2018-03-12 16:43

5 files changed, 84 insertions, 43 deletions

diff --git a/.gitignore b/.gitignore
index 2a47b98..8e9e032 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@
 *.fot
 *.cb
 *.cb2
+*.listing
 
 ## Intermediate documents:
 *.dvi
diff --git a/build.sh b/build.sh
index f098933..bf0c5c0 100755
--- a/build.sh
+++ b/build.sh
@@ -27,7 +27,7 @@ if [[ "$1" = "all" ]] || [[ "$1" = "data" ]] ; then
   #printThenPython "data/TA A.py"
   #printThenPython "data/TA B.py"
   #printThenPython "data/TG A.py"
-  #printThenPython "data/TG B.py"  
+  #printThenPython "data/TG B.py"
 fi
 
 # make figures
diff --git a/dissertation.cls b/dissertation.cls
index 74cd49b..452057b 100644
--- a/dissertation.cls
+++ b/dissertation.cls
@@ -10,7 +10,7 @@
 \RequirePackage[letterpaper, margin=1in]{geometry}  % 1 inch margins required
 \RequirePackage{setspace}
 \RequirePackage{afterpage}
-\RequirePackage{color}
+\RequirePackage{xcolor}
 \RequirePackage{array} 
 
 % --- headers -------------------------------------------------------------------------------------
@@ -49,9 +49,6 @@
 
 \newcommand{\dsignature}[1]{\hfill \normalfont{-- #1}}
   
-% THE FOLLOWING IS DARK MAGIC THAT I DON'T UNDERSTAND
-% I'M SURE I COULD DO BETTER...
-% - Blaise 2018-03-06
 \RequirePackage[shortlabels]{enumitem}
 \setlist[enumerate, 1]{nosep}
 \setlist[enumerate, 2]{nosep, topsep=-5ex}
@@ -78,11 +75,35 @@
 % --- code environment ----------------------------------------------------------------------------
 
 \RequirePackage{etoolbox}
-\RequirePackage[chapter]{minted}
+\RequirePackage[section]{minted}
 \usemintedstyle{colorfuli}
-\BeforeBeginEnvironment{minted}{\begin{singlespace}}
-\AfterEndEnvironment{minted}{\end{singlespace}}
-\setminted[python]{linenos=false, frame=lines}
+\setminted[python]{linenos=false, frame=none}
+
+\definecolor{bg}{rgb}{0.95,0.95,0.95}
+
+\setmintedinline[python]{bgcolor=bg}
+
+\RequirePackage[many]{tcolorbox}
+\tcbuselibrary{minted}
+
+\NewTCBListing{codefragment}{mo}{%
+  colback=bg,
+  boxrule=1pt,
+  colframe=bg,
+  arc=0,
+  shadow=false,
+  boxsep=1ex, top=0pt, left=0pt, right=0pt, bottom=0pt,
+  comment={\hfill(\arabic{chapter}.\arabic{equation})},
+  listing outside comment,
+  righthand width=2.5em,
+  sidebyside gap=0pt,
+  minted language=#1,
+  before skip =-0.5\baselinestretch,
+  after skip=2\baselinestretch,
+}
+
+\BeforeBeginEnvironment{codefragment}{\begin{singlespace}\stepcounter{equation}}
+\AfterEndEnvironment{codefragment}{\end{singlespace}}
 
 % --- tables --------------------------------------------------------------------------------------
 
diff --git a/dissertation.pdf b/dissertation.pdf
index 228593d..3efe0c6 100644
--- a/dissertation.pdf
+++ b/dissertation.pdf
diff --git a/processing/chapter.tex b/processing/chapter.tex
index 9d50bac..a1967c9 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -2,6 +2,8 @@
 

 % TODO: cool quote, if I can think of one

 

+\clearpage

+

 From a data science perspective, CMDS has several unique challenges:

 \begin{ditemize}

   \item Dimensionality of datasets can typically be greater than two, complicating

@@ -27,52 +29,69 @@ each multidimensional (or one-dimensional) spectra.  %
 WrightTools is written in Python, and endeavors to have a ``pythonic'', explicit and ``natural''

 application programming interface (API).  %

 To use WrightTools, simply import:

-

-\begin{minted}{python}

-import numpy as np

- 

-def incmatrix(genl1,genl2):

-    m = len(genl1)

-    n = len(genl2)

-    M = None #to become the incidence matrix

-    VT = np.zeros((n*m,1), int)  #dummy variable

- 

-    #compute the bitwise xor matrix

-    M1 = bitxormatrix(genl1)

-    M2 = np.triu(bitxormatrix(genl2),1) 

- 

-    for i in range(m-1):

-        for j in range(i+1, m):

-            [r,c] = np.where(M2 == M1[i,j])

-            for k in range(len(r)):

-                VT[(i)*n + r[k]] = 1;

-                VT[(i)*n + c[k]] = 1;

-                VT[(j)*n + r[k]] = 1;

-                VT[(j)*n + c[k]] = 1;

- 

-                if M is None:

-                    M = np.copy(VT)

-                else:

-                    M = np.concatenate((M, VT), 1)

- 

-                VT = np.zeros((n*m,1), int)

- 

-    return M

-\end{minted}

+\begin{codefragment}{python}

+>>> import WrightTools as wt

+>>> wt.__version__

+3.0.0

+\end{codefragment}

+I'll discuss more about how exactly WrightTools packaging, distribution, and instillation works in

+\autoref{sec:processing_distbribution}.

+

+We can use the builtin Python function \mintinline{python}{dir} to interrogate the contents of the

+WrightTools package.  %

+\begin{codefragment}{python}

+>>> dir(wt)

+['Collection',

+ 'Data',

+ '__branch__',

+ '__builtins__',

+ '__cached__',

+ '__doc__',

+ '__file__',

+ '__loader__',

+ '__name__',

+ '__package__',

+ '__path__',

+ '__spec__',

+ '__version__',

+ '__wt5_version__',

+ '_dataset',

+ '_group',

+ '_open',

+ '_sys',

+ 'artists',

+ 'collection',

+ 'data',

+ 'diagrams',

+ 'exceptions',

+ 'kit',

+ 'open',

+ 'units']

+\end{codefragment}

+Many of these are dunder (double underscore) attributes---Python internals that are not normally

+used directly.  %

+The ten attributes that do not start with underscore are the public API that users of WrightTools

+typically use.  %

+Within the public API are two classes, \mintinline{python}{Collection} \&

+\mintinline{python}{Data}, which are the two main classes in the WrightTools object model.  %

+\mintinline{python}{Data} stores spectra directly as multidimensional arrays, and

+\mintinline{python}{Collection} stores \textit{groups} of data objects (and other collection

+objects) in a hierarchical way for internal organization purposes.  %

 

 \subsubsection{wt5 file format}  % ----------------------------------------------------------------

 

 

 \section{Artists}  % ==============================================================================

 

+\subsection{Colormaps}  % -------------------------------------------------------------------------

 

+\subsection{Interpolation}  % ---------------------------------------------------------------------

 

 \section{Fitting}  % ==============================================================================

 

 

 

-\section{Distribution and licensing}  % ===========================================================

-

+\section{Distribution and licensing} \label{sec:processing_disbribution}  % =======================

 

 

 \section{Future directions}  % ====================================================================
\ No newline at end of file