Reordered slides describing template

After the previous experience of presenting the slides in Ghent, they
are reordered to be more clear and cause less confusion. In
particular, until this commit, I was describing the software build
steps in the end, so the audience mainly forgot about the analysis
steps and thought this template is just something like Docker or a
virtual machine.

With this commit, the steps are described in the same step that occur:
first how the software are built, then how the input data are
downloaded and finally how the software are run on the data and the
values are written into the paper.

1 files changed, 106 insertions, 27 deletions

diff --git a/tex/project-graph.tex b/tex/project-graph.tex
index 566a9e7..2a0dc66 100644
--- a/tex/project-graph.tex
+++ b/tex/project-graph.tex
@@ -11,6 +11,15 @@
   \draw [white] (0,-4.2) -- (0,4.2);
   \draw [white] (-0.5,0) -- (12,0);
 
+  %% Box showing containers.
+  \ifdefined\containers
+    \filldraw[YellowOrange!20!white, rounded corners=2mm] (-0.1,0.3) rectangle (5.6,3.8);
+    \draw (-0.1,3.6) node [anchor=west] {\scriptsize Existing solutions:};
+    \draw (0.1,3.3) node [anchor=west] {\scriptsize Virtual machines};
+    \draw (0.1,3.0) node [anchor=west] {\scriptsize Containers (e.g., Docker)};
+    \draw (0.1,2.7) node [anchor=west] {\scriptsize OSs (e.g., Nix, GNU Guix)};
+  \fi
+
   \graph[grow right sep, simple] {
     { [nodes={yshift=7mm}]
       soft/Software [gbox] -> build/Build [bbox],
@@ -39,71 +48,141 @@
   \fi
 
   %% Software...
-  \ifdefined\sver
-  \node (sver) [rbox, above=of soft, yshift=-8mm, opacity=\nodeopacity] {What version?};
-  \fi
-  \ifdefined\srep
-  \node (srep) [rbox, above=of sver, yshift=-8mm, opacity=\nodeopacity] {Repository?};
+  \let\ppopacity\undefined
+  \ifdefined\allopacity \newcommand{\ppopacity}{1}
+  \else \ifdefined\focusonpackages
+      \newcommand{\ppopacity}{1}
+    \else
+      \newcommand{\ppopacity}{0.3}
+    \fi
   \fi
 
-  %% Hardware...
-  \ifdefined\db
-  \node (db) [rbox, below=of hard, yshift=+8mm, opacity=\nodeopacity] {Data base?};
-  \fi
-  \ifdefined\calib
-  \node (calib) [rbox, below=of db, yshift=+8mm, opacity=\nodeopacity] {Calibration/version?};
+  \ifdefined\sver
+  \node (sver)
+        [rbox, above=of soft, yshift=-8mm, opacity=\ppopacity]
+        {What version?};
   \fi
-  \ifdefined\corr
-  \node (corr) [rbox, below=of calib, yshift=+8mm, opacity=\nodeopacity] {Integrity?};
+  \ifdefined\srep
+  \node (srep)
+        [rbox, above=of sver, yshift=-8mm, opacity=\ppopacity]
+        {Repository?};
   \fi
 
   %% Build
   \ifdefined\dver
-  \node (dver) [rbox, above=of build, yshift=-8mm, opacity=\nodeopacity] {Dependencies?};
+  \node (dver)
+        [rbox, above=of build, yshift=-8mm, opacity=\ppopacity]
+        {Dependencies?};
   \fi
   \ifdefined\ddver
-  \node (ddver) [rbox, above=of dver, yshift=-8mm, opacity=\nodeopacity] {Dep. versions?};
+  \node (ddver)
+        [rbox, above=of dver, yshift=-8mm, opacity=\ppopacity]
+        {Dep. versions?};
   \fi
   \ifdefined\confopt
-  \node (confopt) [rbox, above=of ddver, yshift=-8mm, opacity=\nodeopacity] {Config options?};
+  \node (confopt)
+        [rbox, above=of ddver, yshift=-8mm, opacity=\ppopacity]
+        {Config options?};
   \fi
   \ifdefined\confenv
-  \node (confenv) [rbox, above=of confopt, yshift=-8mm, opacity=\nodeopacity] {Config environment?};
+  \node (confenv)
+        [rbox, above=of confopt, yshift=-8mm, opacity=\ppopacity]
+        {Config environment?};
+  \fi
+
+  %% Hardware/data
+  \let\ppopacity\undefined
+  \ifdefined\allopacity \newcommand{\ppopacity}{1}
+  \else \ifdefined\focusonhardware
+      \newcommand{\ppopacity}{1}
+    \else
+      \newcommand{\ppopacity}{0.3}
+    \fi
+  \fi
+  \ifdefined\db
+  \node (db)
+        [rbox, below=of hard, yshift=+8mm, opacity=\ppopacity]
+        {Data base, or PID?};
+  \fi
+  \ifdefined\calib
+  \node (calib)
+        [rbox, below=of db, yshift=+8mm, opacity=\ppopacity]
+        {Calibration/version?};
+  \fi
+  \ifdefined\corr
+  \node (corr)
+        [rbox, below=of calib, yshift=+8mm, opacity=\ppopacity]
+        {Integrity?};
   \fi
 
   %% Run software ...
+  \let\ppopacity\undefined
+  \ifdefined\allopacity \newcommand{\ppopacity}{1}
+  \else \ifdefined\focusonrun
+      \newcommand{\ppopacity}{1}
+    \else
+      \newcommand{\ppopacity}{0.3}
+    \fi
+  \fi
   \ifdefined\runord
-  \node (runord) [rbox, above=of srun, yshift=-8mm, opacity=\nodeopacity] {What order?};
+  \node (runord)
+        [rbox, above=of srun, yshift=-8mm, opacity=\ppopacity]
+        {What order?};
   \fi
   \ifdefined\runopt
-  \node (runopt) [rbox, above=of runord, yshift=-8mm, opacity=\nodeopacity] {Runtime options?};
+  \node (runopt)
+        [rbox, above=of runord, yshift=-8mm, opacity=\ppopacity]
+        {Runtime options?};
   \fi
   \ifdefined\humanerr
-  \node (humanerr) [rbox, above=of runopt, yshift=-8mm, opacity=\nodeopacity] {Human error?};
+  \node (humanerr)
+        [rbox, above=of runopt, yshift=-8mm, opacity=\ppopacity]
+        {Human error?};
   \fi
   \ifdefined\depupdate
-  \node (depupdate) [rbox, below=of srun, yshift=+8mm, opacity=\nodeopacity] {Environment update?};
+  \node (depupdate)
+        [rbox, below=of srun, yshift=+8mm, opacity=\ppopacity]
+        {Environment update?};
   \fi
   \ifdefined\coauth
-  \node (coaut) [rbox, below=of depupdate, yshift=+8mm, opacity=\nodeopacity] {In sync with coauthors?};
+  \node (coaut)
+        [rbox, below=of depupdate, yshift=+8mm, opacity=\ppopacity]
+        {In sync with coauthors?};
   \fi
 
   %% Paper ...
+  \let\ppopacity\undefined
+  \ifdefined\allopacity \newcommand{\ppopacity}{1}
+  \else \ifdefined\focusonpaper
+      \newcommand{\ppopacity}{1}
+    \else
+      \newcommand{\ppopacity}{0.3}
+    \fi
+  \fi
   \ifdefined\varsinpaper
-  \node (varsinpaper) [rbox, above=of paper, xshift=-1mm, yshift=-8mm, opacity=1] {Sync with analysis?};
+  \node (varsinpaper)
+        [rbox, above=of paper, xshift=-1mm, yshift=-8mm, opacity=\ppopacity]
+        {Sync with analysis?};
   \fi
   \ifdefined\recordinfo
-  \node (recordinfo) [rbox, above=of varsinpaper, yshift=-8mm, opacity=\nodeopacity] {Report this info?};
+  \node (recordinfo)
+        [rbox, above=of varsinpaper, yshift=-8mm, opacity=\ppopacity]
+        {Report this info?};
   \fi
   \ifdefined\softcite
-  \node (softcite) [rbox, above=of recordinfo, yshift=-8mm, opacity=\nodeopacity] {Cited software?};
+  \node (softcite)
+        [rbox, above=of recordinfo, yshift=-8mm, opacity=\ppopacity]
+        {Cited software?};
   \fi
   \ifdefined\prevchange
-  \node (prevchange) [rbox, above=of softcite, yshift=-8mm, opacity=\nodeopacity] {History recorded?};
+  \node (prevchange)
+        [rbox, above=of softcite, yshift=-8mm, opacity=\ppopacity]
+        {History recorded?};
   \fi
 
   \ifdefined\gitlogo
-  \node [inner sep=0pt, opacity=0.5] at (5.5,0) {\includegraphics[width=10cm]{img/git.png}};
+  \node [inner sep=0pt, opacity=0.5] at (5.5,0)
+        {\includegraphics[width=10cm]{img/git.png}};
   \fi
 \end{tikzpicture}
 }