Analysis phase description started with Final paper and verification

With this commit, the general outline of the analysis phase is given, as
well as a description of the LaTeX macros and their relation to the paper
and thier verification.

Also, the data-lineage figure was updated to have references.tex also and
some resizing of the folders in file-architecture to be more clear.

3 files changed, 49 insertions, 43 deletions

diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex
index d849e8c..aa2a397 100644
--- a/tex/src/figure-data-lineage.tex
+++ b/tex/src/figure-data-lineage.tex
@@ -1,24 +1,25 @@
-\newcommand{\paperpdf}{}
-\newcommand{\papertex}{}
-\newcommand{\projecttex}{}
-\newcommand{\verifytex}{}
-\newcommand{\initializetex}{}
-\newcommand{\downloadtex}{}
-\newcommand{\inputtwo}{}
-\newcommand{\inputsconf}{}
-\newcommand{\analysisonetex}{}
-\newcommand{\outoneb}{}
-\newcommand{\outonebdep}{}
-\newcommand{\inputone}{}
-\newcommand{\inputonedep}{}
-\newcommand{\analysistwotex}{}
-\newcommand{\outtwob}{}
-\newcommand{\outtwobdep}{}
-\newcommand{\analysisthreetex}{}
-\newcommand{\analysisthreeouts}{}
-\newcommand{\outtwoa}{}
-\newcommand{\outtwoadep}{}
-\newcommand{\outthreeadep}{}
+% All macros commented                %  1
+\newcommand{\paperpdf}{}              %  2
+\newcommand{\papertex}{}              %  3
+\newcommand{\projecttex}{}            %  4
+\newcommand{\verifytex}{}             %  5
+\newcommand{\initializetex}{}         %  6
+\newcommand{\downloadtex}{}           %  7
+\newcommand{\inputtwo}{}              %  8
+\newcommand{\inputsconf}{}            %  9
+\newcommand{\analysisonetex}{}        % 10
+\newcommand{\outoneb}{}               % 11
+\newcommand{\outonebdep}{}            % 12
+\newcommand{\inputone}{}              % 13
+\newcommand{\inputonedep}{}           % 14
+\newcommand{\analysistwotex}{}        % 15
+\newcommand{\outtwob}{}               % 16
+\newcommand{\outtwobdep}{}            % 17
+\newcommand{\analysisthreetex}{}      % 18
+\newcommand{\analysisthreeouts}{}     % 19
+\newcommand{\outtwoa}{}               % 20
+\newcommand{\outtwoadep}{}            % 21
+\newcommand{\outthreeadep}{}          % 22
 
 
 
@@ -96,7 +97,10 @@
 
   %% paper.tex
   \ifdefined\papertex
+  \node (reftex) [node-nonterminal, at={(2.67cm,-4.2cm)}] {references.tex};
   \node (papertex) [node-nonterminal, at={(5.47cm,-4.2cm)}] {paper.tex};
+  \node (papertex-north) [node-point, at={(5.47cm,-3.58cm)}] {};
+  \draw [rounded corners] (reftex) |- (papertex-north);
   \draw [->] (papertex) -- (paperpdf);
   \fi
 
diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex
index c892232..a4d4755 100644
--- a/tex/src/figure-file-architecture.tex
+++ b/tex/src/figure-file-architecture.tex
@@ -54,7 +54,7 @@
   \fi
 
   %% reproduce/software/bash
-  \node [dirbox, at={(-5.75cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
+  \node [dirbox, at={(-5.75cm,-0.8cm)}, minimum width=2.6cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {bashrc.sh};
@@ -75,32 +75,34 @@
     label={[shift={(0,-5mm)}]\texttt{analysis/}}, fill=brown!20!white] {};
 
   %% reproduce/analysis/config
-  \node [dirbox, at={(0.15cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
+  \node [dirbox, at={(0.15cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm,
     label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {};
   \node [node-nonterminal-thin, at={(0.15cm,0.8cm)}] {INPUTS.conf};
   \node [node-nonterminal-thin, at={(0.15cm,0.3cm)}] {param-1.conf};
-  \node [node-nonterminal-thin, at={(0.15cm,-0.2cm)}] {param-2.conf};
+  \node [node-nonterminal-thin, at={(0.15cm,-0.2cm)}] {param-2a.conf};
+  \node [node-nonterminal-thin, at={(0.15cm,-0.7cm)}] {param-2b.conf};
 
   %% reproduce/analysis/make
-  \node [dirbox, at={(2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
+  \node [dirbox, at={(2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.6cm,
     label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {};
-  \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {initialize.mk};
-  \node [node-nonterminal-thin, at={(2.95cm,0.3cm)}] {download.mk};
-  \node [node-nonterminal-thin, at={(2.95cm,-0.2cm)}] {analysis-1.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,0.8cm)}] {top-prepare.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,0.3cm)}] {top-make.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,-0.2cm)}] {initialize.mk};
+  \node [node-nonterminal-thin, at={(2.95cm,-0.7cm)}] {analysis1.mk};
 
   %% reproduce/analysis/bash
-  \node [dirbox, at={(0.15cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
+  \node [dirbox, at={(0.15cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.1cm,
     label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
-  \node [node-nonterminal-thin, at={(0.15cm,-1.5cm)}] {process-A.sh};
+  \node [node-nonterminal-thin, at={(0.15cm,-2.0cm)}] {process-A.sh};
   \fi
 
   %% reproduce/analysis/python
-  \node [dirbox, at={(2.95cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
+  \node [dirbox, at={(2.95cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{python/}}, fill=brown!25!white] {};
   \ifdefined\fullfilearchitecture
-  \node [node-nonterminal-thin, at={(2.95cm,-1.5cm)}] {operation-B.py};
-  \node [node-nonterminal-thin, at={(2.95cm,-2.0cm)}] {fitting-plot.py};
+  \node [node-nonterminal-thin, at={(2.95cm,-2.0cm)}] {operation-B.py};
+  \node [node-nonterminal-thin, at={(2.95cm,-2.5cm)}] {fitting-plot.py};
   \fi
 
   %% tex/
@@ -108,28 +110,28 @@
     label={[shift={(0,-5mm)}]\texttt{tex/}}, fill=brown!15!white] {};
 
   %% tex/src
-  \node [dirbox, at={(6cm,2.1cm)}, minimum width=2.5cm, minimum height=2.1cm,
+  \node [dirbox, at={(6cm,2.1cm)}, minimum width=2.5cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{src/}}, fill=brown!20!white] {};
+  \node [node-nonterminal-thin, at={(6cm,1.4cm)}] {references.tex};
   \ifdefined\fullfilearchitecture
-  \node [node-nonterminal-thin, at={(6cm,1.4cm)}] {preamble-1.tex};
   \node [node-nonterminal-thin, at={(6cm,0.9cm)}] {figure-1.tex};
   \fi
 
   %% tex/build
   \ifdefined\fullfilearchitecture
-  \node [dirbox, at={(6cm,-0.2cm)}, minimum width=2.5cm, minimum height=1.3cm,
+  \node [dirbox, at={(6cm,0.1cm)}, minimum width=2.5cm, minimum height=1.3cm,
     label={[shift={(0,-5mm)}]\texttt{build/}}, dashed, , fill=brown!20!white] {};
-  \node [anchor=west, at={(4.7cm,-1.0cm)}] {\scriptsize\sf Symbolic link to};
-  \node [anchor=west, at={(4.7cm,-1.3cm)}] {\scriptsize\sf \LaTeX{} build directory.};
+  \node [anchor=west, at={(4.7cm,-0.7cm)}] {\scriptsize\sf Symbolic link to};
+  \node [anchor=west, at={(4.7cm,-1.0cm)}] {\scriptsize\sf \LaTeX{} build directory.};
   \fi
 
   %% tex/tikz
   \ifdefined\fullfilearchitecture
-  \node [dirbox, at={(6cm,-1.7cm)}, minimum width=2.5cm, minimum height=1.6cm,
+  \node [dirbox, at={(6cm,-1.6cm)}, minimum width=2.5cm, minimum height=1.6cm,
     label={[shift={(0,-5mm)}]\texttt{tikz/}}, dashed, fill=brown!20!white] {};
-  \node [anchor=west, at={(4.67cm,-2.5cm)}] {\scriptsize\sf Symbolic link to TikZ};
-  \node [anchor=west, at={(4.67cm,-2.8cm)}] {\scriptsize\sf directory (figures built};
-  \node [anchor=west, at={(4.67cm,-3.1cm)}] {\scriptsize\sf by \LaTeX).};
+  \node [anchor=west, at={(4.67cm,-2.4cm)}] {\scriptsize\sf Symbolic link to TikZ};
+  \node [anchor=west, at={(4.67cm,-2.7cm)}] {\scriptsize\sf directory (figures built};
+  \node [anchor=west, at={(4.67cm,-3.0cm)}] {\scriptsize\sf by \LaTeX).};
   \fi
 
   %% .local
diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex
index fe36eec..c3aeca2 100644
--- a/tex/src/preamble-style.tex
+++ b/tex/src/preamble-style.tex
@@ -136,4 +136,4 @@
 }
 
 %% Custom macros
-\newcommand{\inlinecode}[1]{`\textcolor{blue!35!black}{\texttt{#1}}'}
+\newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}