No links to main body in the appendices in --supplement mode

Until now, in the appendices we were simply using '\ref' to refer to
different parts of the published paper. However, when built in
'--supplement' mode, the main body of the paper is a separate PDF and
having links to a separate PDF is not impossible, but far too complicated.
However, having the links adds to the richness of the text and helps point
readers to specific parts of the paper.

With this commit, there is a LaTeX conditional anywhere in the appendices
that we want to refer the reader to sections/figures in the main body. When
building a separate PDF, the resepective section/figure is cited in a
descriptive mode (like "Seciton discussing longevity of tools"). However,
when the appendices go into the same PDF as the main body, the '\ref's
remain.

2 files changed, 50 insertions, 9 deletions

diff --git a/tex/src/appendix-existing-solutions.tex b/tex/src/appendix-existing-solutions.tex
index 919f4e5..d7888ad 100644
--- a/tex/src/appendix-existing-solutions.tex
+++ b/tex/src/appendix-existing-solutions.tex
@@ -41,12 +41,22 @@ For more on Popper, please see Section \ref{appendix:popper}.
 For improved reproducibility in Jupyter notebook users, \citeappendix{rule19} propose ten rules to improve reproducibility and also provide links to example implementations.
 These can be very useful for users of Jupyter, but are not generic for non-Jupyter-based computational projects.
 Some criteria (which are indeed very good in a more general context) do not directly relate to reproducibility, for example their Rule 1: ``Tell a Story for an Audience''.
-Generally, as reviewed in Sections \ref{sec:longevityofexisting} and \ref{appendix:jupyter}, Jupyter itself has many issues regarding reproducibility.
-
+Generally, as reviewed in
+\ifdefined\separatesupplement
+the main body of this paper (section on longevity of existing tools)
+\else
+Section \ref{sec:longevityofexisting}
+\fi
+and Section \ref{appendix:jupyter} (below), Jupyter itself has many issues regarding reproducibility.
 To create Docker images, N\"ust et al. propose ``ten simple rules'' in \citeappendix{nust20}.
 They recommend some issues that can indeed help increase the quality of Docker images and their production/usage, such as their rule 7 to ``mount datasets [only] at run time'' to separate the computational environment from the data.
 However, long-term reproducibility of the images is not included as a criterion by these authors.
-For example, they recommend using base operating systems, with version identification limited to a single brief identifier such as \inlinecode{ubuntu:18.04}, which has a serious problem with longevity issues (Section \ref{sec:longevityofexisting}).
+For example, they recommend using base operating systems, with version identification limited to a single brief identifier such as \inlinecode{ubuntu:18.04}, which has a serious problem with longevity issues
+\ifdefined\separatesupplement
+(as discussed in the longevity of existing tools section of the main paper).
+\else
+(Section \ref{sec:longevityofexisting}).
+\fi
 Furthermore, in their proof-of-concept Dockerfile (listing 1), \inlinecode{rocker} is used with a tag (not a digest), which can be problematic due to the high risk of ambiguity (as discussed in Section \ref{appendix:containers}).
 
 \subsection{Reproducible Electronic Documents, RED (1992)}
@@ -82,7 +92,12 @@ Apache Taverna\footnote{\inlinecode{\url{https://taverna.incubator.apache.org}}}
 A workflow is defined as a directed graph, where nodes are called ``processors''.
 Each Processor transforms a set of inputs into a set of outputs and they are defined in the Scufl language (an XML-based language, were each step is an atomic task).
 Other components of the workflow are ``Data links'' and ``Coordination constraints''.
-The main user interface is graphical, where users move processors in the given space and define links between their inputs outputs (manually constructing a lineage like Figure \ref{fig:datalineage}).
+The main user interface is graphical, where users move processors in the given space and define links between their inputs outputs (manually constructing a lineage like
+\ifdefined\separatesupplement
+lineage figure of the main paper.
+\else
+Figure \ref{fig:datalineage}).
+\fi
 Taverna is only a workflow manager and is not integrated with a package manager, hence the versions of the used software can be different in different runs.
 \citeappendix{zhao12} have studied the problem of workflow decays in Taverna.
 
@@ -136,7 +151,12 @@ This is a very nice example of the fragility of solutions that depend on archivi
 
 \subsection{Kepler (2005)}
 Kepler\footnote{\inlinecode{\url{https://kepler-project.org}}} \citeappendix{ludascher05} is a Java-based Graphic User Interface workflow management tool.
-Users drag-and-drop analysis components, called ``actors'', into a visual, directional graph, which is the workflow (similar to Figure \ref{fig:datalineage}).
+Users drag-and-drop analysis components, called ``actors'', into a visual, directional graph, which is the workflow (similar to
+\ifdefined\separatesupplement
+the lineage figure shown in the main paper.
+\else
+Figure \ref{fig:datalineage}).
+\fi
 Each actor is connected to others through the Ptolemy II\footnote{\inlinecode{\url{https://ptolemy.berkeley.edu}}} \citeappendix{eker03}.
 In many aspects, the usage of Kepler and its issues for long-term reproducibility is like Apache Taverna (see Section \ref{appendix:taverna}).
 
@@ -159,7 +179,12 @@ Its design is based on a change-based provenance model using a custom VisTrails
 Since XML is a plane text format, as the user inspects the data and makes changes to the analysis, the changes are recorded as ``trails'' in the project's VisTrails repository that operates very much like common version control systems (see Appendix \ref{appendix:versioncontrol}).
 .
 However, even though XML is in plain text, it is very hard to edit manually.
-VisTrails therefore provides a graphic user interface with a visual representation of the project's inter-dependent steps (similar to Figure \ref{fig:datalineage}).
+VisTrails therefore provides a graphic user interface with a visual representation of the project's inter-dependent steps (similar to
+\ifdefined\separatesupplement
+the data lineage figure of the main paper).
+\else
+Figure \ref{fig:datalineage}).
+\fi
 Besides the fact that it is no longer maintained, VisTrails does not control the software that is run, it only controls the sequence of steps that they are run in.
 
 
diff --git a/tex/src/appendix-existing-tools.tex b/tex/src/appendix-existing-tools.tex
index 794a3fe..b6068e4 100644
--- a/tex/src/appendix-existing-tools.tex
+++ b/tex/src/appendix-existing-tools.tex
@@ -85,7 +85,12 @@ On a more fundamental level, VMs or contains do not store \emph{how} the core en
 This information is usually in a third-party repository, and not necessarily inside container or VM file, making it hard (if not impossible) to track for future users.
 This is a major problem when considering reproducibility which is also highlighted as a major issue in terms of long term reproducibility in \citeappendix{oliveira18}.
 
-The example of \cite{mesnard20} was previously mentioned in Section \ref{criteria}.
+The example of \cite{mesnard20} was previously mentioned in
+\ifdefined\separatesupplement
+the main body of this paper, when discussing the criteria.
+\else
+in Section \ref{criteria}.
+\fi
 Another useful example is the \href{https://github.com/benmarwick/1989-excavation-report-Madjedbebe/blob/master/Dockerfile}{\inlinecode{Dockerfile}} of \citeappendix{clarkso15} (published in June 2015) which starts with \inlinecode{FROM rocker/verse:3.3.2}.
 When we tried to build it (November 2020), the core downloaded image (\inlinecode{rocker/verse:3.3.2}, with image ``digest'' \inlinecode{sha256:c136fb0dbab...}) was created in October 2018 (long after the publication of that paper).
 In principle, it is possible to investigate the difference between this new image and the old one that the authors used, but that would require a lot of effort and may not be possible where the changes are not available in a third public repository or not under version control.
@@ -288,7 +293,12 @@ Hence we will just review Git here, but the general concept of version control i
 \subsubsection{Git}
 With Git, changes in a project's contents are accurately identified by comparing them with their previous version in the archived Git repository.
 When the user decides the changes are significant compared to the archived state, they can ``commit'' the changes into the history/repository.
-The commit involves copying the changed files into the repository and calculating a 40 character checksum/hash that is calculated from the files, an accompanying ``message'' (a narrative description of the purpose/goals of the changes), and the previous commit (thus creating a ``chain'' of commits that are strongly connected to each other like Figure \ref{fig:branching}).
+The commit involves copying the changed files into the repository and calculating a 40 character checksum/hash that is calculated from the files, an accompanying ``message'' (a narrative description of the purpose/goals of the changes), and the previous commit (thus creating a ``chain'' of commits that are strongly connected to each other like
+\ifdefined\separatesupplement
+the figure on Git in the main body of the paper.
+\else
+Figure \ref{fig:branching}).
+\fi
 For example \inlinecode{f4953cc\-f1ca8a\-33616ad\-602ddf\-4cd189\-c2eff97b} is a commit identifier in the Git history of this project.
 Commits are is commonly summarized by the checksum's first few characters, for example \inlinecode{f4953cc}.
 
@@ -313,7 +323,13 @@ There are many tools for managing the sequence of jobs, below we review the most
 The most commonly used workflow system for many researchers is to run the commands, experiment on them and keep the output when they are happy with it.
 As an improvement, some also keep a narrative description of what they ran.
 Atleast in our personal experience with colleagues, this method is still being heavily practiced by many researchers.
-Given that many researchers do not get trained well in computational methods, this is not surprizing and as discussed in Section \ref{discussion}, we believe that improved literacy in computational methods is the single most important factor for the integrity/reproducibility of modern science.
+Given that many researchers do not get trained well in computational methods, this is not surprizing and as discussed in
+\ifdefined\separatesupplement
+the discussion section of the main paper,
+\else
+Section \ref{discussion},
+\fi
+we believe that improved literacy in computational methods is the single most important factor for the integrity/reproducibility of modern science.
 
 \subsubsection{Scripts}
 \label{appendix:scripts}