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).

1 files changed, 139 insertions, 0 deletions

diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
new file mode 100644
index 0000000..5378ee3
--- /dev/null
+++ b/reproduce/analysis/make/paper.mk
@@ -0,0 +1,139 @@
+# Build the final PDF paper/report.
+#
+# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This Makefile 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 Makefile 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.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+# LaTeX macros for paper
+# ----------------------
+#
+# To report the input settings and results, the final report's PDF (final
+# target of this project) uses macros generated from various steps of the
+# project. All these macros are defined through `$(mtexdir)/project.tex'.
+#
+# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# that keep the LaTeX macros related to each workhorse Makefile (in
+# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# `$(mtexdir)/project.tex'. The only workhorse Makefile that doesn't need
+# to produce LaTeX macros is this Makefile (`reproduce/src/make/paper.mk').
+#
+# This file is thus the interface between the processing scripts and the
+# final PDF: when we get to this point, all the processing has been
+# completed.
+#
+# Note that if you don't want the final PDF and just want the processing
+# and file outputs, you can remove the value of `pdf-build-final' in
+# `reproduce/analysis/config/pdf-build.mk'.
+$(mtexdir)/project.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s).tex)
+
+        # If no PDF is requested, or if LaTeX isn't available, don't
+        # continue to building the final PDF. Otherwise, merge all the TeX
+        # macros into one for building the PDF.
+	@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" != x ]; then
+
+          # Put a LaTeX input command for all the necessary macro files.
+	  rm -f $(mtexdir)/project.tex
+	  for t in $(subst paper,,$(makesrc)); do
+	    echo "\input{tex/build/macros/$$t.tex}" >> $(mtexdir)/project.tex
+	  done
+	else
+	  echo
+	  echo "-----"
+	  echo "The processing has COMPLETED SUCCESSFULLY! But the final "
+	  echo "LaTeX-built PDF paper will not be built."
+	  echo
+	  if [ x$(more-on-building-pdf) = x1 ]; then
+	    echo "To do so, make sure you have LaTeX within the project (you"
+	    echo "can check by running './.local/bin/latex --version'), _AND_"
+	    echo "make sure that the 'pdf-build-final' variable has a value."
+	    echo "'pdf-build-final' is defined in: "
+	    echo     "'reproduce/analysis/config/pdf-build.mk'."
+	    echo
+	    echo "If you don't have LaTeX within the project, please re-run"
+	    echo "'./configure' when you have internet access. To speed it up,"
+	    echo "you can keep the previous configuration files (answer 'n'"
+	    echo "when it asks about re-writing previous configuration files)."
+	  else
+	    echo "For more, run './.local/bin/make more-on-building-pdf=1'"
+	  fi
+	  echo
+	  echo "" > $@
+	fi
+
+
+
+
+
+# The bibliography
+# ----------------
+#
+# We need to run the `biber' program on the output of LaTeX to generate the
+# necessary bibliography before making the final paper. So we'll first have
+# one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+#
+# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
+# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
+# recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't
+# been modified, we don't want to re-build the bibliography, only the final
+# PDF.
+$(texbdir)/paper.bbl: tex/src/references.tex                         \
+                      | $(tikzdir) $(texbdir) $(mtexdir)/project.tex
+        # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+	@macros=$$(cat $(mtexdir)/project.tex)
+	if [ x"$$macros" != x ]; then
+
+          # We'll run LaTeX first to generate the `.bcf' file (necessary
+          # for `biber') and then run `biber' to generate the `.bbl' file.
+	  p=$$(pwd);
+	  export TEXINPUTS=$$p:$$TEXINPUTS;
+	  cd $(texbdir);
+	  pdflatex -shell-escape -halt-on-error $$p/paper.tex;
+	  biber paper
+
+	fi
+
+
+
+
+
+# The final paper
+# ---------------
+#
+# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# auxiliary files stay there and keep the top directory clean. To be able
+# to run everything cleanly from there, it is necessary to add the current
+# directory (top project directory) to the `TEXINPUTS' environment
+# variable.
+paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl       \
+	   | $(tikzdir) $(texbdir)
+
+        # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+	@macros=$$(cat $(mtexdir)/project.tex)
+	if [ x"$$macros" != x ]; then
+
+          # Go into the top TeX build directory and make the paper.
+	  p=$$(pwd)
+	  export TEXINPUTS=$$p:$$TEXINPUTS
+	  cd $(texbdir)
+	  pdflatex -shell-escape -halt-on-error $$p/paper.tex
+
+          # Come back to the top project directory and copy the built PDF
+          # file here.
+	  cd $$p
+	  cp $(texbdir)/$@ $(final-paper)
+
+	fi