New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

4 files changed, 5 insertions, 5 deletions

diff --git a/tex/src/delete-me-demo.tex b/tex/src/delete-me-demo.tex
index abd45f6..67024bb 100644
--- a/tex/src/delete-me-demo.tex
+++ b/tex/src/delete-me-demo.tex
@@ -20,7 +20,7 @@
   %% The displayed WFPC2 image.
   \node[anchor=south west] (img) at (0,0)
        {\includegraphics[width=0.5\linewidth]
-         {tex/pipeline/delete-me-demo/wfpc2.pdf}};
+         {tex/build/delete-me-demo/wfpc2.pdf}};
 
   %% Its label
   \node[anchor=south west] at (0.45\linewidth,0.45\linewidth)
@@ -42,7 +42,7 @@
       ]
     \addplot [const plot mark mid, fill=red]
     table [x index=0, y index=1]
-    {tex/pipeline/delete-me-demo/wfpc2-hist.txt}
+    {tex/build/delete-me-demo/wfpc2-hist.txt}
     \closedcycle;
   \end{axis}
 
diff --git a/tex/src/delete-me.tex b/tex/src/delete-me.tex
index 12fd3b7..552e92a 100644
--- a/tex/src/delete-me.tex
+++ b/tex/src/delete-me.tex
@@ -26,7 +26,7 @@
 
     %% A particular plot.
     \addplot+[scatter, only marks]
-    table {tex/pipeline/delete-me/data.txt};
+    table {tex/build/delete-me/data.txt};
 
   \end{axis}
 \end{tikzpicture}
diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex
index b4c02f9..ca54f90 100644
--- a/tex/src/preamble-biblatex.tex
+++ b/tex/src/preamble-biblatex.tex
@@ -56,7 +56,7 @@
 \DeclareFieldFormat[article]{pages}{#1}
 \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
 \addbibresource{tex/src/references.tex}
-\addbibresource{tex/pipeline/macros/dependencies-bib.tex}
+\addbibresource{tex/build/macros/dependencies-bib.tex}
 \renewbibmacro{in:}{}
 \renewcommand*{\bibfont}{\footnotesize}
 \DefineBibliographyStrings{english}{references = {References}}
diff --git a/tex/src/preamble-necessary.tex b/tex/src/preamble-necessary.tex
index 2abcb9e..1deb8ec 100644
--- a/tex/src/preamble-necessary.tex
+++ b/tex/src/preamble-necessary.tex
@@ -24,7 +24,7 @@
 
 
 %% Values from the analysis.
-\input{tex/pipeline/macros/pipeline.tex}
+\input{tex/build/macros/project.tex}