From 6ef4cc854d1df46b719de5d66b45537b0aa11f92 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 28 Jul 2019 02:32:20 +0100
Subject: Single wrapper instead of old ./configure, Makefile and ./for-group

Until now, to work on a project, it was necessary to `./configure' it and
build the software. Then we had to run `.local/bin/make' to run the project
and do the analysis every time. If the project was a shared project between
many users on a large server, it was necessary to call the `./for-group'
script.

This way of managing the project had a major problem: since the user
directly called the lower-level `./configure' or `.local/bin/make' it was
not possible to provide high-level control (for example limiting the
environment variables). This was especially noticed recently with a bug
that was related to environment variables (bug #56682).

With this commit, this problem is solved using a single script called
`project' in the top directory. To configure and build the project, users
can now run these commands:

   $ ./project configure
   $ ./project make

To work on the project with other users in a group these commands can be
used:

  $ ./project configure --group=GROUPNAME
  $ ./project make      --group=GROUPNAME

The old options to both configure and make the project are still valid. Run
`./project --help' to see a list. For example:

  $ ./project configure -e --host-cc
  $ ./project make -j8

The old `configure' script has been moved to
`reproduce/software/bash/configure.sh' and is called by the new `./project'
script. The `./project' script now just manages the options, then passes
control to the `configure.sh' script. For the "make" step, it also reads
the options, then calls Make. So in the lower-level nothing has
changed. Only the `./project' script is now the single/direct user
interface of the project.

On a parallel note: as part of bug #56682, we also found out that on some
macOS systems, the `DYLD_LIBRARY_PATH' environment variable has to be set
to blank. This is no problem because RPATH is automatically set in macOS
and the executables and libraries contain the absolute address of the
libraries they should link with. But having `DYLD_LIBRARY_PATH' can
conflict with some low-level system libraries and cause very hard to debug
linking errors (like that reported in the bug report).

This fixes bug #56682.
---
 reproduce/analysis/make/initialize.mk              |   20 +-
 reproduce/analysis/make/paper.mk                   |    6 +-
 reproduce/analysis/make/top.mk                     |   12 +-
 reproduce/software/bash/configure.sh               | 1224 ++++++++++++++++++++
 reproduce/software/config/installation/LOCAL.mk.in |    4 +-
 reproduce/software/make/atlas-multiple.mk          |    4 +-
 reproduce/software/make/atlas-single.mk            |    4 +-
 reproduce/software/make/basic.mk                   |   10 +-
 reproduce/software/make/high-level.mk              |   13 +-
 reproduce/software/make/python.mk                  |    4 +-
 10 files changed, 1269 insertions(+), 32 deletions(-)
 create mode 100755 reproduce/software/bash/configure.sh

(limited to 'reproduce')

diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index d2b026e..f8a09e6 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -84,8 +84,6 @@ 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
 # built programs).
-sys-path := $(PATH)
-sys-rm   := $(shell which rm)
 curdir   := $(shell echo $$(pwd))
 
 
@@ -97,7 +95,7 @@ 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 `./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
@@ -116,7 +114,11 @@ export LDFLAGS := -L$(installdir)/lib
 export SHELL := $(installdir)/bin/bash
 export CPPFLAGS := -I$(installdir)/include
 export LD_LIBRARY_PATH := $(installdir)/lib
-export DYLD_LIBRARY_PATH := $(installdir)/lib
+
+# 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 :=
 
 
 
@@ -190,15 +192,17 @@ clean: clean-mmap
         # features like ignoring the listing of a file with `!()' that we
         # are using afterwards.
 	shopt -s extglob
-	rm -rf $(BDIR)/!(software)
+	rm -rf $(BDIR)/tex/macros/!(dependencies.tex|dependencies-bib.tex)
+	rm -rf $(BDIR)/!(software|tex) $(BDIR)/tex/!(macros|build)
+	rm -rf $(BDIR)/tex/build/!(tikz) $(BDIR)/tex/build/tikz/*
 
 distclean: clean
         # 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 Makefile .gnuastro .local .build
-	$(sys-rm) -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf
+	$$sys-rm -rf $(BDIR)
+	$$sys-rm -f Makefile .gnuastro .local .build
+	$$sys-rm -f $(pconfdir)/LOCAL.mk $(gconfdir)/gnuastro-local.conf
 
 
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index c17028a..436bac4 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -64,11 +64,9 @@ $(mtexdir)/project.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s)
 	    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)."
+	    echo "'./project configure -e' when you have internet access."
 	  else
-	    echo "For more, run './.local/bin/make more-on-building-pdf=1'"
+	    echo "For more, run './project make more-on-building-pdf=1'"
 	  fi
 	  echo
 	  echo "" > $@
diff --git a/reproduce/analysis/make/top.mk b/reproduce/analysis/make/top.mk
index b753979..7d20800 100644
--- a/reproduce/analysis/make/top.mk
+++ b/reproduce/analysis/make/top.mk
@@ -19,7 +19,8 @@
 
 
 
-# Load the local configuration (created after running `./configure').
+# Load the local configuration (created after running
+# `./project configure').
 include reproduce/software/config/installation/LOCAL.mk
 
 
@@ -49,9 +50,8 @@ include reproduce/software/config/installation/LOCAL.mk
 #
 # Controlling this requires two variables that are available at this stage:
 #
-#   - `GROUP-NAME': from `LOCAL.mk' (which was built by `./configure').
-#   - `reproducible_paper_group_name': from the `./for-group' script (if it
-#     was used to call Make).
+#   - `GROUP-NAME': from `LOCAL.mk' (which was built by `./project configure').
+#   - `reproducible_paper_group_name': value to the `--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
 # when the project isn't being built for a group, both variables will be an
@@ -70,10 +70,10 @@ else
 all:
 	@if [ "x$(GROUP-NAME)" = x ]; then \
 	  echo "Project is NOT configured for groups, please run"; \
-	  echo "   $$ .local/bin/make"; \
+	  echo "   $$ ./project make"; \
 	else \
 	  echo "Project is configured for groups, please run"; \
-	  echo "   $$ ./for-group $(GROUP-NAME) make -j8"; \
+	  echo "   $$ ./project make --group=$(GROUP-NAME) -j8"; \
 	fi
 endif
 
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
new file mode 100755
index 0000000..65b728e
--- /dev/null
+++ b/reproduce/software/bash/configure.sh
@@ -0,0 +1,1224 @@
+#! /bin/bash
+#
+# Necessary preparations/configurations for the reproducible project.
+#
+# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# This script 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 script 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/>.
+
+
+# Script settings
+# ---------------
+# Stop the script if there are any errors.
+set -e
+
+
+
+
+
+# Internal directories
+# --------------------
+#
+# These are defined to help make this script more readable.
+topdir=$(pwd)
+optionaldir="/optional/path"
+adir=reproduce/analysis/config
+cdir=reproduce/software/config
+
+sbdir=$cdir/installation
+
+pconf=$sbdir/LOCAL.mk
+ptconf=$sbdir/LOCAL_tmp.mk
+poconf=$sbdir/LOCAL_old.mk
+depverfile=$cdir/installation/versions.mk
+# --------- Delete for no Gnuastro ---------
+glconf=$cdir/gnuastro/gnuastro-local.conf
+# ------------------------------------------
+
+
+
+
+
+# Notice for top of generated files
+# ---------------------------------
+#
+# In case someone opens the files output from the configuration scripts in
+# a text editor and wants to edit them, it is important to let them know
+# that their changes are not going to be permenant.
+function create_file_with_notice() {
+    if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
+    then
+        echo "#"                                                      >> "$1"
+        echo "# This file was created during configuration"           >> "$1"
+        echo "# ('./project configure'). Therefore, it is not under"  >> "$1"
+        echo "# version control and any manual changes to it will be" >> "$1"
+        echo "# over-written if the project re-configured."           >> "$1"
+        echo "#"                                                      >> "$1"
+    else
+        echo; echo "Can't write to $1"; echo;
+        exit 1
+    fi
+}
+
+
+
+
+
+# Get absolute address
+# --------------------
+#
+# Since the build directory will go into a symbolic link, we want it to be
+# an absolute address. With this function we can make sure of that.
+function absolute_dir() {
+    if stat "$1" 1> /dev/null; then
+        echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
+    else
+        exit 1;
+    fi
+}
+
+
+
+
+
+# Inform the user
+# ---------------
+#
+# Print some basic information so the user gets a feeling of what is going
+# on and is prepared on what will happen next.
+cat <<EOF
+
+-----------------------------
+Project's local configuration
+-----------------------------
+
+Local configuration includes things like top-level directories, or
+processing steps. It is STRONGLY recommended to read the comments, and set
+the best values for your system (where necessary).
+
+EOF
+
+
+
+
+
+# What to do with possibly existing configuration file
+# ----------------------------------------------------
+#
+# `LOCAL.mk' is the top-most local configuration for the project. If it
+# already exists when this script is run, we'll make a copy of it as backup
+# (for example the user might have ran `./project configure' by mistake).
+printnotice=yes
+rewritepconfig=yes
+rewritegconfig=yes
+if [ -f $pconf ] || [ -f $glconf ]; then
+    if [ $existing_conf = 1 ]; then
+        printnotice=no
+        if [ -f $pconf  ]; then rewritepconfig=no; fi
+        if [ -f $glconf ]; then rewritegconfig=no; fi
+    fi
+fi
+
+
+
+
+# Make sure the group permissions satisfy the previous configuration (if it
+# exists and we don't want to re-write it).
+if [ $rewritepconfig = no ]; then
+    oldgroupname=$(awk '/GROUP-NAME/ {print $3; exit 0}' $pconf)
+    if [ "x$oldgroupname" = "x$reproducible_paper_group_name" ]; then
+        just_a_place_holder_to_avoid_not_equal_test=1;
+    else
+        echo "-----------------------------"
+        echo "!!!!!!!!    ERROR    !!!!!!!!"
+        echo "-----------------------------"
+        if [ "x$oldgroupname" = x ]; then
+            status="NOT configured for groups"
+            confcommand="./project configure"
+        else
+            status="configured for '$oldgroupname' group"
+            confcommand="./project configure --group=$oldgroupname"
+        fi
+        echo "Project was previously $status!"
+        echo "Either enable re-write of this configuration file,"
+        echo "or re-run this configuration like this:"
+        echo
+        echo "   $confcommand"; echo
+        exit 1
+    fi
+fi
+
+
+
+
+
+# Identify the downloader tool
+# ----------------------------
+#
+# After this script finishes, we will have both Wget and cURL for
+# downloading any necessary dataset during the processing. However, to
+# complete the configuration, we may also need to download the source code
+# of some necessary software packages (including the downloaders). So we
+# need to check the host's available tool for downloading at this step.
+if [ $rewritepconfig = yes ]; then
+    if type wget > /dev/null 2>/dev/null; then
+        name=$(which wget)
+
+        # By default Wget keeps the remote file's timestamp, so we'll have
+        # to disable it manually.
+        downloader="$name --no-use-server-timestamps -O";
+    elif type curl > /dev/null 2>/dev/null; then
+        name=$(which curl)
+
+        # - cURL doesn't keep the remote file's timestamp by default.
+        # - With the `-L' option, we tell cURL to follow redirects.
+        downloader="$name -L -o"
+    else
+        cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+Couldn't find GNU Wget, or cURL on this system. These programs are used for
+downloading necessary programs and data if they aren't already present (in
+directories that you can specify with this configure script). Therefore if
+the necessary files are not present, the project will crash.
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+        downloader="no-downloader-found"
+    fi;
+fi
+
+
+
+
+
+# Build directory
+# ---------------
+if [ $rewritepconfig = yes ]; then
+    cat <<EOF
+
+===============
+Build directory
+===============
+
+The project's "source" (this directory) and "build" directories are treated
+separately. This greatly helps in managing the many intermediate files that
+are created during the build. The intermediate build files don't need to be
+archived or backed up: you can always re-build them with the contents of
+the source directory. The build directory also needs a relatively large
+amount of free space (atleast serveral Giga-bytes), while the source
+directory (all plain text) will usually be a mega-byte or less.
+
+'.build' (a symbolic link to the build directory) will also be created
+during this configuration. It can help encourage you to set the actual
+build directory in a very different address from this one (one that can be
+deleted and has large volume), while having easy access to it from here.
+
+EOF
+    bdir=
+    junkname=pure-junk-974adfkj38
+    while [ x$bdir == x ]
+    do
+        # Ask the user (if not already set on the command-line).
+        if [ x"$build_dir" = x ]; then
+            read -p"Please enter the top build directory: " build_dir
+        fi
+
+        # If it exists, see if we can write in it. If not, try making it.
+        if [ -d $build_dir ]; then
+            if mkdir $build_dir/$junkname 2> /dev/null; then
+                bdir=$(absolute_dir $build_dir)
+                echo " -- Build directory: '$bdir'"
+                rm -rf $build_dir/$junkname
+            else
+                echo " -- Can't write in '$build_dir'"
+            fi
+        else
+            if mkdir $build_dir 2> /dev/null; then
+                bdir=$(absolute_dir $build_dir)
+                echo " -- Build directory set to (the newly created): '$bdir'"
+            else
+                echo " -- Can't create '$build_dir'"
+            fi
+        fi
+
+        # Reset `build_dir' to blank, so it continues asking when the
+        # previous value wasn't usable.
+        build_dir=
+    done
+fi
+
+
+
+
+
+# Input directory
+# ---------------
+if [ x"$input_dir" = x ]; then
+    indir=$optionaldir
+else
+    indir=$input_dir
+fi
+wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.mk)
+wfpc2md5=$(awk  '!/^#/ && $1=="WFPC2MD5"   {print $3}' $adir/INPUTS.mk)
+wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE"  {print $3}' $adir/INPUTS.mk)
+wfpc2url=$(awk  '!/^#/ && $1=="WFPC2URL"   {print $3}' $adir/INPUTS.mk)
+if [ $rewritepconfig = yes ] && [ x"$input_dir" = x ]; then
+    cat <<EOF
+
+----------------------------------
+(OPTIONAL) Input dataset directory
+----------------------------------
+
+This project needs the dataset(s) listed below. If you already have them,
+please specify the directory hosting them on this system. If you don't,
+they will be downloaded automatically. Each file is shown with its total
+volume and its 128-bit MD5 checksum in parenthesis.
+
+  $wfpc2name ($wfpc2size, $wfpc2md5):
+    A 100x100 Hubble Space Telescope WFPC II image used in the FITS
+    standard webpage as a demonstration of this file format.
+    URL: $wfpc2url/$wfpc2name
+
+NOTE I: This directory, or the datasets above, are optional. If it doesn't
+exist, the files will be downloaded in the build directory and used.
+
+NOTE II: This directory (if given) will only be read, nothing will be
+written into it, so no writing permissions are necessary.
+
+TIP: If you have these files in multiple directories on your system and
+don't want to download them or make duplicates, you can create symbolic
+links to them and put those symbolic links in the given top-level
+directory.
+
+EOF
+    read -p"(OPTIONAL) Input datasets directory ($indir): " inindir
+    if [ x$inindir != x ]; then
+        indir=$inindir
+        echo " -- Using '$indir'"
+    fi
+fi
+
+
+
+
+
+# Dependency tarball directory
+# ----------------------------
+if [ x"$software_dir" = x ]; then
+    ddir=$optionaldir
+else
+    ddir=$software_dir
+fi
+if [ $rewritepconfig = yes ] && [ x"$software_dir" = x ]; then
+    cat <<EOF
+
+---------------------------------------
+(OPTIONAL) Software tarball directory
+---------------------------------------
+
+To ensure an identical build environment, the project will use its own
+build of the programs it needs. Therefore the tarball of the relevant
+programs are necessary. If a tarball isn't present in the specified
+directory, *IT WILL BE DOWNLOADED* automatically.
+
+If you don't specify any directory here, or it doesn't contain the tarball
+of a dependency, it is necessary to have an internet connection. The
+project will download the tarballs it needs automatically.
+
+EOF
+    read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir
+    if [ x"$tmpddir" != x ]; then
+        ddir=$tmpddir
+        echo " -- Using '$ddir'"
+    fi
+fi
+
+
+
+
+
+# Write the parameters into the local configuration file.
+if [ $rewritepconfig = yes ]; then
+
+    # Add commented notice.
+    create_file_with_notice $pconf
+
+    # Write the values.
+    sed -e's|@bdir[@]|'"$bdir"'|' \
+        -e's|@indir[@]|'"$indir"'|' \
+        -e's|@ddir[@]|'"$ddir"'|' \
+        -e's|@downloader[@]|'"$downloader"'|' \
+        -e's|@groupname[@]|'"$reproducible_paper_group_name"'|' \
+        $pconf.in >> $pconf
+else
+    # Read the values from existing configuration file.
+    inbdir=$(awk '$1=="BDIR" {print $3}' $pconf)
+
+    # Read the software directory.
+    ddir=$(awk '$1=="DEPENDENCIES-DIR" {print $3}' $pconf)
+
+    # The downloader command may contain multiple elements, so we'll just
+    # change the (in memory) first and second tokens to empty space and
+    # write the full line (the original file is unchanged).
+    downloader=$(awk '$1=="DOWNLOADER" {$1=""; $2=""; print $0}' $pconf)
+
+    # Make sure all necessary variables have a value
+    err=0
+    verr=0
+    novalue=""
+    if [ x"$inbdir"     = x ]; then novalue="BDIR, ";              fi
+    if [ x"$downloader" = x ]; then novalue="$novalue"DOWNLOADER;  fi
+    if [ x"$novalue"   != x ]; then verr=1; err=1;                 fi
+
+    # Make sure `bdir' is an absolute path and it exists.
+    berr=0
+    ierr=0
+    bdir=$(absolute_dir $inbdir)
+
+    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
+    if [ $err = 1 ]; then
+        cat <<EOF
+
+#################################################################
+########  ERORR reading existing configuration file  ############
+#################################################################
+EOF
+        if [ $verr = 1 ]; then
+            cat <<EOF
+
+These variables have no value: $novalue.
+EOF
+        fi
+        if [ $berr = 1 ]; then
+           cat <<EOF
+
+Couldn't create the build directory '$bdir' (value to 'BDIR') in
+'$pconf'.
+EOF
+        fi
+
+        cat <<EOF
+
+Please run the configure script again (accepting to re-write existing
+configuration file) so all the values can be filled and checked.
+#################################################################
+EOF
+    fi
+fi
+
+
+
+
+
+# --------- Delete for no Gnuastro ---------
+# Get the version of Gnuastro that must be used.
+gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile)
+
+# Gnuastro's local configuration settings
+if [ $rewritegconfig = yes ]; then
+    create_file_with_notice $glconf
+    echo "# Minimum number of bytes to use HDD/SSD instead of RAM." >> $glconf
+    echo " minmapsize $minmapsize"                                  >> $glconf
+    echo                                                            >> $glconf
+    echo "# Version of Gnuastro that must be used."                 >> $glconf
+    echo " onlyversion $gversion"                                   >> $glconf
+else
+    ingversion=$(awk '$1=="onlyversion" {print $NF}' $glconf)
+    if [ x$ingversion != x$gversion ]; then
+           cat <<EOF
+______________________________________________________
+!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!
+
+Gnuastro's version in '$glconf' ($ingversion) doesn't match the tarball
+version that this project was designed to use in '$depverfile'
+($gversion). Please re-run after removing the former file:
+
+   $ rm $glconf
+   $ ./project configure
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+        exit 1
+    fi
+fi
+# ------------------------------------------
+
+
+
+
+
+# Delete final configuration target
+# ---------------------------------
+#
+# We only want to start running the project later if this script has
+# completed successfully. To make sure it hasn't crashed in the middle
+# (without the user noticing), in the end of this script we make a file and
+# we'll delete it here (at the start). Therefore if the script crashed in
+# the middle that file won't exist.
+sdir=$bdir/software
+finaltarget=$sdir/configuration-done.txt
+if ! [ -d $sdir ];  then mkdir $sdir; fi
+rm -f $finaltarget
+
+
+
+
+
+# Project's top-level directories
+# -------------------------------
+#
+# These directories are possibly needed by many steps of process, so to
+# avoid too many directory dependencies throughout the software and
+# analysis Makefiles (thus making them hard to read), we are just building
+# them here
+# Software tarballs
+tardir=$sdir/tarballs
+if ! [ -d $tardir ];  then mkdir $tardir; fi
+
+# Installed software
+instdir=$sdir/installed
+if ! [ -d $instdir ]; then mkdir $instdir; fi
+
+# To record software versions and citation.
+verdir=$instdir/version-info
+if ! [ -d $verdir ]; then mkdir $verdir; fi
+
+# Program and library versions and citation.
+ibidir=$verdir/proglib
+if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+
+# Python module versions and citation.
+ipydir=$verdir/python
+if ! [ -d $ipydir ]; then mkdir $ipydir; fi
+
+# Used software BibTeX entries.
+ictdir=$verdir/cite
+if ! [ -d $ictdir ]; then mkdir $ictdir; fi
+
+# TeXLive versions.
+itidir=$verdir/tex
+if ! [ -d $itidir ]; then mkdir $itidir; fi
+
+# Top-level LaTeX.
+texdir=$bdir/tex
+if ! [ -d $texdir ]; then mkdir $texdir; fi
+
+# LaTeX macros.
+mtexdir=$texdir/macros
+if ! [ -d $mtexdir ]; then mkdir $mtexdir; fi
+
+
+# TeX build directory. If built in a group scenario, the TeX build
+# directory must be separate for each member (so they can work on their
+# relevant parts of the paper without conflicting with each other).
+if [ "x$reproducible_paper_group_name" = x ]; then
+    texbdir=$texdir/build
+else
+    user=$(whoami)
+    texbdir=$texdir/build-$user
+fi
+if ! [ -d $texbdir ]; then mkdir $texbdir; fi
+
+# TiKZ (for building figures within LaTeX).
+tikzdir=$texbdir/tikz
+if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
+
+
+# Set the symbolic links for easy access to the top project build
+# directories. Note that these are put in each user's source/cloned
+# directory, not in the build directory (which can be shared between many
+# users and thus may already exist).
+#
+# Note: if we don't delete them first, it can happen that an extra link
+# will be created in each directory that points to its parent. So to be
+# safe, we are deleting all the links on each re-configure of the project.
+rm -f .build .local tex/build tex/tikz .gnuastro
+ln -s $bdir .build
+ln -s $instdir .local
+ln -s $texdir tex/build
+ln -s $tikzdir tex/tikz
+# --------- Delete for no Gnuastro ---------
+ln -s $topdir/reproduce/software/config/gnuastro .gnuastro
+# ------------------------------------------
+
+
+# Temporary software un-packing/build directory: if the host has the
+# standard `/dev/shm' mounting-point, we'll do it in shared memory (on the
+# RAM), to avoid harming/over-using the HDDs/SSDs. The RAM of most systems
+# today (>8GB) is large enough for the parallel building of the software.
+#
+# For the name of the directory under `/dev/shm' (for this project), we'll
+# use the names of the two parent directories to the current/running
+# directory, separated by a `-' instead of `/'. We'll then appended that
+# with the user's name (in case multiple users may be working on similar
+# project names). Maybe later, we can use something like `mktemp' to add
+# random characters to this name and make it unique to every run (even for
+# a single user).
+tmpblddir=$sdir/build-tmp
+rm -rf $tmpblddir/* $tmpblddir  # If its a link, we need to empty its
+                                # contents first, then itself.
+
+# Set the top-level shared memory location.
+if [ -d /dev/shm ]; then     shmdir=/dev/shm
+else                         shmdir=""
+fi
+
+# If a shared memory mounted directory exists and there is enough space
+# there (in RAM), build a temporary directory for this project.
+needed_space=2000000
+if [ x"$shmdir" != x ]; then
+    available_space=$(df $shmdir | awk 'NR==2{print $4}')
+    if [ $available_space -gt $needed_space ]; then
+        dirname=$(pwd | sed -e's/\// /g' \
+                      | awk '{l=NF-1; printf("%s-%s",$l, $NF)}')
+        tbshmdir=$shmdir/"$dirname"-$(whoami)
+        if ! [ -d $tbshmdir ]; then mkdir $tbshmdir; fi
+    fi
+else
+    tbshmdir=""
+fi
+
+# If a shared memory directory was created set `build-tmp' to be a
+# symbolic link to it. Otherwise, just build the temporary build
+# directory under the project build directory.
+if [ x$tbshmdir = x ]; then mkdir $tmpblddir;
+else                        ln -s $tbshmdir $tmpblddir;
+fi
+
+
+
+
+
+# Check for C/C++ compilers
+# -------------------------
+#
+# To build the software, we'll need some basic tools (the compilers in
+# particular) to be present.
+hascc=0;
+if type cc > /dev/null 2>/dev/null; then
+    if type c++ > /dev/null 2>/dev/null; then hascc=1; fi
+else
+    if type gcc > /dev/null 2>/dev/null; then
+        if type g++ > /dev/null 2>/dev/null; then hascc=1; fi
+    else
+        if type clang > /dev/null 2>/dev/null; then
+            if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi
+        fi
+    fi
+fi
+if [ $hascc = 0 ]; then
+    cat <<EOF
+______________________________________________________
+!!!!!!!       C/C++ Compiler NOT FOUND         !!!!!!!
+
+To build the project's software, the host system needs to have basic C and
+C++ compilers. The executables that were checked are 'cc', 'gcc' and
+'clang' for a C compiler, and 'c++', 'g++' and 'clang++' for a C++
+compiler. If you have a relevant compiler that is not checked, please get
+in touch with us (with the form below) so we add it:
+
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    exit 1
+fi
+
+
+
+
+
+# See if the C compiler can build static libraries
+# ------------------------------------------------
+
+# We are manually only working with shared libraries: because some
+# high-level programs like Wget and cURL need dynamic linking and if we
+# build the libraries statically, our own builds will be ignored and these
+# programs will go and find their necessary libraries on the host system.
+#
+# Another good advantage of shared libraries is that we can actually use
+# the shared library tool of the system (`ldd' with GNU C Library) and see
+# exactly where each linked library comes from. But in static building,
+# unless you follow the build closely, its not easy to see if the source of
+# the library came from the system or our build.
+static_build=no
+
+#oprog=$sdir/static-test
+#cprog=$sdir/static-test.c
+#echo "#include <stdio.h>"          > $cprog
+#echo "int main(void) {return 0;}" >> $cprog
+#if [ x$CC = x ]; then CC=gcc; fi;
+#if $CC $cprog -o$oprog -static &> /dev/null; then
+#    export static_build="yes"
+#else
+#    export static_build="no"
+#fi
+#rm -f $oprog $cprog
+#if [ $printnotice = yes ] && [ $static_build = "no" ]; then
+#    cat <<EOF
+#_________________________________________________________________________
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!      WARNING      !!!!!!!!!!!!!!!!!!!!!!!!!!
+#
+#Your system's C compiler ('$CC') doesn't support building static
+#libraries. Therefore the dependencies will be built dynamically. This means
+#that they will depend more strongly on changes/updates in the host
+#system. For high-level applications (like most research projects in natural
+#sciences), this shouldn't be a significant problem.
+#
+#But generally, for reproducibility, its better to build static libraries
+#and programs. For more on their difference (and generally an introduction
+#on linking), please see the link below:
+#
+#https://www.gnu.org/software/gnuastro/manual/html_node/Linking.html
+#
+#If you have other compilers on your system, you can select a different
+#compiler by setting the 'CC' environment variable before running
+#'./project configure'.
+#
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+#
+#EOF
+#    sleep 5
+#fi
+
+
+
+
+
+# See if the linker accepts -Wl,-rpath-link
+# -----------------------------------------
+#
+# `-rpath-link' is used to write the information of the linked shared
+# library into the shared object (library or program). But some versions of
+# LLVM's linker don't accept it an can cause problems.
+oprog=$sdir/rpath-test
+cprog=$sdir/rpath-test.c
+echo "#include <stdio.h>"          > $cprog
+echo "int main(void) {return 0;}" >> $cprog
+if [ x$CC = x ]; then CC=gcc; fi;
+if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then
+    export rpath_command="-Wl,-rpath-link=$instdir/lib"
+else
+    export rpath_command=""
+fi
+rm -f $oprog $cprog
+
+
+
+
+
+# See if we need the dynamic-linker (-ldl)
+# ----------------------------------------
+#
+# Some programs (like Wget) need dynamic loading (using `libdl'). On
+# GNU/Linux systems, we'll need the `-ldl' flag to link such programs.  But
+# Mac OS doesn't need any explicit linking. So we'll check here to see if
+# it is present (thus necessary) or not.
+oprog=$sdir/ldl-test
+cprog=$sdir/ldl-test.c
+cat > $cprog <<EOF
+#include <stdio.h>
+#include <dlfcn.h>
+int
+main(void) {
+    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
+    return 0;
+}
+EOF
+if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi
+rm -f $oprog $cprog
+
+
+
+
+
+# inform the user that the build process is starting
+# -------------------------------------------------
+if [ $printnotice = yes ]; then
+    tsec=10
+    cat <<EOF
+
+-------------------------
+Building dependencies ...
+-------------------------
+
+Necessary dependency programs and libraries will be built in $tsec sec.
+
+NOTE: the built software will NOT BE INSTALLED on your system (no root
+access is required). They are only for local usage by this project. They
+will be installed in:
+
+  $sdir/installed
+
+EOF
+    sleep $tsec
+fi
+
+
+
+
+
+# If we are on a Mac OS system
+# ----------------------------
+#
+# For the time being, we'll use the existance of `otool' to see if we are
+# on a Mac OS system or not. Some tools (for example OpenSSL) need to know
+# this.
+#
+# On Mac OS, the building of GCC crashes sometimes while building libiberty
+# with CLang's `g++'. Until we find a solution, we'll just use the host's C
+# compiler.
+if type otool > /dev/null 2>/dev/null; then
+    host_cc=1
+    on_mac_os=yes
+else
+    on_mac_os=no
+fi
+
+
+
+
+
+# Build `flock'
+# -------------
+#
+# Flock (or file-lock) is a unique program that is necessary to serialize
+# the (generally parallel) processing of make when necessary. GNU/Linux
+# machines have it as part of their `util-linux' programs. But to be
+# consistent in non-GNU/Linux systems, we will be using our own build.
+#
+# The reason that `flock' is sepecial is that we need it to serialize the
+# download process of the software tarballs.
+flockversion=$(awk '/flock-version/{print $3}' $depverfile)
+flocktar=flock-$flockversion.tar.gz
+flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/
+
+# Prepare/download the tarball.
+if ! [ -f $tardir/$flocktar ]; then
+    if [ -f $ddir/$flocktar ]; then
+        cp $ddir/$flocktar $tardir/$flocktar
+    else
+        if ! $downloader $tardir/$flocktar $flockurl/$flocktar; then
+            rm -f $tardir/$flocktar;
+            echo
+            echo "DOWNLOAD ERROR: Couldn't download the 'flock' tarball:"
+            echo "  $flockurl"
+            echo
+            echo "You can manually place it in '$ddir' to avoid downloading."
+            exit 1
+        fi
+    fi
+fi
+
+# If the tarball is newer than the (possibly existing) program (the version
+# has changed), then delete the program.
+if [ -f .local/bin/flock ]; then
+    if [ $tardir/$flocktar -nt $ibidir/flock ]; then
+        rm $ibidir/flock
+    fi
+fi
+
+# Build `flock' if necessary.
+if ! [ -f $ibidir/flock ]; then
+    cd $tmpblddir
+    tar xf $tardir/$flocktar
+    cd flock-$flockversion
+    ./configure --prefix=$instdir
+    make
+    make install
+    cd $topdir
+    rm -rf $tmpblddir/flock-$flockversion
+    echo "Discoteq flock $flockversion" > $ibidir/flock
+fi
+
+
+
+
+
+# See if GCC can be built
+# -----------------------
+#
+# On some GNU/Linux distros, the C compiler is broken into `multilib' (for
+# 32-bit and 64-bit support, with their own headers). On these systems,
+# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by
+# default. So GCC will crash with different ugly errors! The only solution
+# is that user manually installs the `multilib' part as root, before
+# running the configure script.
+#
+# Note that `sys/cdefs.h' may be available in other directories (for
+# example `/usr/include/x86_64-linux-gnu/') that are automatically included
+# in an installed GCC. HOWEVER during the build of GCC, all those other
+# directories are ignored. So even if they exist, they are useless.
+warningsleep=0
+if [ $host_cc = 0 ]; then
+    if ! [ -f /usr/include/sys/cdefs.h ]; then
+        host_cc=1
+        warningsleep=1
+        cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the
+project can't build its custom GCC to ensure better reproducibility. We
+strongly recommend installing the proper package (for your operating
+system) that installs this necessary file. For example on some Debian-based
+GNU/Linux distros, you need these two packages: 'gcc-multilib' and
+'g++-multilib'.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    fi
+
+    if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then
+        # This is just a place holder
+        host_cc=$host_cc
+    else
+        host_cc=1
+        warningsleep=1
+        cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because
+of this, the project can't build its custom GCC to ensure better
+reproducibility. We strongly recommend installing the proper package (for
+your operating system) that installs this necessary file.
+
+Some possible solutions:
+  1. On some Debian-based GNU/Linux distros, these two packages may fix the
+     problem: 'gcc-multilib' and 'g++-multilib'.
+  2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have
+     '/usr/lib64', then running the following command might fix this
+     particular problem by making a symbolic link.
+         $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
+     After the configure script is finished, delete the link with 'rm
+     /usr/lib64' (you won't need it any more as far as this project is
+     concerned).
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    fi
+
+    if [ $warningsleep = 1 ]; then
+        cat <<EOF
+
+PLEASE SEE THE WARNINGS ABOVE.
+
+Since GCC is pretty low-level, this configuration script will continue in 5
+seconds and use your system's C compiler (it won't build a custom GCC). But
+please consider installing the necessary package(s) to complete your C
+compiler, then re-run './project configure'.
+
+EOF
+        sleep 5
+    fi
+fi
+
+
+
+
+
+# Fortran compiler
+# ----------------
+#
+# If GCC is ultimately build within the project, the user won't need to
+# have a fortran compiler, we'll build it internally for high-level
+# programs. However, when the host C compiler is to be used, the user needs
+# to have a Fortran compiler available.
+if [ $host_cc = 1 ]; then
+    hasfc=0;
+    if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
+
+    if [ $hasfc = 0 ]; then
+        cat <<EOF
+______________________________________________________
+!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!
+
+Because the project won't be building its own GCC (which includes a Fortran
+compiler), you need to have a Fortran compiler available. Fortran is
+commonly necessary for many lower-level scientific programs. Currently we
+search for 'gfortran'. If you have a Fortran compiler that is not checked,
+please get in touch with us (with the form below) so we add it:
+
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+Note: GCC will not be built because you are either using the '--host-cc'
+option, or you are using an operating system that currently has bugs when
+building GCC.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+        exit 1
+    fi
+fi
+
+
+
+
+
+# Number of threads for basic builds
+# ----------------------------------
+#
+# Since the system might not have GNU Make at this stage, and other Make
+# implementations can't deal with parallel build properly, we'll just
+# default to 1 thread. This is because some versions of Make complain about
+# not having enough 'pipe' (memory) on some systems. After some searching,
+# I found out its because of too many threads. GNU Make will be present on
+# GNU systems (that have `nproc', part of GNU Coreutils). So to simplify
+# the test for GNU Make, we'll just try running `nproc'.
+if which nproc &> /dev/null; then
+    if [ $jobs = 0 ]; then
+        numthreads=$(nproc --all);
+    else
+        numthreads=$jobs
+    fi
+else
+    numthreads=1;
+fi
+
+
+
+
+
+# Build basic software
+# --------------------
+#
+# When building these software we don't have our own un-packing software,
+# Bash, Make, or AWK. In this step, we'll install such low-level basic
+# tools, but we have to be very portable (and use minimal features in all).
+make -f reproduce/software/make/basic.mk \
+     rpath_command=$rpath_command \
+     static_build=$static_build \
+     needs_ldl=$needs_ldl \
+     on_mac_os=$on_mac_os \
+     numthreads=$numthreads \
+     host_cc=$host_cc \
+     -j$numthreads
+
+
+
+
+
+# All other software
+# ------------------
+#
+# We will be making all the dependencies before running the top-level
+# Makefile. To make the job easier, we'll do it in a Makefile, not a
+# script. Bash and Make were the tools we need to run Makefiles, so we had
+# to build them in this script. But after this, we can rely on Makefiles.
+if [ $jobs = 0 ]; then
+    numthreads=$($instdir/bin/nproc --all)
+else
+    numthreads=$jobs
+fi
+.local/bin/env -i HOME=$bdir \
+    .local/bin/make -f reproduce/software/make/high-level.mk \
+                    rpath_command=$rpath_command \
+                    static_build=$static_build \
+                    numthreads=$numthreads \
+                    on_mac_os=$on_mac_os \
+                    host_cc=$host_cc \
+                    -j$numthreads
+
+
+
+
+
+# Make sure TeX Live installed successfully
+# -----------------------------------------
+#
+# TeX Live is managed over the internet, so if there isn't any, or it
+# suddenly gets cut, it can't be built. However, when TeX Live isn't
+# installed, the project can do all its processing independent of it. It
+# will just stop at the stage when all the processing is complete and it is
+# only necessary to build the PDF.  So we don't want to stop the project's
+# configuration and building if its not present.
+if [ -f $itidir/texlive-ready-tlmgr ]; then
+    texlive_result=$(cat $itidir/texlive-ready-tlmgr)
+else
+    texlive_result="NOT!"
+fi
+if [ x"$texlive_result" = x"NOT!" ]; then
+    cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+TeX Live couldn't be installed during the configuration (probably because
+there were downloading problems). TeX Live is only necessary in making the
+final PDF (which is only done after all the analysis has been complete). It
+is not used at all during the analysis.
+
+Therefore, if you don't need the final PDF, and just want to do the
+analysis, you can safely ignore this warning and continue.
+
+If you later have internet access and would like to add TeX live to your
+project, please delete the respective files, then re-run configure as shown
+below. Within configure, answer 'n' (for "no") when asked to re-write the
+configuration files.
+
+    rm .local/version-info/tex/texlive-ready-tlmgr
+    ./project configure
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+fi
+
+
+
+
+
+# Citation of installed software
+#
+# After everything is installed, we'll put all the names and versions in a
+# human-readable paragraph and also prepare the BibTeX citation for the
+# software.
+function prepare_name_version() {
+
+    # First see if the (possible) `*' in the input arguments corresponds to
+    # anything. Note that some of the given directories may be empty (no
+    # software installed).
+    hasfiles=0
+    for f in $@; do
+        if [ -f $f ]; then hasfiles=1; break; fi;
+    done
+
+    # If there are any files, merge all the names in a paragraph.
+    if [ $hasfiles = 1 ]; then
+
+        # Count how many names there are. This is necessary to identify the
+        # last element.
+        num=$(.local/bin/cat $@ \
+                  | .local/bin/sed '/^\s*$/d' \
+                  | .local/bin/wc -l)
+
+        # Put them all in one paragraph.
+        .local/bin/cat $@ \
+            | .local/bin/sort \
+            | sed 's/_/\\_/' \
+            | .local/bin/awk 'NF>0 { \
+                  c++; \
+                  if(c==1) \
+                    { \
+                      if('$num'==1) printf("%s", $0); \
+                      else          printf("%s", $0); \
+                    } \
+                  else if(c=='$num') printf(" and %s\n", $0); \
+                  else printf(", %s", $0) \
+                }'
+    fi
+}
+
+# Report the different software in separate contexts (separating Python and
+# TeX packages from the C/C++ programs and libraries).
+proglibs=$(prepare_name_version $verdir/proglib/*)
+pymodules=$(prepare_name_version $verdir/python/*)
+texpkg=$(prepare_name_version $verdir/tex/texlive)
+
+# Write them as one paragraph for LaTeX.
+pkgver=$mtexdir/dependencies.tex
+.local/bin/echo "This research was done with the following free" > $pkgver
+.local/bin/echo "software programs and libraries: $proglibs."   >> $pkgver
+if [ x"$pymodules" != x ]; then
+    .local/bin/echo "Within Python, the following modules"      >> $pkgver
+    echo "were used: $pymodules."                               >> $pkgver
+fi
+.local/bin/echo "The \LaTeX{} source of the paper was compiled" >> $pkgver
+.local/bin/echo "to make the PDF using the following packages:" >> $pkgver
+.local/bin/echo "$texpkg. We are very grateful to all their"    >> $pkgver
+.local/bin/echo "creators for freely providing this necessary"  >> $pkgver
+.local/bin/echo "infrastructure. This research (and many "      >> $pkgver
+.local/bin/echo "others) would not be possible without them."   >> $pkgver
+
+# Prepare the BibTeX entries for the used software (if there are any).
+hasentry=0
+bibfiles="$ictdir/*"
+for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done;
+
+# Make sure we start with an empty output file.
+pkgbib=$mtexdir/dependencies-bib.tex
+echo "" > $pkgbib
+
+# Fill it in with all the BibTeX entries in this directory. We'll just
+# avoid writing any comments (usually copyright notices) and also put an
+# empty line after each file's contents to make the output more readable.
+if [ $hasentry = 1 ]; then
+    for f in $bibfiles; do
+        awk '!/^%/{print} END{print ""}' $f >> $pkgbib
+    done
+fi
+
+
+
+
+
+# Clean the temporary build directory
+# ---------------------------------
+#
+# By the time the script reaches here the temporary software build
+# directory should be empty, so just delete it. Note `tmpblddir' may be a
+# symbolic link to shared memory. So, to work in any scenario, first delete
+# the contents of the directory (if it has any), then delete `tmpblddir'.
+.local/bin/rm -rf $tmpblddir/* $tmpblddir
+
+
+
+
+
+# Register successful completion
+# ------------------------------
+echo `.local/bin/date` > $finaltarget
+
+
+
+
+
+
+# Final notice
+# ------------
+#
+# The configuration is now complete, we can inform the user on the next
+# step(s) to take.
+if [ x$reproducible_paper_group_name = x ]; then
+    buildcommand="./project make -j8"
+else
+    buildcommand="./project make --group=$reproducible_paper_group_name -j8"
+fi
+cat <<EOF
+
+----------------
+The project and its environment are configured with no errors.
+
+Please run the following command to start.
+(Replace '8' with the number of CPU threads)
+
+    $buildcommand
+
+To change the configuration later, please re-run './project configure', DO
+NOT manually edit the relevant files.
+
+EOF
diff --git a/reproduce/software/config/installation/LOCAL.mk.in b/reproduce/software/config/installation/LOCAL.mk.in
index 785bb6a..132d961 100644
--- a/reproduce/software/config/installation/LOCAL.mk.in
+++ b/reproduce/software/config/installation/LOCAL.mk.in
@@ -1,7 +1,7 @@
 # Local project configuration.
 #
-# This is just a template for the `./configure' script to fill in. Please
-# don't make any change to this file.
+# This is just a template for the `./project configure' script to fill
+# in. Please don't make any change to this file.
 #
 # Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
diff --git a/reproduce/software/make/atlas-multiple.mk b/reproduce/software/make/atlas-multiple.mk
index fef25c7..f5efb35 100755
--- a/reproduce/software/make/atlas-multiple.mk
+++ b/reproduce/software/make/atlas-multiple.mk
@@ -3,8 +3,8 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run during the initial `./configure' script. It is
-# not included into the reproduction pipe after that.
+# This Makefile will be run during the initial `./project configure'
+# script. It is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
diff --git a/reproduce/software/make/atlas-single.mk b/reproduce/software/make/atlas-single.mk
index dde2926..c4621ce 100755
--- a/reproduce/software/make/atlas-single.mk
+++ b/reproduce/software/make/atlas-single.mk
@@ -3,8 +3,8 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run during the initial `./configure' script. It is
-# not included into the reproduction pipe after that.
+# This Makefile will be run during the initial `./project configure'
+# script. It is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index bab37ed..e4ab55a 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -4,8 +4,8 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run by the initial `./configure' script. It is not
-# included into the project after that.
+# This Makefile will be run by the initial `./project configure' script. It
+# is not included into the project after that.
 #
 # This Makefile builds very low-level and basic tools like GNU Tar, GNU
 # Bash, GNU Make, GCC and etc. Therefore this is the only Makefile in the
@@ -58,7 +58,11 @@ export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
 export CPPFLAGS := -I$(idir)/include $(CPPFLAGS)
 export LD_LIBRARY_PATH := $(ildir):$(LD_LIBRARY_PATH)
 export LDFLAGS := $(rpath_command) -L$(ildir) $(LDFLAGS)
-export DYLD_LIBRARY_PATH := $(ildir):$(DYLD_LIBRARY_PATH)
+
+# 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 :=
 
 # Define the top-level basic programs (that don't depend on any other).
 top-level-programs = low-level-links gcc
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index dee23ca..b9a70de 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -3,8 +3,8 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run by the initial `./configure' script. It is not
-# included into the reproduction pipe after that.
+# This Makefile will be run by the initial `./project configure' script. It
+# is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
@@ -76,7 +76,11 @@ export LD_RUN_PATH := $(ildir):$(il64dir)
 export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export LD_LIBRARY_PATH := $(ildir):$(il64dir)
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
-export DYLD_LIBRARY_PATH := $(ildir):$(il64dir)
+
+# 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 :=
 
 # Building flags:
 #
@@ -90,6 +94,9 @@ export CXXFLAGS          := -liconv
 endif
 
 
+
+
+
 # We want the download to happen on a single thread. So we need to define a
 # lock, and call a special script we have written for this job. These are
 # placed here because we want them both in the `high-level.mk' and
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 22b668f..ed1c87d 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -3,8 +3,8 @@
 # ------------------------------------------------------------------------
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
-# This Makefile will be run by the initial `./configure' script. It is not
-# included into the reproduction pipe after that.
+# This Makefile will be run by the initial `./project configure' script. It
+# is not included into the reproduction pipe after that.
 #
 # ------------------------------------------------------------------------
 #
-- 
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