Git commits in slide now have a checksum

The fact that we only displayed the Git checksum before showing it in
the paper could be a little confusing to people not much familiar with
Git. So a commit checksum (taken randomly from the history of these
slides) was added to it.

Also, some minor changes were done here and there.

4 files changed, 148 insertions, 122 deletions

diff --git a/img/verified.png b/img/verified.png
new file mode 100644
index 0000000..7c03c44
--- /dev/null
+++ b/img/verified.png
diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index 413b72d..ca039ec 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -27,8 +27,8 @@
 }
 
 %% Set the date and insitutional logos.
-\date{\scriptsize \href{https://ifas5.sciencesconf.org}{5th
-    Indo-French Astronomy School}, \href{http://www.iucaa.in}{IUCAA}, Pune (India),\\August 21st, 2019\\
+\date{\scriptsize August 21st, 2019\\\href{https://ifas5.sciencesconf.org}{5th
+    Indo-French Astronomy School}, \href{http://www.iucaa.in}{IUCAA}, Pune (India),\\
   \vspace{0.1cm} Slides available at
   \textcolor{blue}{\url{http://akhlaghi.org/pdf/reproducible-paper.pdf}}}
 
@@ -100,7 +100,7 @@
 
 
   \newcommand{\imgtdir}{/home/mohammad/documents/personal/professional/astronomy/talks/in-prep/images}
-  \begin{frame}{Reproducibility is critically important for astronomy}
+  \begin{frame}{Reproducibility is critically important in the sciences (example from astronomy)}
     \small
     \begin{columns}
       \column{6cm} Example: Detecting outer regions of M51 in a
@@ -209,56 +209,6 @@
 
 
 
-  \begin{frame}[t]{Types of reproducibility}
-    \vspace{-5mm}
-    \begin{columns}[t]
-      \column{0.5\linewidth}
-      \begin{center}
-        \large\textbf{Hardware/Statistical reproducibility}
-        \rule{0.5\linewidth}{1pt}
-      \end{center}
-      \begin{itemize}
-        \setlength\itemsep{0.5em}
-      \item Involves data \alert{collection}.
-      \item Inherently includes \alert{measurements errors}\\(can
-        never be exactly reproduced).
-      \item Example: Raw telescope image/spectra.
-      \item \alert{\textbf{NOT DISCUSSED HERE.}}
-      \end{itemize}
-
-      \vspace{3.5mm}
-      \begin{center}
-        \vspace{-5mm}
-        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
-        \vspace{-0.6mm}
-        \tiny \href{http://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/L07/index.html}{http://slittlefair.staff.shef.ac.uk}
-      \end{center}
-
-      \column{0.5\linewidth}
-      \begin{center}
-        \large\textbf{Software/Deterministic reproducibility}
-        \rule{0.5\linewidth}{1pt}
-      \end{center}
-      \begin{itemize}
-        \setlength\itemsep{1em}
-      \item Involves data \alert{analysis}, or simulations.
-      \item Starts \alert{after} data is collected/digitized.
-      \item Example: $2+2=4$ (i.e., sum of datasets).
-      \item \textbf{\textcolor{green!50!black}{DISCUSSED HERE.}}
-      \end{itemize}
-
-      \centering
-      \vspace{3mm}
-      \includegraphics[width=0.8\linewidth]{img/digital-tunnel.jpg}\\
-      \vspace{-0.6mm}
-      \tiny \href{https://tsongas.com/newsletter_articles/the-new-electronic-version-of-the-advantage/digital-tunnel-wallpaper/}{https://tsongas.com}
-    \end{columns}
-  \end{frame}
-
-
-
-
-
   %% Step-by-step slides.
   \newcommand{\allopacity}{1}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
@@ -323,6 +273,8 @@
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\humanerr}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
+  \newcommand{\confirmbias}{}
+  \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\depupdate}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \newcommand{\coauth}{}
@@ -399,6 +351,57 @@
 
 
 
+
+  \begin{frame}[t]{Types of reproducibility}
+    \vspace{-5mm}
+    \begin{columns}[t]
+      \column{0.5\linewidth}
+      \begin{center}
+        \large\textbf{Hardware/Statistical reproducibility}
+        \rule{0.5\linewidth}{1pt}
+      \end{center}
+      \begin{itemize}
+        \setlength\itemsep{0.5em}
+      \item Involves data \alert{collection}.
+      \item Inherently includes \alert{measurements errors}\\(can
+        never be exactly reproduced).
+      \item Example: Raw telescope image/spectra.
+      \item \alert{\textbf{NOT DISCUSSED HERE.}}
+      \end{itemize}
+
+      \vspace{3.5mm}
+      \begin{center}
+        \vspace{-5mm}
+        \includegraphics[width=0.7\linewidth]{img/hale-prime-focus.jpg}\\
+        \vspace{-0.6mm}
+        \tiny \href{http://slittlefair.staff.shef.ac.uk/teaching/phy217/lectures/telescopes/L07/index.html}{http://slittlefair.staff.shef.ac.uk}
+      \end{center}
+
+      \column{0.5\linewidth}
+      \begin{center}
+        \large\textbf{Software/Deterministic reproducibility}
+        \rule{0.5\linewidth}{1pt}
+      \end{center}
+      \begin{itemize}
+        \setlength\itemsep{1em}
+      \item Involves data \alert{analysis}, or simulations.
+      \item Starts \alert{after} data is collected/digitized.
+      \item Example: $2+2=4$ (i.e., sum of datasets).
+      \item \textbf{\textcolor{green!50!black}{DISCUSSED HERE.}}
+      \end{itemize}
+
+      \centering
+      \vspace{3mm}
+      \includegraphics[width=0.8\linewidth]{img/digital-tunnel.jpg}\\
+      \vspace{-0.6mm}
+      \tiny \href{https://tsongas.com/newsletter_articles/the-new-electronic-version-of-the-advantage/digital-tunnel-wallpaper/}{https://tsongas.com}
+    \end{columns}
+  \end{frame}
+
+
+
+
+
   \newcommand{\focusonpackages}{}
   \begin{frame}{General outline of a project} \include{tex/project-graph} \end{frame}
   \let\focusonpackages\undefined
@@ -847,6 +850,8 @@
 
 
 
+
+
   \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
   \newcommand{\projinit}{}
   \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
@@ -860,22 +865,8 @@
   \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
   \newcommand{\githappy}{}
   \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
-
-
-
-
-  \begin{frame}{Project source and its execution}
-    \begin{tcolorbox}
-      Programs \textcolor{gray}{[here: Scientific projects]} must be
-      written for \alert{people to read}...
-
-      \hfill ...and only \emph{incidentally} for machines to
-      \emph{execute}.
-
-      \vspace{2mm}
-      \hfill \footnotesize Harold Abelson, Structure and Interpretation of Computer Programs
-    \end{tcolorbox}
-  \end{frame}
+  \newcommand{\gitverified}{}
+  \begin{frame}{New projects branch from template} \include{tex/git-branch} \end{frame}
 
 
 
@@ -913,6 +904,23 @@
 
 
 
+  \begin{frame}{Project source and its execution}
+    \begin{tcolorbox}
+      Programs \textcolor{gray}{[here: Scientific projects]} must be
+      written for \alert{people to read}...
+
+      \hfill ...and only \emph{incidentally} for machines to
+      \emph{execute}.
+
+      \vspace{2mm}
+      \hfill \footnotesize Harold Abelson, Structure and Interpretation of Computer Programs
+    \end{tcolorbox}
+  \end{frame}
+
+
+
+
+
   \begin{frame}{Future prospects...}
     \large Adoption of reproducibility by many researchers will enable
     the following:
diff --git a/tex/git-branch.tex b/tex/git-branch.tex
index 9a2666a..9f1bc37 100644
--- a/tex/git-branch.tex
+++ b/tex/git-branch.tex
@@ -45,50 +45,59 @@
     %% circles.
 
     %% Template commits.
-    \ifdefined\tofuture
-      \foreach \y in {0.55,...,7}
-      \draw [fill=green!80!blue, opacity=0.5] (0,\y) circle [radius=2.1mm];
-    \else
-      \ifdefined\tempevolve
-        \foreach \y in {0.55,...,5}
-        \draw [fill=green!80!blue, opacity=0.5] (0,\y) circle [radius=2.1mm];
-      \else
-        \foreach \y in {0.55,...,2.5}
-        \draw [fill=green!80!blue, opacity=0.5] (0,\y) circle [radius=2.1mm];
+    \draw[anchor=north] (0,0) node {\textbf{Template}};
+    \draw [fill=green!80!blue, opacity=0.5] (0,0.55cm) circle [radius=2.1mm];
+    \draw[anchor=east] (-5pt,0.55cm) node {\tiny\texttt{ad2c476}};
+    \draw [fill=green!80!blue, opacity=0.5] (0,1.55cm) circle [radius=2.1mm];
+    \draw[anchor=east] (-5pt,1.55cm) node {\tiny\texttt{706c644}};
+    \ifdefined\tempevolve
+      \draw [fill=green!80!blue, opacity=0.5] (0,2.55cm) circle [radius=2.1mm];
+      \draw[anchor=east] (-5pt,2.55cm) node {\tiny\texttt{fa2ac10}};
+      \draw [fill=green!80!blue, opacity=0.5] (0,3.55cm) circle [radius=2.1mm];
+      \draw[anchor=east] (-5pt,3.55cm) node {\tiny\texttt{1e06fe2}};
+      \draw [fill=green!80!blue, opacity=0.5] (0,4.55cm) circle [radius=2.1mm];
+      \draw[anchor=east] (-5pt,4.55cm) node {\tiny\texttt{32043ee}};
+      \ifdefined\tofuture
+        \draw [fill=green!80!blue, opacity=0.5] (0,5.55cm) circle [radius=2.1mm];
+        \draw[anchor=east] (-5pt,5.55cm) node {\tiny\texttt{2d808f2}};
+        \draw [fill=green!80!blue, opacity=0.5] (0,6.55cm) circle [radius=2.1mm];
+        \draw[anchor=east] (-5pt,6.55cm) node {\tiny\texttt{a4d96c0}};
       \fi
     \fi
 
+
     %% Project commits.
     \ifdefined\projinit
-      \draw[anchor=north] (1,1.7) node {Project};
-
-      \ifdefined\tofuture
-        \foreach \y in {2,...,6}
-        \draw [fill=red!60!green, opacity=0.5] (0.95,\y) circle [radius=2.1mm];
-      \else
+      \draw[anchor=north] (1,1.7) node {\textbf{Project}};
+      \draw [fill=red!60!green, opacity=0.5] (0.95,2) circle [radius=2.1mm];
+      \draw[anchor=west] (1.1,2) node {\tiny\texttt{53b53d6}};
+      \ifdefined\projwork
+        \draw [fill=red!60!green, opacity=0.5] (0.95,3) circle [radius=2.1mm];
+        \draw[anchor=west] (1.1,3) node {\tiny\texttt{9f8cc74}};
+        \draw [fill=red!60!green, opacity=0.5] (0.95,4) circle [radius=2.1mm];
+        \draw[anchor=west] (1.1,4) node {\tiny\texttt{8ebb784}};
         \ifdefined\mergewithtemp
-          \foreach \y in {2,...,5}
-          \draw [fill=red!60!green, opacity=0.5] (0.95,\y) circle [radius=2.1mm];
-        \else
-          \ifdefined\projwork
-            \foreach \y in {2,...,4.9}
-            \draw [fill=red!60!green, opacity=0.5] (0.95,\y) circle [radius=2.1mm];
-          \else
-            \foreach \y in {2,...,2.9}
-            \draw [fill=red!60!green, opacity=0.5] (0.95,\y) circle [radius=2.1mm];
+          \draw [fill=red!60!green, opacity=0.5] (0.95,5) circle [radius=2.1mm];
+          \draw[anchor=west] (1.1,5) node {\tiny\texttt{01ce2cc}};
+          \ifdefined\tofuture
+            \draw [fill=red!60!green, opacity=0.5] (0.95,6) circle [radius=2.1mm];
+            \draw[anchor=west] (1.1,6) node {\tiny\texttt{b52cc6f}};
           \fi
         \fi
       \fi
     \fi
 
-    \draw[anchor=north] (0,0) node {Template};
-
     %% Happy scientist
     \ifdefined\githappy
     \node [inner sep=0pt] at (3.5,4) {\includegraphics[width=2cm]{img/happy.jpg}};
     \node [inner sep=0pt] at (4.15,5.3) {\includegraphics[width=0.2cm]{img/checkmark.png}};
-    \draw[anchor=east] (2.4,6) node {\footnotesize\texttt{5cfe2eab}};
-    \draw[anchor=south] (4.5,5) node [rotate=20] {\tiny\texttt{5cfe2eab}};
+    \draw [<->, red, line width=0.2mm] plot [smooth, tension=2] coordinates
+          { (1.9,6.15) (4,6) (4.8,5.25) };
+    \draw[anchor=south] (4.5,5) node [rotate=20] {\tiny\texttt{b52cc6f}};
+
+    \ifdefined\gitverified
+      \node [inner sep=0pt] at (3.5,1.5) {\includegraphics[width=3cm]{img/verified.png}};
+    \fi
     \fi
 
   \end{tikzpicture}
@@ -98,29 +107,33 @@
   \begin{itemize}
     \setlength\itemsep{0.3cm}
   \item Template's history is recorded.
-    \ifdefined\projinit
-  \item New project: a branch from the template.
-    \fi
-    \ifdefined\projwork
-  \item Research progresses in the project branch.
-    \fi
-    \ifdefined\tempevolve
-  \item Template will evolve (improved infrastructure).
-    \fi
-    \ifdefined\mergewithtemp
-  \item Template can be imported/merged back into project.
-    \fi
-    \ifdefined\tofuture
-  \item The template and project will \alert{evolve}.
-    \fi
-    \ifdefined\githappy
-  \item During research this \alert{encourages creative tests}\\
-    (previous research states can easily be retrieved).
-  \item \alert{Coauthors} can work on same project in parallel
-    \\(separate project branches).
-  \item Upon publication, the \alert{Git hash} is enough to verify the
-    integrity of the result.
-
-    \fi
+  \ifdefined\projinit
+    \item New project: a branch from the template.
+  \fi
+  \ifdefined\projwork
+    \item Research progresses in the project branch.
+  \fi
+  \ifdefined\tempevolve
+    \item Template will evolve (improved infrastructure).
+  \fi
+  \ifdefined\mergewithtemp
+    \item Template can be imported/merged back into project.
+  \fi
+  \ifdefined\tofuture
+    \item The template and project will \alert{evolve}.
+    \item During research this \alert{encourages creative tests}\\
+      (previous research states can easily be retrieved).
+    \item \alert{Coauthors} can work on same project in parallel
+      \\(separate project branches).
+  \fi
+  \ifdefined\githappy
+    \item Upon \alert{publication}, the \alert{Git checksum} is enough
+      to verify the integrity of the result.
+  \fi
   \end{itemize}
+
+  \ifdefined\gitapproved
+  \vspace{4mm}
+  \tiny ``Verified'' image from \href{https://www.vectorstock.com/royalty-free-vector/red-vintage-verified-stamp-retro-style-on-white-vector-22770076}{vectorstock.com}
+  \fi
 \end{columns}
diff --git a/tex/project-graph.tex b/tex/project-graph.tex
index 1ed5b73..07d5d67 100644
--- a/tex/project-graph.tex
+++ b/tex/project-graph.tex
@@ -140,6 +140,11 @@
         [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]