997a,

   author =       {Carolyn B. Seaman and Victor R. Basili},

   title =        {An empirical study of communication in code inspections},

@@ -2001,6 +2044,7 @@ year = {1998}
   month =        {oct},

 }

 

+

 @article{WrightJohnCurtis1997a,

   author =       {Wright, John C.},

   title =        {{New selective nonlinear vibrational spectroscopies}},

@@ -2014,7 +2058,6 @@ year = {1998}
   month =        {jun},

 }

 

-

 @article{WrightJohnCurtis1997b,

   author =       {Wright, John C. and Chen, Peter C. and Hamilton, James P. and Zilian, Arne and

                   Labuda, Mitchell J.},

@@ -2196,20 +2239,22 @@ year = {1998}
   url =          {https://git.chem.wisc.edu/},

 }

 

+@misc{h5py,

+  note =         {Accessed: 2018-04-04},

+  title =        {h5py: HDF5 for Python},

+  url =          {https://www.h5py.org/},

+}

+

+

 @misc{h5py.Group,

   note =         {Accessed: 2018-03-25},

   title =        {h5py Groups documentation.},

   url =          {http://docs.h5py.org/en/latest/high/group.html#groups},

 }

 

-@misc{FITS,

-  note =         {Accessed: 2018-03-27},

-  title =        {FITS: Flexable image transport},

-  url =          {https://fits.gsfc.nasa.gov/},

-}

-

 @misc{pyqtgraph,

   note =         {Accessed: 2018-03-27},

   title =        {PyQtGraph: Scientific Graphics and GUI Library for Python},

   url =          {http://pyqtgraph.org/},

-}
\ No newline at end of file
+}

+

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}  %