Analysis and configuration file sections complete

With this commit a description of these two important parts have been added
to the project, along with several figures showing various parts of the
files that are discussed. I also done some other restructuring of the
figures and files to make things fit better into the the description of the
paper.

8 files changed, 126 insertions, 28 deletions

diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex
index 010a0be..7379b2f 100644
--- a/tex/src/figure-data-lineage.tex
+++ b/tex/src/figure-data-lineage.tex
@@ -58,11 +58,11 @@
   \node (downloadmk)   [node-makefile, at={(-2.93cm,-1.3cm)},
     label={[shift={(0,-5mm)}]\texttt{download.mk}}] {};
   \node (analysis1mk)  [node-makefile, at={(-0.13cm,-1.3cm)},
-    label={[shift={(0,-5mm)}]\texttt{analysis1.mk}}] {};
+    label={[shift={(0,-5mm)}]\texttt{format.mk}}] {};
   \node (analysis2mk)  [node-makefile, at={(2.67cm,-1.3cm)},
-    label={[shift={(0,-5mm)}]\texttt{analysis2.mk}}] {};
-  \node (analysis2mk)  [node-makefile, at={(5.47cm,-1.3cm)},
-    label={[shift={(0,-5mm)}]\texttt{analysis3.mk}}] {};
+    label={[shift={(0,-5mm)}]\texttt{demo-plot.mk}}] {};
+  \node (analysis3mk)  [node-makefile, at={(5.47cm,-1.3cm)},
+    label={[shift={(0,-5mm)}]\texttt{another-step.mk}}] {};
 
   %% verify.mk
   \node [at={(-5.3cm,-2.8cm)},
@@ -149,7 +149,7 @@
 
   %% analysis1.tex
   \ifdefined\analysisonetex
-  \node (a1tex) [node-terminal, at={(-0.13cm,-0.8cm)}] {analysis1.tex};
+  \node (a1tex) [node-terminal, at={(-0.13cm,-0.8cm)}] {format.tex};
   \draw [rounded corners, -] (a1tex) |- (initialize-south);
   \fi
 
@@ -167,14 +167,17 @@
 
   %% analysis2.tex
   \ifdefined\analysistwotex
-  \node (a2tex) [node-terminal, at={(2.67cm,-0.8cm)}] {analysis2.tex};
+  \node (a2tex) [node-terminal, at={(2.67cm,-0.8cm)}] {demo-plot.tex};
   \draw [rounded corners, -] (a2tex) |- (initialize-south);
   \fi
 
   %% out-2b.dat
   \ifdefined\outtwob
-  \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {out-2b.dat};
+  \node (menkedemoyear) [node-nonterminal, at={(2.67cm,4.6cm)}] {menke-demo-year.conf};
+  \node (a2tex-west) [node-point, at={(1.27cm,-0.8cm)}] {};
+  \node (out2b) [node-terminal, at={(2.67cm,0.3cm)}] {tools-per-year.txt};
   \draw [->] (out2b) -- (a2tex);
+  \draw [->,rounded corners] (menkedemoyear.west) -| (a2tex-west) |- (a2tex);
   \fi
 
   %% out-2b dependencies
@@ -184,39 +187,36 @@
 
   %% analysis3.tex
   \ifdefined\analysisthreetex
-  \node (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {analysis3.tex};
-  \draw [rounded corners, -] (a3tex) |- (initialize-south);
+  \node [opacity=0.6] (a3tex) [node-terminal, at={(5.47cm,-0.8cm)}] {another-step.tex};
+  \draw [opacity=0.6, rounded corners, -, dashed] (a3tex) |- (initialize-south);
   \fi
 
   %% Outputs of analysis3
   \ifdefined\analysisthreeouts
-  \node (out3a) [node-terminal, at={(5.47cm,2.7cm)}] {out-3a.dat};
-  \node (out3b) [node-terminal, at={(5.47cm,1.1cm)}] {out-3b.dat};
+  \node [opacity=0.6] (out3a) [node-terminal, at={(5.47cm,2.7cm)}] {out-3a.dat};
+  \node [opacity=0.6] (out3b) [node-terminal, at={(5.47cm,1.1cm)}] {out-3b.dat};
   \node (a3tex-east) [node-point, at={(6.87cm,-0.8cm)}] {};
-  \draw [->,rounded corners] (out3a.east) -| (a3tex-east) |- (a3tex);
-  \draw [->] (out3b) -- (a3tex);
+  \draw [opacity=0.6, ->,rounded corners, dashed] (out3a.east) -| (a3tex-east) |- (a3tex);
+  \draw [opacity=0.6, ->, dashed] (out3b) -- (a3tex);
   \fi
 
   %% out-2a.dat
   \ifdefined\outtwoa
-  \node (out2a) [node-terminal, at={(2.67cm,1.9cm)}] {out-2a.dat};
-  \draw [->, rounded corners] (out2a.south) |- (out3b);
+  \node [opacity=0.6] (out2a) [node-terminal, at={(2.67cm,1.9cm)}] {demo-out.dat};
+  \draw [opacity=0.6, ->, rounded corners, dashed] (out2a.south) |- (out3b);
   \fi
 
   %% Dependencies of out-2a
   \ifdefined\outtwoadep
-  \node (a2conf1) [node-nonterminal, at={(2.67cm,5.3cm)}]  {param-2a.conf};
-  \node (a2conf2) [node-nonterminal, at={(2.67cm,4.6cm)}]  {param-2b.conf};
   \node (out2a-west) [node-point, at={(1.27cm,1.9cm)}] {};
-  \draw [->,rounded corners] (a2conf1.west) -| (out2a-west) |- (out2a);
-  \draw [->,rounded corners] (a2conf2.west) -| (out2a-west) |- (out2a);
-  %\draw [->] (input1) -- (out2a);
+  \draw [opacity=0.6, ->, dashed] (input2) -- (out2a);
   \fi
 
   %% Dependencies of out-3a
   \ifdefined\outthreeadep
-  \node (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {};
-  \node (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}]  {param-3.conf};
-  \draw [rounded corners] (a3conf1.west) -| (out3a-west) |- (out3a);
+  \node [opacity=0.6] (out3a-west) [node-point, at={(4.07cm,2.7cm)}] {};
+  \draw [opacity=0.6, ->,rounded corners, dashed] (input2) |- (out3a);
+  \node [opacity=0.6] (a3conf1) [node-nonterminal, at={(5.47cm,4.6cm)}]  {param-3.conf};
+  \draw [opacity=0.6, rounded corners, dashed] (a3conf1.west) -| (out3a-west) |- (out3a);
   \fi
 \end{tikzpicture}
diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex
index 8fb1a6d..1fc26c5 100644
--- a/tex/src/figure-file-architecture.tex
+++ b/tex/src/figure-file-architecture.tex
@@ -88,7 +88,7 @@
   \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};
+  \node [node-nonterminal-thin, at={(2.95cm,-0.7cm)}] {format.mk};
 
   %% reproduce/analysis/bash/
   \node [dirbox, at={(0.15cm,-1.3cm)}, minimum width=2.6cm, minimum height=1.1cm,
diff --git a/tex/src/figure-inputconf.tex b/tex/src/figure-inputconf.tex
new file mode 100644
index 0000000..f09bebd
--- /dev/null
+++ b/tex/src/figure-inputconf.tex
@@ -0,0 +1,8 @@
+\begin{tcolorbox}
+  \footnotesize
+  \texttt{\mkvar{MK20DATA} = menke20.xlsx}\\
+  \texttt{\mkvar{MK20MD5}{ }  = 8e4eee64791f351fec58680126d558a0}\\
+  \texttt{\mkvar{MK20SIZE} = 1.9MB}\\
+  \texttt{\mkvar{MK20URL}{ }  = https://the.full.url/is/too/large/for/here/media-1.xlsx}\\
+  \vspace{-3mm}
+\end{tcolorbox}
diff --git a/tex/src/figure-src-demoplot.tex b/tex/src/figure-src-demoplot.tex
new file mode 100644
index 0000000..6d788f5
--- /dev/null
+++ b/tex/src/figure-src-demoplot.tex
@@ -0,0 +1,32 @@
+\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{demo-plot.mk}}\hfill(Simplified contents)]
+  \footnotesize
+  \texttt{\mkcomment{1ST MAKE RULE: build the directory hosting the converted table.}}\\
+  \texttt{\mkvar{a2dir} = \$(\mkvar{texdir})/tools-per-year}\\
+  \texttt{\mktarget{\$(a2dir)}:; \mkprog{mkdir} \$@}
+
+  \vspace{2em}
+  \texttt{\mkcomment{2ND MAKE RULE: extract necessary info from raw table.}}\\
+  \texttt{\mkvar{a2mk20f1c} = \$(\mkvar{a2dir})/tools-per-year.txt}\\
+  \texttt{\mktarget{\$(a2mk20f1c)}: \$(\mkvar{mk20tab3}) | \$(\mkvar{a2dir})}\\
+  \texttt{\mktab{}\mkprog{awk} '!/\^{}\#/ \{all[\$\$1]+=\$\$2; id[\$\$1]+=\$\$3;\}} \textbackslash\\
+  \texttt{\mktab{}{ }{ }{ }{ }{ }END\{ for(year in all) print year, 100*id[year]/all[year], all[year] \}}' \textbackslash\\
+  \texttt{\mktab{}{ }{ }{ }{ }> \$@}
+
+  \vspace{2em}
+  \texttt{\mkcomment{3RD MAKE RULE: Main LaTeX macro file for reported values in text.}}\\
+  \texttt{\mkvar{pconfdir} = reproduce/analysis/config}\\
+  \texttt{\mktarget{\$(mtexdir)/demo-plot.tex}: \$(\mkvar{a2mk20f1c}) \$(\mkvar{pconfdir})/menke-demo-year.conf}
+
+  %% We need an empty line here for the extra space to work.
+  \texttt{\recipecomment{First year data were taken (first column of first row).}}\\
+  \texttt{\mktab{}v=\$\$(awk 'NR==1\{print \$\$1\}' \$(\mkvar{a2mk20f1c}))}\\
+  \texttt{\mktab{}\mkprog{echo} "\textbackslash{}newcommand\{\textbackslash{}menkefirstyear\}\{\$\$v\}" > \$@}
+
+  %% We need an empty line here for the extra space to work.
+  \texttt{\recipecomment{Number of papers in the demonstration year. The year is defined in}}
+
+  \texttt{\recipecomment{`\$(pconfdir)/menke-demo-year.conf' as `menke-demo-year' and also passed onto LaTeX.}}\\
+  \texttt{\mktab{}v=\$\$(awk '\$\$1==\$(\mkvar{menke-demo-year})\{print \$\$3\}' \$(\mkvar{a2mk20f1c}))}\\
+  \texttt{\mktab{}\mkprog{echo} "\textbackslash{}newcommand\{\textbackslash{}menkenumpapersdemocount\}\{\$\$v\}"{ }>> \$@} \\
+  \texttt{\mktab{}\mkprog{echo} "\textbackslash{}newcommand\{\textbackslash{}menkenumpapersdemoyear\}\{\$(\mkvar{menke-demo-year})\}"{ }>> \$@}
+\end{tcolorbox}
diff --git a/tex/src/figure-download.tex b/tex/src/figure-src-download.tex
index b9da02f..74026b8 100644
--- a/tex/src/figure-download.tex
+++ b/tex/src/figure-src-download.tex
@@ -1,4 +1,4 @@
-\begin{tcolorbox}
+\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{download.mk}} \textcolor{white}{(only \LaTeX{} macro's rule.}]
   \footnotesize
   \texttt{\mkcomment{Write download URL into the paper (through a LaTeX macro).}}
 
diff --git a/tex/src/figure-mk20tab3.tex b/tex/src/figure-src-format.tex
index 3cc0cd3..ba4458e 100644
--- a/tex/src/figure-mk20tab3.tex
+++ b/tex/src/figure-src-format.tex
@@ -1,8 +1,8 @@
-\begin{tcolorbox}
+\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{format.mk}}\hfill(Simplified contents)]
   \footnotesize
   \texttt{\mkcomment{1ST MAKE RULE: build the directory hosting the converted table.}}
 
-  \texttt{\mkvar{a1dir} = \$(\mkvar{BDIR})/analysis-1}
+  \texttt{\mkvar{a1dir} = \$(\mkvar{BDIR})/format}
 
   \texttt{\mktarget{\$(a1dir)}:}
 
@@ -40,7 +40,7 @@
   \vspace{2em}
   \texttt{\mkcomment{3RD MAKE RULE: Main LaTeX macro file for reported values.}}
 
-  \texttt{\mktarget{\$(mtexdir)/analysis1.tex}: \$(\mkvar{mk20tab3)}}
+  \texttt{\mktarget{\$(mtexdir)/format.tex}: \$(\mkvar{mk20tab3)}}
 
   \texttt{\recipecomment{Count the total number of papers in their study to report in this paper.}}
 
diff --git a/tex/src/figure-src-topmake.tex b/tex/src/figure-src-topmake.tex
new file mode 100644
index 0000000..bd4b67d
--- /dev/null
+++ b/tex/src/figure-src-topmake.tex
@@ -0,0 +1,24 @@
+\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{top-make.mk}}\hfill\textcolor{white}{(simplified)}]
+  \footnotesize
+
+  \texttt{\mkcomment{Ultimate target/purpose of project (`paper.pdf' is the final target of the final subMakefile}}\par
+  \texttt{\mkcomment{that is loaded/included below)}}\par
+  \texttt{\mktarget{all}: paper.pdf}
+
+  \vspace{1em}
+  \texttt{\mkcomment{List of subMakefiles to be loaded in order.}}\par
+  \texttt{\mkvar{makesrc} = initialize \textbackslash}\par
+  \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }download \textbackslash}\par
+  \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }format \textbackslash}\par
+  \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }demo-plot \textbackslash}\par
+  \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }verify \textbackslash}\par
+  \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }paper}\par
+
+  \vspace{1em}
+  \texttt{\mkcomment{Load all the configuration files.}}\par
+  \texttt{\textcolor{purple}{include} reproduce/analysis/config/*.conf}
+
+  \vspace{1em}
+  \texttt{\mkcomment{Load/include the subMakefiles in the specified order.}}\par
+  \texttt{\textcolor{purple}{include} \$(\textcolor{blue}{foreach} s, \$(\mkvar{makesrc}), reproduce/analysis/make/\$(\mkvar{s}).mk)}
+\end{tcolorbox}
diff --git a/tex/src/figure-tools-per-year.tex b/tex/src/figure-tools-per-year.tex
new file mode 100644
index 0000000..75557ac
--- /dev/null
+++ b/tex/src/figure-tools-per-year.tex
@@ -0,0 +1,34 @@
+\begin{tikzpicture}
+  \begin{axis}[
+      ymin=0,
+      ymax=100,
+      width=\linewidth,
+      height=0.3\linewidth,
+      xlabel={Year},
+      ylabel={Frac. papers with tools},
+      axis y line*=left,
+      enlarge x limits = false,
+      yticklabel=\pgfmathprintnumber{\tick}\,\%,
+      x tick label style={/pgf/number format/1000 sep=},
+    ]
+
+    %% Linear plot, showing the number of papers mentioning tools.
+    \addplot+ [mark=none, very thick, green!60!black]
+    table {tex/build/tools-per-year/tools-per-year.txt};
+  \end{axis}
+
+  %% Add the right-side Y axis.
+  \begin{axis}[
+      ymode=log,
+      width=\linewidth,
+      height=0.3\linewidth,
+      axis x line=none,
+      axis y line*=right,
+      enlarge x limits = false,
+      ylabel=Num. papers (log-scale),
+      max space between ticks=20,
+    ]
+    \addplot+ [ybar, mark=none, fill=red!50!white, red, opacity=0.25]
+    table [x index=0, y index=2] {tex/build/tools-per-year/tools-per-year.txt};
+    \end{axis}
+\end{tikzpicture}