From f8c9747d3b6425b420839ff06931b63692318f03 Mon Sep 17 00:00:00 2001
From: Blaise Thompson <blaise@untzag.com>
Date: Thu, 5 Apr 2018 09:47:06 -0500
Subject: 2018-04-05 09:47

---
 processing/chapter.tex | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

(limited to 'processing/chapter.tex')

diff --git a/processing/chapter.tex b/processing/chapter.tex
index baca84c..c1e46f4 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -33,8 +33,7 @@ enough to be a foundational tool.  %
 
 When creating a toolkit for CMDS, there are several challenges worth considering:
 \begin{ditemize}
-  \item Dimensionality of datasets can typically be greater than two, complicating
-    \textbf{representation}.
+  \item Dimensionality of datasets can typically be greater than two, complicating representation.
   \item Shape and dimensionality change, and relevant axes can be different from the scanned
     dimensions.  %
   \item Data can be awkwardly large-ish (several million pixels), and can become legitimately large
@@ -45,10 +44,10 @@ The biggest challenge is to find a really good definition for what constitutes a
 Once understood, this common denominator can be enshrined into software and built upon.  %
 
 WrightTools is a software package written in Python, built using the excellent tools provided by
-the scientific Python collection of packages, especially Scipy and Numpy.  % TODO: cite cite cite
+the scientific Python collection of packages, especially Scipy and Numpy. [CITE?]  %
 WrightTools defines a universal file-format that is flexible enough to encompass the diversity of
 CMDS while still being entirely self-describing.  %
-This file format is based on the popular binary format ``HDF5''.  % TODO: cite
+This file format is based on the popular binary format ``HDF5''. \cite{h5py}  %
 This format allows for computers to interact with the arrays piece-by-piece in a very fast and
 reliable way, without loading the entire array in and out of memory.  %
 WrightTools piggybacks on this, allowing users to interact with legitimately large CMDS datasets
@@ -59,7 +58,7 @@ coordinate spaces.  %
 
 WrightTools is written to be used in scripts and in the command line.  %
 It does not have any graphical components built in, except for the ability to generate plots using
-matplotlib.  % TODO: cite
+matplotlib. [CITE?]  %
 Being built in this way gives WrightTools users maximum flexibility, and allows for rapid
 collaborative development.  %
 It also allows other software packages to use WrightTools as a ``back-end'' foundational software,
@@ -77,7 +76,7 @@ To use WrightTools, simply import:
 3.0.0
 \end{codefragment}
 I'll discuss more about how exactly WrightTools packaging, distribution, and instillation works in
-\autoref{pro:sec:processing_distribution}.
+\autoref{pro:sec:distribution}.
 
 We can use the builtin Python function \python{dir} to interrogate the contents of the
 WrightTools package.  %
@@ -929,6 +928,7 @@ This license is incredibly permissive and puts as few restrictions as possible o
 Because the license is short, it is reproduced below.  %
 
 \begin{dquote}
+
   The MIT License (MIT)
 
   Copyright (c) 2016-2018 WrightTools Developers.
@@ -948,6 +948,7 @@ Because the license is short, it is reproduced below.  %
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
   DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
 \end{dquote}
 
 As an aside, since Python is an interpreted language the source code of a library \emph{must} be
@@ -957,7 +958,7 @@ However many Python libraries end up being interfaces to compiled code that coul
 closed-source.  %
 The Scientific Python Stack have MIT-compatible licenses, including BSD-like licenses.  %
 
-\subsection{Distribution}  % ----------------------------------------------------------------------
+\subsection{Distribution} \label{pro:sec:distribution}  % ------------------------------------------
 
 How does WrightTools get onto end-users machines?  %
 Distribution...
-- 
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