Raw draft (until now as a separate repository) imported

Until now, I was writing the paper without the template. But we will soon
be adding a tutorial to the template, and I thought it will be good to have
an example demonstration here too. So I just brought the hole project into
the template structure, allowing us to add the template analysis later when
its ready, and also allowing us to easily reproduce this paper ofcourse
(without having to worry about the host's TeXLive installation.

1 files changed, 229 insertions, 0 deletions

diff --git a/tex/src/figure-project-outline.tex b/tex/src/figure-project-outline.tex
new file mode 100644
index 0000000..4cd933d
--- /dev/null
+++ b/tex/src/figure-project-outline.tex
@@ -0,0 +1,229 @@
+% Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%
+% This LaTeX source is free software: you can redistribute it and/or
+% modify it under the terms of the GNU General Public License as
+% published by the Free Software Foundation, either version 3 of the
+% License, or (at your option) any later version.
+%
+% This LaTeX source is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+% General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this LaTeX source.  If not, see <https://www.gnu.org/licenses/>.
+
+%% Environment variables.
+\newcommand{\allopacity}{1}
+\newcommand{\sver}{}
+\newcommand{\srep}{}
+\newcommand{\dver}{}
+\newcommand{\ddver}{}
+\newcommand{\confopt}{}
+\newcommand{\confenv}{}
+\newcommand{\containers}{}
+\newcommand{\db}{}
+\newcommand{\calib}{}
+\newcommand{\corr}{}
+\newcommand{\runord}{}
+\newcommand{\runopt}{}
+\newcommand{\humanerr}{}
+\newcommand{\confirmbias}{}
+\newcommand{\depupdate}{}
+\newcommand{\coauth}{}
+\newcommand{\varsinpaper}{}
+\newcommand{\recordinfo}{}
+\newcommand{\softcite}{}
+\newcommand{\prevchange}{}
+
+\begin{tikzpicture}[>=stealth, thick, black!50, text=black,
+    every new ->/.style={shorten >=1pt},
+    hv path/.style={to path={-| (\tikztotarget)}},
+    graphs/every graph/.style={edges=rounded corners}]
+
+    \footnotesize
+
+  %% This white line is only added to fix the vertical position of the
+  %% figure so it doesn't change as we add more boxes.
+  \draw [white] (0,-4.3) -- (0,3.8);
+  \draw [white] (-0.5,0) -- (12,0);
+
+  %% Box showing containers.
+  \ifdefined\containers
+    \filldraw[orange!20!white, rounded corners=2mm] (-0.1,0.3) rectangle (5.6,3.8);
+    \draw (-0.1,3.65) node [anchor=west] {\scriptsize Existing solutions:};
+    \draw (0,3.35) node [anchor=west] {\scriptsize Virtual machines};
+    \draw (0,3.05) node [anchor=west] {\scriptsize Containers};
+    \draw (0,2.75) node [anchor=west] {\scriptsize Package managers};
+  \fi
+
+  \graph[grow right sep, simple] {
+    { [nodes={yshift=7mm}]
+      soft/Software [gbox] -> build/Build [bbox],
+      hard/Hardware/data [gbox, yshift=-0.5cm] --
+      p1 [coordinate, xshift=2cm, yshift=-0.5cm]
+    } -- [hv path]
+    p2 [coordinate] ->
+    srun/Run software on data [bbox] ->
+    paper/Paper [bbox]
+  };
+
+  \ifdefined\paperfinal
+    \node (happy) [inner sep=0pt, below=of paper, yshift=+8mm]
+          {\includegraphics[width=2cm]{img/happy-question.jpg}};
+    \node (happyurl) [below=of happy, xshift=-9.5mm, yshift=+1cm]
+          {\tiny \url{https://heywhatwhatdidyousay.wordpress.com}};
+    \node (qurl) [below=of happyurl, xshift=10.5mm, yshift=+1.2cm]
+          {\tiny \url{http://pngimages.net}};
+  \else
+    \ifdefined\paperinit
+      \node (happy) [inner sep=0pt, below=of paper, yshift=+8mm]
+            {\includegraphics[width=2cm]{img/happy.jpg}};
+      \node (happyurl) [below=of happy, xshift=-9.5mm, yshift=+1cm]
+            {\tiny \url{https://heywhatwhatdidyousay.wordpress.com}};
+    \fi
+  \fi
+
+  %% Software...
+  \let\ppopacity\undefined
+  \ifdefined\allopacity \newcommand{\ppopacity}{1}
+  \else \ifdefined\focusonpackages
+      \newcommand{\ppopacity}{1}
+    \else
+      \newcommand{\ppopacity}{0.3}
+    \fi
+  \fi
+
+  \ifdefined\sver
+  \node (sver)
+        [rbox, above=of soft, yshift=-8mm, opacity=\ppopacity]
+        {What version?};
+  \fi
+  \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=\ppopacity]
+        {Dependencies?};
+  \fi
+  \ifdefined\ddver
+  \node (ddver)
+        [rbox, above=of dver, yshift=-8mm, opacity=\ppopacity]
+        {Dep. versions?};
+  \fi
+  \ifdefined\confopt
+  \node (confopt)
+        [rbox, above=of ddver, yshift=-8mm, opacity=\ppopacity]
+        {Config options?};
+  \fi
+  \ifdefined\confenv
+  \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=\ppopacity]
+        {What order?};
+  \fi
+  \ifdefined\runopt
+  \node (runopt)
+        [rbox, above=of runord, yshift=-8mm, opacity=\ppopacity]
+        {Runtime options?};
+  \fi
+  \ifdefined\humanerr
+  \node (humanerr)
+        [rbox, above=of runopt, yshift=-8mm, opacity=\ppopacity]
+        {Human error?};
+  \fi
+  \ifdefined\confirmbias
+  \node (confirmbias)
+        [rbox, above=of humanerr, yshift=-8mm, opacity=\ppopacity]
+        {Confirmation bias?};
+  \fi
+  \ifdefined\depupdate
+  \node (depupdate)
+        [rbox, below=of srun, yshift=+8mm, opacity=\ppopacity]
+        {Environment update?};
+  \fi
+  \ifdefined\coauth
+  \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=\ppopacity]
+        {Sync with analysis?};
+  \fi
+  \ifdefined\recordinfo
+  \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=\ppopacity]
+        {Cited software?};
+  \fi
+  \ifdefined\prevchange
+  \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}};
+  \fi
+\end{tikzpicture}