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, 117 insertions, 104 deletions

diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index bc73df8..7f0c514 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
 # Project initialization.
 #
-# 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
@@ -25,10 +25,10 @@
 # Basic directories that are used throughout the project.
 #
 # Locks are used to make sure that an operation is done in series not in
-# parallel (even if Make is run in parallel with the `-j' option). The most
+# parallel (even if Make is run in parallel with the '-j' option). The most
 # common case is downloads which are better done in series and not in
 # parallel. Also, some programs may not be thread-safe, therefore it will
-# be necessary to put a lock on them. This project uses the `flock' program
+# be necessary to put a lock on them. This project uses the 'flock' program
 # to achieve this.
 #
 # To help with modularity and clarity of the build directory (not mixing
@@ -43,7 +43,7 @@ bsdir=$(BDIR)/software
 texdir      = $(badir)/tex
 lockdir     = $(bsdir)/locks
 indir       = $(badir)/inputs
-prepdir     = $(padir)/prepare
+prepdir     = $(badir)/prepare
 mtexdir     = $(texdir)/macros
 installdir  = $(bsdir)/installed
 bashdir     = reproduce/analysis/bash
@@ -56,10 +56,10 @@ pconfdir    = reproduce/analysis/config
 # Preparation phase
 # -----------------
 #
-# This Makefile is loaded both for the `prepare' phase and the `make'
+# This Makefile is loaded both for the 'prepare' phase and the 'make'
 # phase. But the preparation files should be dealt with differently
-# (depending on the phase). In the `prepare' phase, the main directory
-# should be created, and in the `make' phase, its contents should be
+# (depending on the phase). In the 'prepare' phase, the main directory
+# should be created, and in the 'make' phase, its contents should be
 # loaded.
 #
 # If you don't need any preparation, please simply comment these lines.
@@ -87,6 +87,14 @@ endif
 # (independent parts of the paper can be added to it independently). To fix
 # this problem, when we are in a group setting, we'll use the user's ID to
 # create a separate LaTeX build directory for each user.
+#
+# The same logic applies to the final paper PDF: each user will create a
+# separte final PDF (for example 'paper-user1.pdf' and 'paper-user2.pdf')
+# and no 'paper.pdf' will be built. This isn't a problem because
+# 'initialize.tex' is a .PHONY prerequisite, so the rule to build the final
+# paper is always executed (even if it is present and nothing has
+# changed). So in terms of over-all efficiency and processing steps, this
+# doesn't change anything.
 ifeq (x$(GROUP-NAME),x)
 texbtopdir  = build
 else
@@ -104,7 +112,7 @@ tikzdir     = $(texbdir)/tikz
 # ---------------------------
 #
 # Before defining the local sub-environment here, we'll need to save the
-# system's environment for some scenarios (for example after `clean'ing the
+# system's environment for some scenarios (for example after 'clean'ing the
 # built programs).
 curdir   := $(shell echo $$(pwd))
 
@@ -117,16 +125,16 @@ curdir   := $(shell echo $$(pwd))
 #
 # We want the full recipe to be executed in one call to the shell. Also we
 # want Make to run the specific version of Bash that we have installed
-# during `./project configure' time.
+# during './project configure' time.
 #
 # Regarding the directories, this project builds its major dependencies
 # itself and doesn't use the local system's default tools. With these
 # environment variables, we are setting it to prefer the software we have
 # build here.
 #
-# `TEXINPUTS': we have to remove all possible user-specified directories to
-# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'),
-# we are also going to overwrite `TEXINPUTS' just before `pdflatex'.
+# 'TEXINPUTS': we have to remove all possible user-specified directories to
+# avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'),
+# we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'.
 .ONESHELL:
 .SHELLFLAGS = -ec
 export TERM=xterm
@@ -144,12 +152,12 @@ export LD_LIBRARY_PATH := $(installdir)/lib
 # will be empty.
 export CPATH := $(SYS_CPATH)
 
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
 
-# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because
+# OpenMPI can depend on an existing 'ssh' or 'rsh' binary. However, because
 # of security reasons, its best to not install them, disable any
 # remote-shell accesss through this environment variable.
 export OMPI_MCA_plm_rsh_agent=/bin/false
@@ -163,7 +171,7 @@ export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 # Python enviroment
 # -----------------
 #
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
 # have found several other Python-related environment variables on some
 # systems which might interfere. To be safe, we are removing all their
 # values.
@@ -187,10 +195,10 @@ export MPI_PYTHON3_SITEARCH   :=
 # directories (or possible sub-directories) for individual steps will be
 # defined and added within their own Makefiles.
 #
-# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the
+# The '.SUFFIXES' rule with no prerequisite is defined to eliminate all the
 # default implicit rules. The default implicit rules are to do with
-# programming (for example converting `.c' files to `.o' files). The
-# problem they cause is when you want to debug the make command with `-d'
+# programming (for example converting '.c' files to '.o' files). The
+# problem they cause is when you want to debug the make command with '-d'
 # option: they add too many extra checks that make it hard to find what you
 # are looking for in the outputs.
 .SUFFIXES:
@@ -201,8 +209,11 @@ $(lockdir): | $(bsdir); mkdir $@
 
 
 # Version and distribution tarball definitions
-project-commit-hash := $(shell if [ -d .git ]; then \
-    echo $$(git describe --dirty --always --long); else echo NOGIT; fi)
+project-commit-hash := $(shell \
+    if [ -d .git ]; then \
+      export LD_LIBRARY_PATH="$(installdir)/lib"; \
+      echo $$($(installdir)/bin/git describe --dirty --always --long); \
+    else echo NOGIT; fi)
 project-package-name := maneaged-$(project-commit-hash)
 project-package-contents = $(texdir)/$(project-package-name)
 
@@ -213,10 +224,10 @@ project-package-contents = $(texdir)/$(project-package-name)
 # High-level Makefile management
 # ------------------------------
 #
-# About `.PHONY': these are targets that must be built even if a file with
+# About '.PHONY': these are targets that must be built even if a file with
 # their name exists.
 #
-# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because
+# Only '$(mtexdir)/initialize.tex' corresponds to a file. This is because
 # we want to ensure that the file is always built in every run: it contains
 # the project version which may change between two separate runs, even when
 # no file actually differs.
@@ -229,14 +240,20 @@ texclean:
 	mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
 
 clean:
-        # Delete the top-level PDF file.
+#	Delete the top-level PDF file.
 	rm -f *.pdf
 
-        # Delete all the built outputs except the dependency
-        # programs. We'll use Bash's extended options builtin (`shopt') to
-        # enable "extended glob" (for listing of files). It allows extended
-        # features like ignoring the listing of a file with `!()' that we
-        # are using afterwards.
+#	Delete possible LaTeX output in top directory. This can happen when
+#	the user has run LaTeX with applications other than maneage. For
+#	example, when opening 'paper.tex' file with 'texstudio' and
+#	executing 'build'.
+	rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf
+
+#	Delete all the built outputs except the dependency programs. We'll
+#	use Bash's extended options builtin ('shopt') to enable "extended
+#	glob" (for listing of files). It allows extended features like
+#	ignoring the listing of a file with '!()' that we are using
+#	afterwards.
 	shopt -s extglob
 	rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
 	rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
@@ -244,14 +261,13 @@ clean:
 	rm -rf $(bsdir)/preparation-done.mk
 
 distclean: clean
-        #  Without cleaning the Git hooks, we won't be able to easily
-        #  commit or checkout after this task is done. So we'll remove them
-        #  first.
+#	Without cleaning the Git hooks, we won't be able to easily commit
+#	or checkout after this task is done. So we'll remove them first.
 	rm -f .git/hooks/post-checkout .git/hooks/pre-commit
 
-        # We'll be deleting the built environent programs and just need the
-        # `rm' program. So for this recipe, we'll use the host system's
-        # `rm', not our own.
+#	We'll be deleting the built environent programs and just need the
+#	'rm' program. So for this recipe, we'll use the host system's 'rm',
+#	not our own.
 	$$sys_rm -rf $(BDIR)
 	$$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
 
@@ -268,15 +284,15 @@ distclean: clean
 # without having to worry about the technicalities of the analysis.
 $(project-package-contents): paper.pdf | $(texdir)
 
-        # Set up the output directory, delete it if it exists and remake it
-        # to fill with new contents.
+#	Set up the output directory, delete it if it exists and remake it
+#	to fill with new contents.
 	dir=$@
 	rm -rf $$dir
 	mkdir $$dir
 	curdir=$$(pwd)
 
-        # Build a small Makefile to help in automatizing the paper building
-        # (including the bibliography).
+#	Build a small Makefile to help in automatizing the paper building
+#	(including the bibliography).
 	m=$$dir/Makefile
 	echo   "paper.pdf: paper.tex paper.bbl"                   > $$m
 	printf "\tlatex -shell-escape -halt-on-error paper\n"    >> $$m
@@ -291,94 +307,92 @@ $(project-package-contents): paper.pdf | $(texdir)
 	printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n"           >> $$m
 	printf "\trm -f *.blg *.log *.out *.run.xml\n"           >> $$m
 
-        # Copy the top-level contents (see next step for `paper.tex').
+#	Copy the top-level contents (see next step for 'paper.tex').
 	cp COPYING project README.md README-hacking.md $$dir/
 
-        # Since the packaging is mainly intended for high-level building of
-        # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
-        # the paper. This will disable usage of TiKZ.
+#	Since the packaging is mainly intended for high-level building of
+#	the PDF with LaTeX, we'll comment the 'makepdf' LaTeX macro in the
+#	paper. This will disable usage of TiKZ.
 	sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
 	    paper.tex > $$dir/paper.tex
 
-        # Copy ONLY the version-controlled files in 'reproduce' and
-        # 'tex/src'. This is important because files like 'LOCAL.conf' (in
-        # 'reproduce/software/config') should not be archived, they contain
-        # information about the host computer and are irrelevant for
-        # others. Also some project authors may have temporary files here
-        # that are not under version control and thus shouldn't be archived
-        # (although this is bad practice, but that is up to the user).
-        #
-        # To keep the sub-directory structure, we are packaging the files
-        # with Tar, piping it, and unpacking it in the archive
-        # directory. So afterwards we need to come back to the current
-        # directory.
+#	Copy ONLY the version-controlled files in 'reproduce' and
+#	'tex/src'. This is important because files like 'LOCAL.conf' (in
+#	'reproduce/software/config') should not be archived, they contain
+#	information about the host computer and are irrelevant for
+#	others. Also some project authors may have temporary files here
+#	that are not under version control and thus shouldn't be archived
+#	(although this is bad practice, but that is up to the user).
+#
+#	To keep the sub-directory structure, we are packaging the files
+#	with Tar, piping it, and unpacking it in the archive directory. So
+#	afterwards we need to come back to the current directory.
 	tar -c -f - $$(git ls-files peer-review reproduce tex/src) \
 	    | (cd $$dir ; tar -x -f -)
 	cd $(curdir)
 
-        # Build the other two subdirectories of 'tex/' that we need in the
-        # archive (in the actual project, these are symbolic links to the
-        # build directory).
+#	Build the other two subdirectories of 'tex/' that we need in the
+#	archive (in the actual project, these are symbolic links to the
+#	build directory).
 	mkdir $$dir/tex/tikz $$dir/tex/build
 
-        # Copy the 'tex/build' directory into the archive (excluding the
-        # temporary archive directory that we are now copying to). We will
-        # be using Bash's extended globbing ('extglob') for excluding this
-        # directory.
+#	Copy the 'tex/build' directory into the archive (excluding the
+#	temporary archive directory that we are now copying to). We will be
+#	using Bash's extended globbing ('extglob') for excluding this
+#	directory.
 	shopt -s extglob
 	cp -r tex/img                              $$dir/tex/img
 	cp tex/tikz/*.eps                          $$dir/tex/tikz
 	cp -r tex/build/!($(project-package-name)) $$dir/tex/build
 
-        # Clean up the $(texdir)/build* directories in the archive (when
-        # building in a group structure, there will be `build-user1',
-        # `build-user2' and etc). These are just temporary LaTeX build
-        # files and don't have any relevant/hand-written files in them.
+#	Clean up the $(texdir)/build* directories in the archive (when
+#	building in a group structure, there will be 'build-user1',
+#	'build-user2' and etc). These are just temporary LaTeX build files
+#	and don't have any relevant/hand-written files in them.
 	rm -rf $$dir/tex/build/build*
 
-        # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
-        # PGFPlots was used to generate them), copy them too.
+#	If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
+#	PGFPlots was used to generate them), copy them too.
 	if ls tex/tikz/*.pdf &> /dev/null; then
 	  cp tex/tikz/*.pdf $$dir/tex/tikz
 	fi
 
-        # When submitting to places like arXiv, they will just run LaTeX
-        # once and won't run `biber'. So we need to also keep the `.bbl'
-        # file into the distributing tarball. However, BibLaTeX is
-        # particularly sensitive to versioning (a `.bbl' file has to be
-        # read by the same BibLaTeX version that created it). This is hard
-        # to do with non-up-to-date places like arXiv. Therefore, we thus
-        # just copy the whole of BibLaTeX's source (the version we are
-        # using) into the top tarball directory. In this way, arXiv's LaTeX
-        # engine will use the same BibLaTeX version to interpret the `.bbl'
-        # file. TIP: you can use the same strategy for other LaTeX packages
-        # that may cause problems on the arXiv server.
+#	When submitting to places like arXiv, they will just run LaTeX once
+#	and won't run 'biber'. So we need to also keep the '.bbl' file into
+#	the distributing tarball. However, BibLaTeX is particularly
+#	sensitive to versioning (a '.bbl' file has to be read by the same
+#	BibLaTeX version that created it). This is hard to do with
+#	non-up-to-date places like arXiv. Therefore, we thus just copy the
+#	whole of BibLaTeX's source (the version we are using) into the top
+#	tarball directory. In this way, arXiv's LaTeX engine will use the
+#	same BibLaTeX version to interpret the '.bbl' file. TIP: you can
+#	use the same strategy for other LaTeX packages that may cause
+#	problems on the arXiv server.
 	cp tex/build/build/paper.bbl $$dir/
 	tltopdir=.local/texlive/maneage/texmf-dist/tex/latex
         #find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
         #     | xargs -0 cp -t $$dir
 
-        # Just in case the package users want to rebuild some of the
-        # figures (manually un-comment the `makepdf' command we commented
-        # above), correct the TikZ external directory, so the figures can
-        # be rebuilt.
+#	Just in case the package users want to rebuild some of the figures
+#	(manually un-comment the 'makepdf' command we commented above),
+#	correct the TikZ external directory, so the figures can be rebuilt.
 	pgfsettings="$$dir/tex/src/preamble-pgfplots.tex"
 	sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
 	mv $$pgfsettings.new $$pgfsettings
 
-        # PROJECT SPECIFIC
-        # ----------------
-        # Put any project-specific distribution steps here.
+#	PROJECT SPECIFIC
+#	----------------
+#	Put any project-specific distribution steps here.
 	cd $$curdir
 	cp tex/build/build/appendix.bbl $$dir/
-        # ----------------
+#	----------------
 
-        # Clean temporary files that may have been created by text editors.
+#	Clean temporary files that may have been created by text editors.
 	cd $(texdir)
 	find $(project-package-name) -name \*~ -delete
 	find $(project-package-name) -name \*.swp -delete
 
-# Package into `.tar.gz' or '.tar.lz'.
+# Package into '.tar.gz' or '.tar.lz'.
 dist dist-lzip: $(project-package-contents)
 	curdir=$$(pwd)
 	cd $(texdir)
@@ -394,7 +408,7 @@ dist dist-lzip: $(project-package-contents)
 	cd $$curdir
 	mv $(texdir)/$(project-package-name).tar.$$suffix ./
 
-# Package into `.zip'.
+# Package into '.zip'.
 dist-zip: $(project-package-contents)
 	curdir=$$(pwd)
 	cd $(texdir)
@@ -495,13 +509,13 @@ print-general-metadata = \
 # This file will store some basic info about the project that is necessary
 # for the final PDF. Since these are not version controlled, it must be
 # calculated everytime the project is run. So even though this file
-# actually exists, it is also aded as a `.PHONY' target above.
+# actually exists, it is also aded as a '.PHONY' target above.
 $(mtexdir)/initialize.tex: | $(mtexdir)
 
-        # Version and title of project. About the starting '@': since these
-        # commands are run every time with './project make', it is annoying
-        # to print them on the standard output every time. With the '@',
-        # make will not print the commands that it runs in this recipe.
+#	Version and title of project. About the starting '@': since these
+#	commands are run every time with './project make', it is annoying
+#	to print them on the standard output every time. With the '@', make
+#	will not print the commands that it runs in this recipe.
 	@d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}')
 	echo "\newcommand{\projectdate}{$$d}" > $@
 	echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
@@ -514,16 +528,15 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	v=$$(echo $(metadata-doi-zenodo) | sed -e's/\./ /g' | awk '{print $$NF}')
 	echo "\newcommand{\projectzenodoid}{$$v}" >> $@
 
-        # Calculate the latest Maneage commit used to build this
-        # project:
-        #  - The project may not have the 'maneage' branch (for example
-        #    after cloning from a fork that didn't include it!). In this
-        #    case, we'll print a descriptive warning, telling the user what
-        #    should be done (reporting the last merged commit and its date
-        #    is very useful for the future).
-        #  - The '--dirty' option (used in 'project-commit-hash') isn't
-        #    applicable to "commit-ishes" (direct quote from Git's error
-        #    message!).
+#	Calculate the latest Maneage commit used to build this project:
+#	  - The project may not have the 'maneage' branch (for example
+#	    after cloning from a fork that didn't include it!). In this
+#	    case, we'll print a descriptive warning, telling the user what
+#	    should be done (reporting the last merged commit and its date
+#	    is very useful for the future).
+#	  - The '--dirty' option (used in 'project-commit-hash') isn't
+#	    applicable to "commit-ishes" (direct quote from Git's error
+#	    message!).
 	if git log maneage -1 &> /dev/null; then
 	  c=$$(git merge-base HEAD maneage)
 	  v=$$(git describe --always --long $$c)