Section on starting new projects, and publishing project added

With the main structure of Maneage explained, I have started to explain how
a new project is created, along with a schematic diagram that shows two
scenarios of how Git can help with project management.

7 files changed, 165 insertions, 5 deletions

diff --git a/tex/img/collaboration-icon.pdf b/tex/img/collaboration-icon.pdf
new file mode 100644
index 0000000..7bb5795
--- /dev/null
+++ b/tex/img/collaboration-icon.pdf
diff --git a/tex/img/paper-icon.pdf b/tex/img/paper-icon.pdf
new file mode 100644
index 0000000..db7660c
--- /dev/null
+++ b/tex/img/paper-icon.pdf
diff --git a/tex/src/figure-branching.tex b/tex/src/figure-branching.tex
new file mode 100644
index 0000000..bc6fb41
--- /dev/null
+++ b/tex/src/figure-branching.tex
@@ -0,0 +1,140 @@
+% Copyright (C) 2020 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/>.
+
+
+
+
+
+%% To simplify the adding of new commits.
+\newcommand{\branchcommit}[4]{
+  \draw [fill=#1, opacity=0.8] (#2,#3) circle [x radius=5.5mm, y radius=2.1mm];
+  \draw [anchor=center] (#2,#3) node {\textcolor{white}{\scriptsize\texttt{#4}}};
+}
+
+
+
+
+
+\begin{tikzpicture}
+
+  %% Just for a reference (so the image size always remains fixed). It also
+  %% helps in defining easy coordinates for all the other elements.
+  \draw [white] (0,0) -- (0,10cm);
+  \draw [white] (0,0) -- (\linewidth,0);
+
+  %% Maneage branch line.
+  \draw [black!40!white, dashed, line width=2mm] (2cm,0) -- (2cm,0.6cm);
+  \draw [->, black!40!white, line width=2mm] (2cm,0.6cm) -- (2cm,7.9cm);
+  \draw [anchor=south, black!20!white] (2cm,4cm) node [rotate=90, scale=2]
+        {\bf Maneage branch};
+
+  %% Project branch line.
+  \draw [->, black!40!white, rounded corners, line width=2mm]
+        (2cm,2cm) -- (3.5cm,2.5cm) -- (3.5cm,7.9cm);
+  \draw [black!40!white, line width=2mm] (2cm,5cm) -- (3.5cm,5.5cm);
+  \draw [anchor=south, black!20!white] (3.5cm,5cm) node [rotate=90, scale=2]
+        {\bf Project branch};
+
+  %% Derivative project
+  \draw [black!40!white, rounded corners, line width=2mm]
+        (3.5cm,4.5cm) -- (5cm,5cm) -- (5cm,6cm) -- (3.5cm,6.5cm);
+
+  %% Maneage commits.
+  \branchcommit{green!70!blue}{2cm}{1cm}{1d72e26}
+  \branchcommit{green!70!blue}{2cm}{2cm}{0c120cb}
+  \branchcommit{green!70!blue}{2cm}{3cm}{5781173}
+  \branchcommit{green!70!blue}{2cm}{4cm}{0774aac}
+  \branchcommit{green!70!blue}{2cm}{5cm}{3c05235}
+  \branchcommit{green!70!blue}{2cm}{6cm}{6ec4881}
+  \branchcommit{green!70!blue}{2cm}{7cm}{852d996}
+
+  %% Project commits.
+  \branchcommit{red!60!green}{3.5cm}{2.5cm}{4483a81}
+  \branchcommit{red!60!green}{3.5cm}{3.5cm}{5e830f5}
+  \branchcommit{red!60!green}{3.5cm}{4.5cm}{01dd812}
+  \branchcommit{red!60!green}{3.5cm}{5.5cm}{2ed0c82}
+  \branchcommit{red!60!green}{3.5cm}{6.5cm}{f62596e}
+
+  %% Derivate project commits.
+  \branchcommit{red!60!green}{5cm}{5cm}{f69e1f4}
+  \branchcommit{red!60!green}{5cm}{6cm}{716b56b}
+  \node[inner sep=0pt] at (4.5cm,7cm)
+       {\includegraphics[width=9mm]{tex/img/collaboration-icon.pdf}};
+
+
+  %% Description of this scenario:
+  \draw [anchor=west, black] (2.7cm,1.5cm) node {\textbf{Scenario 1} (pre-publication):};
+  \draw [anchor=west, black] (2.8cm,1.1cm) node {\small Collaborating on a project while};
+  \draw [anchor=west, black] (2.8cm,0.7cm) node {\small working in parallel, then merging.};
+
+
+
+  %% Middle line.
+  \draw [black] (8cm,0.5) -- (8cm,7.5cm);
+
+
+
+
+  %% Maneage branch line.
+  \draw [black!40!white, dashed, line width=2mm] (10cm,0) -- (10cm,0.6cm);
+  \draw [->, black!40!white, line width=2mm] (10cm,0.6cm) -- (10cm,9.9cm);
+  \draw [anchor=south, black!20!white] (10cm,4cm) node [rotate=90, scale=2]
+        {\bf Maneage branch};
+
+  %% Project branch line.
+  \draw [black!40!white, rounded corners, line width=2mm]
+        (10cm,2cm) -- (11.5cm,2.5cm) -- (11.5cm,6.9cm);
+  \draw [black!40!white, line width=2mm] (10cm,5cm) -- (11.5cm,5.5cm);
+  \draw [anchor=south, black!20!white] (11.5cm,5cm) node [rotate=90, scale=2]
+        {\bf Project branch};
+
+  %% Derivative project
+  \draw [->, black!40!white, rounded corners, line width=2mm]
+        (11.5cm,6.5cm) -- (13cm,7cm) -- (13cm,9.9cm);
+  \draw [black!40!white, line width=2mm] (10cm,8cm) -- (13cm,9cm);
+  \draw [anchor=south, black!20!white] (13cm,6.5cm) node [rotate=90, scale=2]
+        {\bf Derivative branch};
+
+  %% Maneage commits.
+  \branchcommit{green!70!blue}{10cm}{1cm}{1d72e26}
+  \branchcommit{green!70!blue}{10cm}{2cm}{0c120cb}
+  \branchcommit{green!70!blue}{10cm}{3cm}{5781173}
+  \branchcommit{green!70!blue}{10cm}{4cm}{0774aac}
+  \branchcommit{green!70!blue}{10cm}{5cm}{3c05235}
+  \branchcommit{green!70!blue}{10cm}{6cm}{6ec4881}
+  \branchcommit{green!70!blue}{10cm}{7cm}{852d996}
+  \branchcommit{green!70!blue}{10cm}{8cm}{13a1881}
+  \branchcommit{green!70!blue}{10cm}{9cm}{61b6b01}
+
+  %% Project commits.
+  \branchcommit{red!60!green}{11.5cm}{2.5cm}{4483a81}
+  \branchcommit{red!60!green}{11.5cm}{3.5cm}{5e830f5}
+  \branchcommit{red!60!green}{11.5cm}{4.5cm}{01dd812}
+  \branchcommit{red!60!green}{11.5cm}{5.5cm}{2ed0c82}
+  \branchcommit{red!60!green}{11.5cm}{6.5cm}{f62596e}
+  \node[inner sep=0pt] at (11.5cm,7.2cm) {\includegraphics[width=9mm]{tex/img/paper-icon.pdf}};
+  \draw [anchor=north, black] (11.5cm,8cm) node {\scriptsize Published};
+
+  %% Derivate project commits.
+  \branchcommit{purple!60!yellow}{13cm}{7cm}{b177c7e}
+  \branchcommit{purple!60!yellow}{13cm}{8cm}{5ae1fdc}
+  \branchcommit{purple!60!yellow}{13cm}{9cm}{bcf4512}
+
+  %% Description of this scenario:
+  \draw [anchor=west, black] (10.7cm,1.5cm) node {\textbf{Scenario 2} (post-publication):};
+  \draw [anchor=west, black] (10.8cm,1.1cm) node {\small Other researchers building upon};
+  \draw [anchor=west, black] (10.8cm,0.7cm) node {\small previously published work.};
+
+\end{tikzpicture}
diff --git a/tex/src/figure-data-lineage.tex b/tex/src/figure-data-lineage.tex
index 7379b2f..146a833 100644
--- a/tex/src/figure-data-lineage.tex
+++ b/tex/src/figure-data-lineage.tex
@@ -61,8 +61,8 @@
     label={[shift={(0,-5mm)}]\texttt{format.mk}}] {};
   \node (analysis2mk)  [node-makefile, at={(2.67cm,-1.3cm)},
     label={[shift={(0,-5mm)}]\texttt{demo-plot.mk}}] {};
-  \node (analysis3mk)  [node-makefile, at={(5.47cm,-1.3cm)},
-    label={[shift={(0,-5mm)}]\texttt{another-step.mk}}] {};
+  \node [opacity=0.6] (analysis3mk)  [node-makefile, at={(5.47cm,-1.3cm)},
+    label={[shift={(0,-5mm)}, opacity=0.6]\texttt{another-step.mk}}] {};
 
   %% verify.mk
   \node [at={(-5.3cm,-2.8cm)},
diff --git a/tex/src/figure-src-download.tex b/tex/src/figure-src-download.tex
index 74026b8..4d4b755 100644
--- a/tex/src/figure-src-download.tex
+++ b/tex/src/figure-src-download.tex
@@ -1,4 +1,4 @@
-\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{download.mk}} \textcolor{white}{(only \LaTeX{} macro's rule.}]
+\begin{tcolorbox}[title=\inlinecode{\textcolor{white}{download.mk}} \hfill\textcolor{white}{(only \LaTeX{} macro's rule)}]
   \footnotesize
   \texttt{\mkcomment{Write download URL into the paper (through a LaTeX macro).}}
 
diff --git a/tex/src/figure-src-topmake.tex b/tex/src/figure-src-topmake.tex
index bd4b67d..6ed315b 100644
--- a/tex/src/figure-src-topmake.tex
+++ b/tex/src/figure-src-topmake.tex
@@ -15,10 +15,10 @@
   \texttt{{ }{ }{ }{ }{ }{ }{ }{ }{ }{ }paper}\par
 
   \vspace{1em}
-  \texttt{\mkcomment{Load all the configuration files.}}\par
+  \texttt{\mkcomment{Include all the configuration files.}}\par
   \texttt{\textcolor{purple}{include} reproduce/analysis/config/*.conf}
 
   \vspace{1em}
-  \texttt{\mkcomment{Load/include the subMakefiles in the specified order.}}\par
+  \texttt{\mkcomment{Include the subMakefiles in the specified order.}}\par
   \texttt{\textcolor{purple}{include} \$(\textcolor{blue}{foreach} s, \$(\mkvar{makesrc}), reproduce/analysis/make/\$(\mkvar{s}).mk)}
 \end{tcolorbox}
diff --git a/tex/src/references.tex b/tex/src/references.tex
index 6e1de41..510fc89 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -1428,6 +1428,26 @@ Reproducible Research in Image Processing},
 
 
 
+@Article{matplotlib2007,
+  Author    = {Hunter, J. D.},
+  Title     = {Matplotlib: A 2D graphics environment},
+  Journal   = {CiSE},
+  Volume    = {9},
+  Number    = {3},
+  Pages     = {90},
+  abstract  = {Matplotlib is a 2D graphics package used for Python
+  for application development, interactive scripting, and
+  publication-quality image generation across user
+  interfaces and operating systems.},
+  publisher = {IEEE COMPUTER SOC},
+  doi       = {10.1109/MCSE.2007.55},
+  year      = 2007
+}
+
+
+
+
+
 @ARTICLE{witten2007,
      author = {Ben Witten and Bill Curry and Jeff Shragge},
       title = {A New Build Environment for SEP},