From a6be72cca6b29794c4ed3ce7e66a815f90b8854a Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Tue, 21 Jan 2020 13:41:48 +0000
Subject: File architecture plot in two phases, commands printed

The file architecture plot was a little crowded, so I am now first
showing the files discussed in previous plots, and then showing the
whole thing. Also, the 4 commands necessary to reproduce a project are
added.
---
 img/figure-file-architecture-1.pdf | Bin 0 -> 7922 bytes
 img/figure-file-architecture-2.pdf | Bin 0 -> 15813 bytes
 reproducible-paper.tex             |  38 +++++++++++++++++++++++++++++++++++--
 3 files changed, 36 insertions(+), 2 deletions(-)
 create mode 100644 img/figure-file-architecture-1.pdf
 create mode 100644 img/figure-file-architecture-2.pdf

diff --git a/img/figure-file-architecture-1.pdf b/img/figure-file-architecture-1.pdf
new file mode 100644
index 0000000..dac3225
Binary files /dev/null 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
new file mode 100644
index 0000000..c6b6a9a
Binary files /dev/null and b/img/figure-file-architecture-2.pdf differ
diff --git a/reproducible-paper.tex b/reproducible-paper.tex
index 09f7d7d..5818448 100644
--- a/reproducible-paper.tex
+++ b/reproducible-paper.tex
@@ -1094,9 +1094,14 @@
     \end{itemize}
   \end{frame}
 
-  \begin{frame}{Organization of project source files in its top directory}
+  \begin{frame}{Files organized in directories by context (here are some of the files discussed before)}
     \centering
-    \includegraphics[width=0.9\linewidth]{img/figure-file-architecture.pdf}
+    \includegraphics[width=0.9\linewidth]{img/figure-file-architecture-1.pdf}
+  \end{frame}
+
+  \begin{frame}{Files organized in directories by context (now with other project files and symbolic links)}
+    \centering
+    \includegraphics[width=0.9\linewidth]{img/figure-file-architecture-2.pdf}
   \end{frame}
 
 
@@ -1115,6 +1120,8 @@
 
 
 
+
+
   \newcommand{\allopacity}{1}
   \begin{frame}{All questions have an answer now (in
         \alert{plain text}: human \& computer readable/archivable).}
@@ -1220,6 +1227,33 @@
 
 
 
+  \begin{frame}[t]{General outline of using this system (for example \href{https://arxiv.org/abs/1909.11230}{arXiv:1909.11230})}
+    \vspace{1cm}
+    \texttt{\$ git clone http://gitlab.com/makhlaghi/iau-symposium-355{ }{ }{ }{ }\textcolor{gray}{\# Import the project.}}\\
+
+    \pause
+    \vspace{1.2cm}
+    \texttt{\$ ./project configure { }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# You will specify the build directory on your system,}}\\
+    \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# and it will build all software (about 1.5 hours).}}
+
+    \pause
+    \vspace{1.2cm}
+    \texttt{\$ ./project prepare { }{ }{ }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# In case data prepartion is necessary.}}\\
+
+    \pause
+    \vspace{1.2cm}
+    \texttt{\$ ./project make { }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }\textcolor{gray}{\# Does all the analysis and makes final PDF.}}\\
+  \end{frame}
+
+
+
+
+
+
+
+
+
+
   \begin{frame}{Future prospects...}
     \large Adoption of reproducibility by many researchers will enable
     the following:
-- 
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