7 files changed, 85 insertions, 45 deletions
diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk
index 325280d..a20abc6 100644
--- a/reproduce/analysis/make/delete-me.mk
+++ b/reproduce/analysis/make/delete-me.mk
@@ -1,6 +1,6 @@
 # Dummy Makefile to create a random dataset for plotting.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 9e8db4a..b57b3a9 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
 # Project initialization.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -41,7 +41,7 @@ bsdir=$(BDIR)/software
 # Derived directories (the locks directory can be shared with software
 # which already has this directory.).
 texdir      = $(badir)/tex
-lockdir     = $(bsdir)/locks
+lockdir     = $(badir)/.locks
 indir       = $(badir)/inputs
 prepdir     = $(badir)/prepare
 mtexdir     = $(texdir)/macros
@@ -73,7 +73,7 @@ pconfdir    = reproduce/analysis/config
 ifeq (x$(project-phase),xprepare)
 $(prepdir):; mkdir $@
 else
--include $(bsdir)/preparation-done.mk
+-include $(badir)/preparation-done.mk
 ifeq (x$(include-prepare-results),xyes)
 -include $(prepdir)/*.mk $(prepdir)/*.conf
 endif
@@ -265,16 +265,8 @@ clean:
 #	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))
-	rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/*
-	rm -rf $(bsdir)/preparation-done.mk
+#	Delete the full 'badir' (containing all analysis outputs).
+	rm -rf $(badir)
 
 distclean: clean
 #	Without cleaning the Git hooks, we won't be able to easily commit
@@ -285,7 +277,7 @@ distclean: clean
 #	'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
+	$$sys_rm -f .local .build
 
 
 
@@ -329,12 +321,11 @@ $(project-package-contents): paper.pdf | $(texdir)
 	    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).
+#	'tex/src'. This is important because the git commit hash goes in
+#	the tarball name (should correspond to it) and 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
@@ -362,17 +353,20 @@ $(project-package-contents): paper.pdf | $(texdir)
 	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.
+#	PGFPlots was used to generate them), copy them too. Note that in
+#	the main project source, 'tex/tikz' is just a symbolic link to
+#	'tex/build/tikz'. But inside the tarball we do not want to have
+#	symbolic links and they should be independent.
 	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
+#	and won't run 'biber' or 'biblatex'. 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 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
@@ -469,7 +463,7 @@ dist-software:
 # process with a file and make sure that only one downloading event is in
 # progress at every moment.
 $(indir):; mkdir $@
-downloadwrapper = $(bashdir)/download-multi-try
+downloadwrapper = $(bashdir)/download-multi-try.sh
 inputdatasets := $(foreach i, \
                    $(patsubst INPUT-%-sha256,%, \
                      $(filter INPUT-%-sha256,$(.VARIABLES))) \
@@ -521,7 +515,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
 #	    Unrecognized format.
 	    *)
-	    echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;;
+	    printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! "
+	    printf "Please see the description of this variable in "
+	    printf "'$(bsdir)/config/LOCAL.conf' for the acceptable "
+	    printf "values."; exit 1;;
 	  esac
 	fi
 
@@ -672,7 +669,7 @@ print-general-metadata = \
 # 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.
-$(mtexdir)/initialize.tex: | $(mtexdir)
+$(mtexdir)/initialize.tex:
 
 #	Version and title of project. About the starting '@': since these
 #	commands are run every time with './project make', it is annoying
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 791108b..a399637 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) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -18,6 +18,7 @@
 
 
 
+
 # LaTeX macros for paper
 # ----------------------
 #
@@ -92,6 +93,38 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
 
 
+# TeX build directory
+# -------------------
+#
+# If built in a group scenario, the TeX build directory must be separate
+# for each member (so they can work on their relevant parts of the paper
+# without conflicting with each other).
+ifeq ($(strip $(maneage_group_name)),)
+texbdir:=$(texdir)/build
+else
+texbdir:=$(texdir)/build-$(shell whoami)
+endif
+tikzdir:=$(texbdir)/tikz
+
+
+
+
+
+# Software info in TeX
+# --------------------
+#
+# The information of the installed software is placed in the
+# '.build/software' directory (which the TeX build should not depend
+# on). Therefore, we should copy those macros here in the LaTeX build
+# directory, so the TeX directory is completely independent from each
+# other.
+$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
+	cp $(bsdir)/config/*.tex $(mtexdir)/
+
+
+
+
+
 # The bibliography
 # ----------------
 #
@@ -104,8 +137,9 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 # recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
+$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \
                       | $(mtexdir)/project.tex
+
 #	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
@@ -128,9 +162,13 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 #	  use PGFPlots, then you should remove the '-shell-escape' option
 #	  for better security. See https://savannah.nongnu.org/task/?15694
 #	  for details.
+#
+#	  We need the modification to 'LD_LIBRARY_PATH' because we do not
+#	  build LaTeX from source and it (or its packages) may use
+#	  '/bin/sh' (among other possible system-wide things).
+	  export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 	  biber paper
-
 	fi
 
 
@@ -158,6 +196,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
 #	  See above for a warning and brief discussion on the the pdflatex
 #	  option '-shell-escape'.
+#
+#	  We need the modification to 'LD_LIBRARY_PATH' because we do not
+#	  build LaTeX from source and it (or its packages) may use
+#	  '/bin/sh' (among other possible system-wide things).
+	  export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 
 #	  Come back to the top project directory and copy the built PDF
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index 36f5294..ffb2a3c 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
 # Basic preparations, called by './project make'.
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
@@ -25,7 +25,7 @@
 #
 # We need to remove the 'prepare' word from the list of 'makesrc'.
 prepare-dep = $(filter-out prepare, $(makesrc))
-$(bsdir)/preparation-done.mk: \
+$(badir)/preparation-done.mk: \
                 $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
 
 #	If you need to add preparations (mainly automatically generated
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 460433b..e87aed8 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -1,6 +1,6 @@
 # Top-level Makefile (first to be loaded).
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -19,9 +19,9 @@
 
 
 
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf
 
 
 
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index 930c2a9..d2d1c14 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -4,7 +4,7 @@
 # are not included here. Please see that file for thorough comments on each
 # step.
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
@@ -23,9 +23,9 @@
 
 
 
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf
 
 
 
@@ -36,7 +36,7 @@ include reproduce/software/config/LOCAL.conf
 #
 # See 'top-make.mk' for complete explanation.
 ifeq (x$(maneage_group_name),x$(GROUP-NAME))
-all: $(BDIR)/software/preparation-done.mk
+all: $(BDIR)/analysis/preparation-done.mk
 	@echo "Project preparation is complete.";
 else
 all:
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index aa026b5..c74f8ca 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -1,6 +1,6 @@
 # Verify the project outputs before building the paper.
 #
-# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 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