Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 65 insertions, 65 deletions

diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 00bd3b5..da2702c 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -1,6 +1,6 @@
 # Build the final PDF paper/report.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -24,14 +24,14 @@
 #
 # 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 `$(mtexdir)/project.tex'.
+# project. All these macros are defined through '$(mtexdir)/project.tex'.
 #
-# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# '$(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
-# `$(mtexdir)/verify.tex' which will check them before starting to build
+# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# '$(mtexdir)/verify.tex' which will check them before starting to build
 # the paper. The only workhorse Makefile that doesn't need to produce LaTeX
-# macros is this Makefile (`reproduce/src/make/paper.mk').
+# macros is this Makefile ('reproduce/src/make/paper.mk').
 #
 # This file is thus the interface between the analysis/processing steps and
 # the final PDF: when we get to this point, all the processing has been
@@ -39,38 +39,38 @@
 #
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can give any value other than 'yes' to
-# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
 $(mtexdir)/project.tex: $(mtexdir)/verify.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 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/latex ] && [ x"$(pdf-build-final)" = xyes ]; then
 
-          # Put a LaTeX input command for all the necessary macro files.
-          # 'hardware-parameters.tex' is created in 'configure.sh'.
+#	  Put a LaTeX input command for all the necessary macro files.
+#	  'hardware-parameters.tex' is created in 'configure.sh'.
 	  projecttex=$(mtexdir)/project.tex
 	  rm -f $$projecttex
 	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
 	    echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
 	  done
 
-          # Possibly print the appendix in the final PDF.
+#	  Possibly print the appendix in the final PDF.
 	  if [ x"$(separatesupplement)" = x1 ]; then
 	    echo "\newcommand{\separatesupplement}{}" >> $$projecttex
 	  fi
 
-          # Possibly highlight the '\new' parts of the text.
+#	  Possibly highlight the '\new' parts of the text.
 	  if [ x"$(highlightnew)" = x1 ]; then
 	    echo "\newcommand{\highlightnew}{}" >> $$projecttex
 	  fi
 
-          # Possibly show the text within '\tonote'.
+#	  Possibly show the text within '\tonote'.
 	  if [ x"$(highlightnotes)" = x1 ]; then
 	    echo "\newcommand{\highlightnotes}{}" >> $$projecttex
 	  fi
 
-        # The paper shouldn't be built.
+#	The paper shouldn't be built.
 	else
 	  echo
 	  echo "-----"
@@ -101,76 +101,76 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 # The bibliography
 # ----------------
 #
-# We need to run the `bibtex' program on the output of LaTeX to generate
+# We need to run the 'bibtex' program on the output of LaTeX to generate
 # the necessary bibliography before making the final paper. So we'll first
-# have one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# have one run of LaTeX (similar to the 'paper.pdf' recipe), then 'bibtex'.
 #
-# NOTE: `$(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.bib' hasn't
+# 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.
 bbls = $(foreach t,$(subst .pdf,,$(top-pdfs)),$(texbdir)/$(t).bbl)
 $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
          $(mtexdir)/dependencies-bib.tex | $(mtexdir)/project.tex
 
-        # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+#	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
 
-          # Unfortunately I can't get bibtex to look into a special
-          # directory for the references, so we'll copy it into the LaTeX
-          # building directory.
+#	  Unfortunately I can't get bibtex to look into a special directory
+#	  for the references, so we'll copy it into the LaTeX building
+#	  directory.
 	  p=$$(pwd)
 	  if ! [ -L $(texbdir)/references.bib ]; then
 	    ln -sf $$p/tex/src/references.tex $(texbdir)/references.bib
 	  fi
 
-          # Copy the improved IEEE bst file into the build directory.
-          # The improved bst file provides ArXiv clickable URLs and
-          # if available, open-access URLs based on the DOIs, with
-          # closed-access URLs as a fallback, via https://oadoi.org .
+#	  Copy the improved IEEE bst file into the build directory. The
+#	  improved bst file provides ArXiv clickable URLs and if available,
+#	  open-access URLs based on the DOIs, with closed-access URLs as a
+#	  fallback, via https://oadoi.org .
 	  ln -sf $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)/
 
-          # We'll run LaTeX first to generate the `.bcf' file (necessary
-          # for `biber') and then run `biber' to generate the `.bbl' file.
+#	  We'll run LaTeX first to generate the '.bcf' file (necessary for
+#	  'bibtex') and then run 'bibtex' to generate the '.bbl' file.
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
 
-          # Delete any possibly existing target (a '.bbl' file) to avoid
-          # complications with LaTeX being run before the command that
-          # generates it. Otherwise users will have to manually delete
-          # it. It will be built anyway once this rule is done.
+#	  Delete any possibly existing target (a '.bbl' file) to avoid
+#	  complications with LaTeX being run before the command that
+#	  generates it. Otherwise users will have to manually delete it. It
+#	  will be built anyway once this rule is done.
 	  rm -f $@
 
-          # Put a link to the main LaTeX source that we want to build.
+#	  Put a link to the main LaTeX source that we want to build.
 	  if [ $* = paper ]; then sdir="$$p"
 	  else                    sdir="$$p"/tex/src
 	  fi
 	  ln -sf "$$sdir"/$*.tex ./
 
-          # The pdflatex option '-shell-escape' is "normally disallowed for
-          # security reasons" according to the `info pdflatex' manual, but
-          # is enabled here in order to allow the use of PGFPlots. If you
-          # do not use PGFPlots, then you can remove the `-shell-escape'
-          # option for better security. See
-          # https://savannah.nongnu.org/task/?15694 for details.
+#	  The pdflatex option '-shell-escape' is "normally disallowed for
+#	  security reasons" according to the 'info pdflatex' manual, but is
+#	  enabled here in order to allow the use of PGFPlots. If you do not
+#	  use PGFPlots, then you should remove the '-shell-escape' option
+#	  for better security. See https://savannah.nongnu.org/task/?15694
+#	  for details.
 	  latex -shell-escape -halt-on-error $*.tex
 
-          # When we are building the main paper and the appendices are to
-          # be built within the main paper's PDF, we need two
-          # bibliographies: one for the main body, and one for the
-          # appendix. For this, we use 'multibib'. Multibib creates a
-          # separate '.aux' file for each bibliography.
+#	  When we are building the main paper and the appendices are to be
+#	  built within the main paper's PDF, we need two bibliographies:
+#	  one for the main body, and one for the appendix. For this, we use
+#	  'multibib'. Multibib creates a separate '.aux' file for each
+#	  bibliography.
 	  bibtex $*
 	  if [ x"$(separatesupplement)" != x1 ]; then
 	    bibtex appendix
 	  fi
 
-          # Hack: tidy up eprint+doi style that didn't work in .bst file.
-          # TODO (better): read Part 4 of
-          # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
-          # and fix the .bst style properly.
+#	  Hack: tidy up eprint+doi style that didn't work in .bst file.
+#	  TODO (better): read Part 4 of
+#	  http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf and
+#	  fix the .bst style properly.
 	  cp -pv $*.bbl $*-tmp.bbl \
 	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
@@ -188,7 +188,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 	      | sed -e 's/EOLINE/\n/g' > appendix.bbl
 	  fi
 
-	  # Paper-specific hacks for reducing very-long author lists.
+#	  Paper-specific hacks for reducing very-long author lists.
 	  cp -pv $*.bbl $*-tmp.bbl \
 	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
@@ -196,7 +196,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 	    | sed -e 's;, V\..Khodiyar[^{]*Whyte; et al.\\/;' \
 	    | sed -e 's/EOLINE/\n/g' > $*.bbl
 
-          # The pre-final run of LaTeX after 'paper.bbl' was created.
+#	  The pre-final run of LaTeX after 'paper.bbl' was created.
 	  latex -shell-escape -halt-on-error $*.tex
 	fi
 
@@ -207,36 +207,36 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 # The final paper
 # ---------------
 #
-# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# 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
+# directory (top project directory) to the 'TEXINPUTS' environment
 # variable.
 $(top-pdfs): %.pdf: $(mtexdir)/project.tex paper.tex \
          tex/src/appendix-*.tex $(texbdir)/%.bbl
 
-        # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+#	If '$(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.
+#	  Go into the top TeX build directory and make the paper.
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir)
 
-          # See above for a warning and brief discussion on the the
-          # pdflatex option `-shell-escape'.
+#	  See above for a warning and brief discussion on the the pdflatex
+#	  option '-shell-escape'.
 	  latex -shell-escape -halt-on-error $*.tex
 
-          # Convert the DVI to PostScript, and the PostScript to PDF. The
-          # `-dNOSAFER' option to GhostScript allows transparencies in the
-          # conversion from PostScript to PDF, see
-          # https://www.ghostscript.com/doc/current/Language.htm#Transparency
+#	  Convert the DVI to PostScript, and the PostScript to PDF. The
+#	  '-dNOSAFER' option to GhostScript allows transparencies in the
+#	  conversion from PostScript to PDF, see
+#	  https://www.ghostscript.com/doc/current/Language.htm#Transparency
 	  dvips $*.dvi
 	  ps2pdf $*.ps
 
-          # Come back to the top project directory and copy the built PDF
-          # file here.
+#	  Come back to the top project directory and copy the built PDF
+#	  file here.
 	  cd "$$p"
 	  cp $(texbdir)/$*.pdf $@
 	fi