From 310f254ee1557824174e0327eb10120cd7377385 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sat, 1 Feb 2020 23:25:25 +0100
Subject: Added principles before starting to describe the solution

Until now, there wasn't any good transition onto the project, so the
principles have now been added.
---
 Makefile                           |   2 +-
 img/figure-file-architecture-1.pdf | Bin 8755 -> 8782 bytes
 img/figure-file-architecture-2.pdf | Bin 16061 -> 16099 bytes
 reproducible-paper.tex             |  51 ++++++++++++++++++++++++++-----------
 4 files changed, 37 insertions(+), 16 deletions(-)

diff --git a/Makefile b/Makefile
index 55ef6b2..dd4171b 100644
--- a/Makefile
+++ b/Makefile
@@ -23,7 +23,7 @@ reproducible-paper.pdf: reproducible-paper.tex tex/*.tex
 	else                 v=NO-GIT; fi; \
 	echo "\newcommand{\gitcommit}{$$v}" > git-commit.tex
 	pdflatex reproducible-paper
-	pdflatex reproducible-paper
+#	pdflatex reproducible-paper
 
 # Clean all extra files
 .PHONY: clean-latex clean
diff --git a/img/figure-file-architecture-1.pdf b/img/figure-file-architecture-1.pdf
index cae5b83..dfeb94c 100644
Binary files a/img/figure-file-architecture-1.pdf and b/img/figure-file-architecture-1.pdf differ
diff --git a/img/figure-file-architecture-2.pdf b/img/figure-file-architecture-2.pdf
index e51426a..19f1fe9 100644
Binary files a/img/figure-file-architecture-2.pdf and b/img/figure-file-architecture-2.pdf differ
diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index d0b3f66..fe8817d 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -444,7 +444,7 @@
 
 
 
-\begin{frame}
+  \begin{frame}
     \begin{tcolorbox}[title={Buckheit \& Donoho (1996) \small Lecture Notes in Statistics (vol 103, DOI:\textcolor{blue!10!white}{\href{https://doi.org/10.1007/978-1-4612-2544-7\_5}{10.1007/978-1-4612-2544-7\_5}})}]
       \centering ``An \alert{article} about computational science [\emph{today: almost all sciences}] ... is not the scholarship itself, it is merely \textbf{ADVERTISING} of the \textbf{SCHOLARSHIP}.
 
@@ -452,31 +452,52 @@
       \pause
       The \textbf{ACTUAL SCHOLARSHIP} is the \alert{complete software development environment} and the \alert{complete set of instructions} which generated the figures.''
     \end{tcolorbox}
-\end{frame}
+  \end{frame}
 
 
 
 
 
-  \begin{frame}{Necessity of (exactly) reproducible research}
+  \begin{frame}{Principles behind proposed solution}
     \begin{tcolorbox}[title=Basic/simple principle:]
       \centering Science is defined by its METHOD, \alert{not} its
       result.
     \end{tcolorbox}
 
-    \vspace{0.5cm}
+    \pause
     \begin{itemize}
-      \setlength\itemsep{0.6cm}
-    \item The software(s) used, configuration file(s), the order of
-      steps taken, along with the input data are necessary for
-      reproducibility.
-    \item \alert{A solution} is proposed here, which if adopted from
-      the start, can greatly \alert{simplify a scientific research
-        project} and \alert{allow full/exact reproducibility} once it
-      is published.
-    \item In the next slides, we'll review the template from the
-      highest level (final research paper) to the lowest (setting up
-      the research environment).
+    \item \textbf{Complete/self-contained:}
+      \begin{itemize}
+        \pause
+      \item The project's \alert{only dependencies} should be \alert{POSIX} \textcolor{gray}{(discards Conda or Jupyter which need Python)}.
+        \pause
+      \item Project's source should be in \alert{plain-text}: a binary format neeeds special software.
+        \pause
+      \item Should be \alert{non-interactive} or runnable in batch (user interaction is an incompleteness).
+        \pause
+      \item Must \alert{not require root} permissions \textcolor{gray}{(discards tools like Docker or Nix/Guix)}.
+        \pause
+      \item Should \alert{not require internet} connection.
+        \pause
+      \item \alert{Version control} (e.g., with Git) can track project's history.
+      \end{itemize}
+
+      \pause
+    \item \textbf{Modularity:} Parts of the project should be \alert{re-usable} in other projects.
+      \pause
+    \item \textbf{Minimal complexity:} Occum’s rasor: “Never posit pluralities without necessity”.
+      \begin{itemize}
+        \pause
+      \item Avoiding the \alert{fashionable} tool of the day (other tools can also do the job).
+      \pause
+      \item Easier \alert{learning curve}, also doesn't create a \alert{generational gap}.
+      \pause
+      \item Is \alert{compatible} and \alert{extensible}.
+      \end{itemize}
+      \pause
+    \item \textbf{Verifable inputs and outputs:} Inputs and Outputs must be \alert{automatically verified}.
+      \pause
+    \item \textbf{Free and open source software:} \alert{Free software} is essential: non-free software is not tracable, not configurable, not distributable, dependent on non-free provider.
     \end{itemize}
   \end{frame}
 
-- 
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