General project structure and configuration described

In the last few days I have been writing these two sections in the middle
of other work. But I am making this commit because it has already become a
lot! I am now going onto the description of `./project make'.

1 files changed, 62 insertions, 35 deletions

diff --git a/tex/src/figure-file-architecture.tex b/tex/src/figure-file-architecture.tex
index 5c00e6e..c892232 100644
--- a/tex/src/figure-file-architecture.tex
+++ b/tex/src/figure-file-architecture.tex
@@ -1,3 +1,5 @@
+\newcommand{\fullfilearchitecture}{}
+
 \begin{tikzpicture}[
   line width=1.5pt,
   black!50,
@@ -10,118 +12,143 @@
   %% project/
   \node [dirbox, at={(0,4cm)}, minimum width=15cm, minimum height=9cm,
     label={[shift={(0,-5mm)}]\texttt{project/}}] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-6.0cm,3.3cm)}] {COPYING};
+  \fi
   \node [node-nonterminal-thin, at={(-3.5cm,3.3cm)}] {paper.tex};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-1.0cm,3.3cm)}] {project};
   \node [node-nonterminal-thin, at={(+1.5cm,3.3cm)}] {README.md};
   \node [node-nonterminal-thin, at={(+4.25cm,3.3cm)},
-         text width=2.5cm, text depth=-3pt] {README-hacking.md};
+    text width=2.5cm, text depth=-3pt] {README-hacking.md};
+  \fi
 
   %% reproduce/
   \node [dirbox, at={(-1.4cm,2.6cm)}, minimum width=11.9cm, minimum height=6cm,
-    label={[shift={(0,-5mm)}]\texttt{reproduce/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{reproduce/}}, fill=brown!15!white] {};
 
   %% reproduce/software/
   \node [dirbox, at={(-4.35cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm,
-    label={[shift={(0,-5mm)}]\texttt{software/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{software/}}, fill=brown!20!white] {};
 
   %% reproduce/software/config
   \node [dirbox, at={(-5.75cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{config/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{config/}}, fill=brown!25!white] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-5.75cm,0.8cm)}] {LOCAL.conf.in};
+  \fi
   \node [node-nonterminal-thin, at={(-5.75cm,0.3cm)}] {versions.conf};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-5.75cm,-0.2cm)}] {checksums.conf};
+  \fi
 
   %% reproduce/software/make
   \node [dirbox, at={(-2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{make/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{make/}}, fill=brown!25!white] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-2.95cm,0.8cm)}] {basic.mk};
+  \fi
   \node [node-nonterminal-thin, at={(-2.95cm,0.3cm)}] {high-level.mk};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-2.95cm,-0.2cm)}] {python.mk};
+  \fi
 
   %% reproduce/software/bash
   \node [dirbox, at={(-5.75cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-5.75cm,-1.5cm)}] {bashrc.sh};
   \node [node-nonterminal-thin, at={(-5.75cm,-2.0cm)}] {configure.sh};
-  \node [node-nonterminal-thin, at={(-5.75cm,-2.5cm)}] {git-pre-comit};
+  \fi
 
   %% reproduce/software/bibtex
   \node [dirbox, at={(-2.95cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{bibtex/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{bibtex/}}, fill=brown!25!white] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(-2.95cm,-1.5cm)}] {fftw.tex};
   \node [node-nonterminal-thin, at={(-2.95cm,-2.0cm)}] {numpy.tex};
   \node [node-nonterminal-thin, at={(-2.95cm,-2.5cm)}] {gnuastro.tex};
+  \fi
 
   %% reproduce/analysis/
   \node [dirbox, at={(1.55cm,2.1cm)}, minimum width=5.7cm, minimum height=5.3cm,
-    label={[shift={(0,-5mm)}]\texttt{analysis/}}] {};
+    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,
-    label={[shift={(0,-5mm)}]\texttt{config/}}] {};
+    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};
 
   %% reproduce/analysis/make
   \node [dirbox, at={(2.95cm,1.5cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{make/}}] {};
+    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};
 
   %% reproduce/analysis/bash
   \node [dirbox, at={(0.15cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{bash/}}] {};
-  \node [node-nonterminal-thin, at={(0.15cm,-1.5cm)}] {process-1.sh};
-  \node [node-nonterminal-thin, at={(0.15cm,-2.0cm)}] {process-2.sh};
-  \node [node-nonterminal-thin, at={(0.15cm,-2.5cm)}] {process-3.sh};
+    label={[shift={(0,-5mm)}]\texttt{bash/}}, fill=brown!25!white] {};
+  \ifdefined\fullfilearchitecture
+  \node [node-nonterminal-thin, at={(0.15cm,-1.5cm)}] {process-A.sh};
+  \fi
 
   %% reproduce/analysis/python
   \node [dirbox, at={(2.95cm,-0.8cm)}, minimum width=2.6cm, minimum height=2.1cm,
-    label={[shift={(0,-5mm)}]\texttt{python/}}] {};
-  \node [node-nonterminal-thin, at={(2.95cm,-1.5cm)}] {operation-1.py};
-  \node [node-nonterminal-thin, at={(2.95cm,-2.0cm)}] {operation-2.py};
-  \node [node-nonterminal-thin, at={(2.95cm,-2.5cm)}] {fitting-plot.py};
+    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};
+  \fi
 
   %% tex/
   \node [dirbox, at={(6cm,2.6cm)}, minimum width=2.7cm, minimum height=6cm,
-    label={[shift={(0,-5mm)}]\texttt{tex/}}] {};
+    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,
-    label={[shift={(0,-5mm)}]\texttt{src/}}] {};
+    label={[shift={(0,-5mm)}]\texttt{src/}}, fill=brown!20!white] {};
+  \ifdefined\fullfilearchitecture
   \node [node-nonterminal-thin, at={(6cm,1.4cm)}] {preamble-1.tex};
-  \node [node-nonterminal-thin, at={(6cm,0.9cm)}] {preamble-2.tex};
-  \node [node-nonterminal-thin, at={(6cm,0.4cm)}] {figure-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,
-    label={[shift={(0,-5mm)}]\texttt{build/}}, dashed] {};
+    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.};
+  \fi
 
-  %% tex/build
+  %% tex/tikz
+  \ifdefined\fullfilearchitecture
   \node [dirbox, at={(6cm,-1.7cm)}, minimum width=2.5cm, minimum height=1.6cm,
-    label={[shift={(0,-5mm)}]\texttt{tikz/}}, dashed] {};
+    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).};
+  \fi
 
   %% .local
-  \node [dirbox, at={(-3.6cm,-3.7cm)}, minimum width=7cm, minimum height=1.2cm,
-    label={[shift={(0,-5mm)}]\texttt{.local/}}, dashed] {};
-  \node [anchor=west, at={(-7.1cm,-4.4cm)}]
+  \ifdefined\fullfilearchitecture
+  \node [dirbox, at={(-3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm,
+    label={[shift={(0,-5mm)}]\texttt{.local/}}, dashed, fill=brown!15!white] {};
+  \node [anchor=west, at={(-7.1cm,-4.3cm)}]
         {\scriptsize\sf Symbolic link to project's software environment, e.g., };
-  \node [anchor=west, at={(-7.1cm,-4.7cm)}]
+  \node [anchor=west, at={(-7.1cm,-4.6cm)}]
         {\scriptsize\sf Python or R, run `\texttt{.local/bin/python}' or `\texttt{.local/bin/R}'};
+  \fi
 
   %% .build
-  \node [dirbox, at={(3.6cm,-3.7cm)}, minimum width=7cm, minimum height=1.2cm,
-    label={[shift={(0,-5mm)}]\texttt{.build/}}, dashed] {};
-  \node [anchor=west, at={(0.1cm,-4.4cm)}]
+  \ifdefined\fullfilearchitecture
+  \node [dirbox, at={(3.6cm,-3.6cm)}, minimum width=7cm, minimum height=1.2cm,
+    label={[shift={(0,-5mm)}]\texttt{.build/}}, dashed, fill=brown!15!white] {};
+  \node [anchor=west, at={(0.1cm,-4.3cm)}]
         {\scriptsize\sf Symbolic link to project's top-level build directory.};
-  \node [anchor=west, at={(0.1cm,-4.7cm)}]
-        {\scriptsize\sf Enabling easy access to built project components.};
+  \node [anchor=west, at={(0.1cm,-4.6cm)}]
+        {\scriptsize\sf Enabling easy access to all of project's built components.};
+  \fi
 \end{tikzpicture}