Acknowledged contributions of Marios Karouzos

Marios had read the first draft of the paper (Commit f990bba) and provided
valuable feedback (shown below) that ultimately helped in the current
version. But because of all the work that was necessary in those days, I
forgot to actually thank him in the acknowledgment, while I had implemented
most of his thoughts.

Following Marios' thoughts on the Git branching figure, with this commit, I
am also adding a few sentences at the end of the caption with a very rough
summary of Git.

I also changed the branch commit-colors to shades of brown (incrementally
becoming lighter as higher-level branches are shown) to avoid the confusion
with the blue and green signs within the schematic papers shown in the
figure.

Marios' comments (April 28th, 2020, on Commit f990bba)
------------------------------------------------------

I think the structure of the paper is more or less fine. There are two
places that I thought could be improved:

1) Section 3 (Principles) was somewhat confusing to me in the way that it
was structured. I think the main source of confusion is the mixing of what
Maeage is about and what other programs have done. I would suggest to
separate the two. I would have short intro for the section, similar to what
you have now. However, I would suggest to highlight the underlying goals
motivating the principles that follow: reproducibility, open science,
something else? Then I would go into the details of the seven principles.

Some of the principles are less clear to me than others. For example, why
is simplicity a guiding principle? Then some other principles appear to be
related, for example modularity, minimal complexity and scalability to my
eyes are not necessarily separate.

Finally, I would separate the comparison with other software and either
dedicate a section to that somewhere toward the end of the paper (perhaps a
subsection for section 5) or at least condense it and put it as a closing
paragraph for Section 3. As it is now I think it draws focus from Maneage
and also includes some repetitions.

2) Section 4 (Maneage) was at times confusing because it is written, I
think in part as a demonstration of Maneage (i.e., including examples that
showed how Maneage was used to write this or other papers) and a
manual/description of the software. I wonder whether these two aspects can
be more cleanly separated. Perhaps it would be possible to first have a
section 4 where each of the modules/units of Maneage are listed and
explained and then have the following section discuss a working example of
Maneage using this or another paper.

3) I found Figure 7 [the git branching figure] and its explanation not very
intuitive. This probably has to do with my zero knowledge of github and how
versioning there works, but perhaps the description can be a bit more "user
friendly" even for those who are not familiar with the tool.

4) I find Section 6 to be rather inconsequential. It does not add anything
and it more or less is just a summary of what was discussed. I would
personally remove it and include a very short summary of the
ideals/principles/goals of Maneage at the beginning of Section 5, before
the discussion.

2 files changed, 29 insertions, 28 deletions

diff --git a/tex/src/figure-branching.tex b/tex/src/figure-branching.tex
index 56a76e8..56c1652 100644
--- a/tex/src/figure-branching.tex
+++ b/tex/src/figure-branching.tex
@@ -17,12 +17,14 @@
 
 
 
-%% To simplify the adding of new commits.
+%% Basic definitions to facilitate the plot code.
 \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}}};
 }
-
+\definecolor{maneagebranchcolor}{HTML}{46211A}
+\definecolor{projectbranchcolor}{HTML}{BA5536}
+\definecolor{derivedbranchcolor}{HTML}{C28556}
 
 
 
@@ -61,24 +63,24 @@
         (3cm,4.5cm) -- (4.5cm,5cm) -- (4.5cm,6cm) -- (3cm,6.5cm);
 
   %% Maneage commits.
-  \branchcommit{green!70!blue}{1.5cm}{1cm}{1d72e26}
-  \branchcommit{green!70!blue}{1.5cm}{2cm}{0c120cb}
-  \branchcommit{green!70!blue}{1.5cm}{3cm}{5781173}
-  \branchcommit{green!70!blue}{1.5cm}{4cm}{0774aac}
-  \branchcommit{green!70!blue}{1.5cm}{5cm}{3c05235}
-  \branchcommit{green!70!blue}{1.5cm}{6cm}{6ec4881}
-  \branchcommit{green!70!blue}{1.5cm}{7cm}{852d996}
+  \branchcommit{maneagebranchcolor}{1.5cm}{1cm}{1d72e26}
+  \branchcommit{maneagebranchcolor}{1.5cm}{2cm}{0c120cb}
+  \branchcommit{maneagebranchcolor}{1.5cm}{3cm}{5781173}
+  \branchcommit{maneagebranchcolor}{1.5cm}{4cm}{0774aac}
+  \branchcommit{maneagebranchcolor}{1.5cm}{5cm}{3c05235}
+  \branchcommit{maneagebranchcolor}{1.5cm}{6cm}{6ec4881}
+  \branchcommit{maneagebranchcolor}{1.5cm}{7cm}{852d996}
 
   %% Project commits.
-  \branchcommit{red!60!green}{3cm}{2.5cm}{4483a81}
-  \branchcommit{red!60!green}{3cm}{3.5cm}{5e830f5}
-  \branchcommit{red!60!green}{3cm}{4.5cm}{01dd812}
-  \branchcommit{red!60!green}{3cm}{5.5cm}{2ed0c82}
-  \branchcommit{red!60!green}{3cm}{6.5cm}{f62596e}
+  \branchcommit{projectbranchcolor}{3cm}{2.5cm}{4483a81}
+  \branchcommit{projectbranchcolor}{3cm}{3.5cm}{5e830f5}
+  \branchcommit{projectbranchcolor}{3cm}{4.5cm}{01dd812}
+  \branchcommit{projectbranchcolor}{3cm}{5.5cm}{2ed0c82}
+  \branchcommit{projectbranchcolor}{3cm}{6.5cm}{f62596e}
 
   %% Derivate project commits.
-  \branchcommit{red!60!green}{4.5cm}{5cm}{f69e1f4}
-  \branchcommit{red!60!green}{4.5cm}{6cm}{716b56b}
+  \branchcommit{projectbranchcolor}{4.5cm}{5cm}{f69e1f4}
+  \branchcommit{projectbranchcolor}{4.5cm}{6cm}{716b56b}
 
   %% Paper being processed icon. The white rectangle over it is to blend it
   %% into the background.
@@ -128,23 +130,23 @@
         {\bf project};
 
   %% Maneage commits.
-  \branchcommit{green!70!blue}{9.5cm}{1cm}{1d72e26}
-  \branchcommit{green!70!blue}{9.5cm}{2cm}{0c120cb}
-  \branchcommit{green!70!blue}{9.5cm}{4cm}{b47b2a3}
-  \branchcommit{green!70!blue}{9.5cm}{5cm}{340a7ec}
-  \branchcommit{green!70!blue}{9.5cm}{6cm}{a92b25a}
-  \branchcommit{green!70!blue}{9.5cm}{7cm}{6e1e3ff}
+  \branchcommit{maneagebranchcolor}{9.5cm}{1cm}{1d72e26}
+  \branchcommit{maneagebranchcolor}{9.5cm}{2cm}{0c120cb}
+  \branchcommit{maneagebranchcolor}{9.5cm}{4cm}{b47b2a3}
+  \branchcommit{maneagebranchcolor}{9.5cm}{5cm}{340a7ec}
+  \branchcommit{maneagebranchcolor}{9.5cm}{6cm}{a92b25a}
+  \branchcommit{maneagebranchcolor}{9.5cm}{7cm}{6e1e3ff}
 
   %% Project commits.
-  \branchcommit{red!60!green}{11cm}{2.5cm}{4483a81}
-  \branchcommit{red!60!green}{11cm}{4.5cm}{\projectversion}
+  \branchcommit{projectbranchcolor}{11cm}{2.5cm}{4483a81}
+  \branchcommit{projectbranchcolor}{11cm}{4.5cm}{\projectversion}
   \node[anchor=south, inner sep=0pt, color=white] at (11cm,4.8cm)
        {\includegraphics[width=1cm]{tex/img/icon-complete.eps}};
 
   %% Derivate project commits.
-  \branchcommit{purple!60!yellow}{12.5cm}{5cm}{b177c7e}
-  \branchcommit{purple!60!yellow}{12.5cm}{6cm}{5ae1fdc}
-  \branchcommit{purple!60!yellow}{12.5cm}{7cm}{bcf4512}
+  \branchcommit{derivedbranchcolor}{12.5cm}{5cm}{b177c7e}
+  \branchcommit{derivedbranchcolor}{12.5cm}{6cm}{5ae1fdc}
+  \branchcommit{derivedbranchcolor}{12.5cm}{7cm}{bcf4512}
 
   %% Description of this scenario:
   \draw [rounded corners, fill=black!10!white] (11.1cm,0) rectangle (15.3cm,1.25cm);
diff --git a/tex/src/preamble-project.tex b/tex/src/preamble-project.tex
index e14fbf6..16a9ddc 100644
--- a/tex/src/preamble-project.tex
+++ b/tex/src/preamble-project.tex
@@ -55,7 +55,6 @@
 %% Custom macros
 \newcommand{\inlinecode}[1]{\textcolor{blue!35!black}{\texttt{#1}}}
 
-
 \newcommand\eprint[1]{\href{https://arXiv.org/abs/#1}{{arXiv:#1}}}
 
 \newcommand\doi[1]{\href{https://oadoi.org/#1}{{DOI:#1}}}