IMPORTANT: reproduce/software/bash renamed to reproduce/software/shell

Until now the shell scripts in the software building phase were in the
`reproduce/software/bash' directory. But given our recent change to a
POSIX-only start, the `configure.sh' shell script (which is the main
component of this directory) is no longer written with Bash.

With this commit, to fix that problem, that directory's name has been
changed to `reproduce/software/shell'.

4 files changed, 0 insertions, 1601 deletions

diff --git a/reproduce/software/bash/bashrc.sh b/reproduce/software/bash/bashrc.sh
deleted file mode 100755
index b2a151f..0000000
--- a/reproduce/software/bash/bashrc.sh
+++ /dev/null
@@ -1,45 +0,0 @@
-# Bash startup file for better control of project environment.
-#
-# To have better control over the environment of each analysis step (Make
-# recipe), besides having environment variables (directly included from
-# Make), it may also be useful to have a Bash startup file (this file). All
-# of the Makefiles set this file as the `BASH_ENV' environment variable, so
-# it is loaded into all the Make recipes within the project.
-#
-# The special `PROJECT_STATUS' environment variable is defined in every
-# top-level Makefile of the project. It defines the the state of the Make
-# that is calling this script. It can have three values:
-#
-#    configure_basic
-#    ---------------
-#       When doing basic configuration, therefore the executed steps cannot
-#       make any assumptions about the version of Bash (or any other
-#       program). Therefore it is important for any step in this step to be
-#       highly portable.
-#
-#    configure_highlevel
-#    -------------------
-#       When building the higher-level programs, so the versions of the
-#       most basic tools are set and you may safely assume certain
-#       features.
-#
-#    make
-#    ----
-#       When doing the project's analysis: all software have known
-#       versions.
-#
-#
-# Copyright (C) 2019-2020 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/>.
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
deleted file mode 100755
index a6fbc4e..0000000
--- a/reproduce/software/bash/configure.sh
+++ /dev/null
@@ -1,1407 +0,0 @@
-#! /bin/sh
-#
-# Necessary preparations/configurations for the reproducible project.
-#
-# Copyright (C) 2018-2020 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=$sbdir/LOCAL.conf
-ptconf=$sbdir/LOCAL_tmp.conf
-poconf=$sbdir/LOCAL_old.conf
-depverfile=$cdir/installation/versions.conf
-depshafile=$cdir/installation/checksums.conf
-# --------- Delete for no Gnuastro ---------
-glconf=$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.
-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.
-absolute_dir ()
-{
-    if stat "$1" 1> /dev/null; then
-        echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
-    else
-        exit 1;
-    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 export CC=cc; hascc=1; fi
-else
-    if type gcc > /dev/null 2>/dev/null; then
-        if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
-    else
-        if type clang > /dev/null 2>/dev/null; then
-            if type clang++ > /dev/null 2>/dev/null; then export CC=clang; 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
-
-
-
-
-
-# Special directory for compiler testing
-# --------------------------------------
-#
-# This directory will be deleted when the compiler testing is finished.
-compilertestdir=.compiler_test_dir_please_delete
-if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; fi
-
-
-
-
-
-# Check C compiler
-# ----------------
-gcc_works=0
-testprog=$compilertestdir/test
-testsource=$compilertestdir/test.c
-echo; echo; echo "Checking host C compiler...";
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void){printf("...C compiler works.\n");
-               return EXIT_SUCCESS;}
-EOF
-if $CC $testsource -o$testprog && $testprog; then
-    rm $testsource $testprog
-else
-    rm $testsource
-    cat <<EOF
-
-______________________________________________________
-!!!!!!!        C compiler doesn't work         !!!!!!!
-
-Host C compiler ('gcc') can't build a simple program.
-
-A working C compiler is necessary for building the project's software.
-Please use the error message above to find a good solution and re-run the
-project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
-   $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    exit 1
-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.
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void) {return EXIT_SUCCESS;}
-EOF
-if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
-    export rpath_command="-Wl,-rpath-link=$instdir/lib"
-else
-    export rpath_command=""
-fi
-rm -f $testprog $testsource
-
-
-
-
-
-# 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.
-cat > $testsource <<EOF
-#include <stdio.h>
-#include <dlfcn.h>
-int
-main(void) {
-    void *handle=dlopen ("/lib/CEDD_LIB.so.6", RTLD_LAZY);
-    return 0;
-}
-EOF
-if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
-    needs_ldl=no;
-else
-    needs_ldl=yes;
-fi
-rm -f $testprog $testsource
-
-
-
-
-
-# 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
-
-
-
-
-
-# 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
-    host_cc=0
-    on_mac_os=no
-fi
-
-
-
-
-
-# Necessary C library element positions
-# -------------------------------------
-#
-# On some systems (in particular Debian-based OSs), the static C library
-# and necessary headers in a non-standard place, and we can't build GCC. So
-# we need to find them first. The `sys/cdefs.h' header is also in a
-# similarly different location.
-sys_cpath=""
-sys_library_path=""
-if [ x"$$on_mac_os" != xyes ]; then
-
-    # Get the GCC target name of the compiler, when its given, special
-    # C libraries and headers are in a sub-directory of the host.
-    gcctarget=$(gcc -v 2>&1 \
-                    | tr ' ' '\n' \
-                    | awk '/\-\-target/' \
-                    | sed -e's/\-\-target=//')
-    if [ x"$gcctarget" != x ]; then
-        if [ -f /usr/lib/$gcctarget/libc.a ]; then
-            export sys_library_path=/usr/lib/$gcctarget
-            export sys_cpath=/usr/include/$gcctarget
-        fi
-    fi
-
-    # For a check:
-    #echo "sys_library_path: $sys_library_path"
-    #echo "sys_cpath: $sys_cpath"
-fi
-
-
-
-
-
-# See if a link-able static C library exists
-# ------------------------------------------
-#
-# After building GCC, we must use PatchELF to correct its RPATHs. However,
-# PatchELF links internally with `libstdc++'. So a dynamicly linked
-# PatchELF cannot be used to correct the links to `libstdc++' in general
-# (on some systems this causes no problem, but on others it doesn't!).
-#
-# However, to build a Static PatchELF, we need to be able to link with the
-# static C library, which is not always available on some GNU/Linux
-# systems. Therefore we need to check this here. If we can't build a static
-# PatchELF, we won't build any GCC either.
-if [ x"$host_cc" = x0 ]; then
-    echo; echo; echo "Checking if static C library is available...";
-    cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/cdefs.h>
-int main(void){printf("...yes\n");
-               return EXIT_SUCCESS;}
-EOF
-    cc_call="$CC $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
-    if $cc_call && $testprog; then
-        gccwarning=0
-        good_static_libc=1
-        rm $testsource $testprog
-    else
-        echo; echo "Compilation command:"; echo "$cc_call"
-        good_static_libc=0
-        rm $testsource
-        gccwarning=1
-        host_cc=1
-        cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-The 'sys/cdefs.h' header cannot be included, or a usable static C library
-('libc.a', in any directory) cannot be used with the current settings of
-this system. SEE THE ERROR MESSAGE ABOVE.
-
-Because of this, we can't build GCC. You either 1) don't have them, or 2)
-the default system environment aren't enough to find them.
-
-1) If you don't have them, your operating system provides them as separate
-packages that you must manually install. Please look into your operating
-system documentation or contact someone familiar with it. For example on
-some Redhat-based GNU/Linux distributions, the static C library package can
-be installed with this command:
-
-    $ sudo yum install glibc-static
-
-2) If you have 'libc.a' and 'sys/cdefs.h', but in a non-standard location (for
-example in '/PATH/TO/STATIC/LIBC/libc.a' and
-'/PATH/TO/SYS/CDEFS_H/sys/cdefs.h'), please run the commands below, then
-re-configure the project to fix this problem.
-
-    $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
-    $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    fi
-fi
-
-# Print a warning if GCC is not meant to be built.
-if [ x"$gccwarning" = x1 ]; 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
-
-
-
-
-
-# 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
-
-    # See if a Fortran compiler exists.
-    hasfc=0;
-    if type gfortran > /dev/null 2>/dev/null; then hasfc=1; fi
-    if [ $hasfc = 0 ]; then
-        cat <<EOF
-______________________________________________________
-!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!
-
-Because the project won't be building its own GCC (which includes a Fortran
-compiler), you need to have a Fortran compiler available. Fortran is
-commonly necessary for many lower-level scientific programs. Currently we
-search for 'gfortran'. If you have a Fortran compiler that is not checked,
-please get in touch with us (with the form below) so we add it:
-
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-Note: GCC will not be built because you are either using the '--host-cc'
-option, or you are using an operating system that currently has bugs when
-building GCC.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-        exit 1
-    fi
-
-    # See if the Fortran compiler works
-    testsource=$compilertestdir/test.f
-    echo; echo; echo "Checking host Fortran compiler...";
-    echo "      PRINT *, \"... Fortran Compiler works.\""  > $testsource
-    echo "      END"                                      >> $testsource
-    if gfortran $testsource -o$testprog && $testprog; then
-        rm $testsource $testprog
-    else
-        rm $testsource
-        cat <<EOF
-
-______________________________________________________
-!!!!!!!     Fortran compiler doesn't work      !!!!!!!
-
-Host Fortran compiler ('gfortran') can't build a simple program.
-
-A working Fortran compiler is necessary for building some of the project's
-software.  Please use the error message above to find a good solution and
-re-run the project configuration.
-
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
-
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
-
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
-
-   $ ./project configure -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-        exit 1
-    fi
-fi
-
-
-
-
-
-# Delete the compiler testing directory
-# -------------------------------------
-#
-# This directory was made above to make sure the necessary compilers can be
-# run.
-rm -rf $compilertestdir
-
-
-
-
-
-# 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.conf' 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 [ $rewritepconfig = yes ]; then
-    cat <<EOF
-
-===============
-Build directory
-===============
-
-The project's "source" (this directory) and "build" directories are treated
-separately. This greatly helps in managing the many intermediate files that
-are created during the build. The intermediate build files don't need to be
-archived or backed up: you can always re-build them with the contents of
-the source directory. The build directory also needs a relatively large
-amount of free space (atleast serveral Giga-bytes), while the source
-directory (all plain text) will usually be a mega-byte or less.
-
-'.build' (a symbolic link to the build directory) will also be created
-during this configuration. It can help encourage you to set the actual
-build directory in a very different address from this one (one that can be
-deleted and has large volume), while having easy access to it from here.
-
---- CAUTION ---
-Do not choose any directory under the top source directory (this
-directory). The build directory cannot be a subdirectory of the source.
----------------
-
-EOF
-    bdir=
-    currentdir=$(pwd)
-    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
-                instring="the already existing"
-                bdir=$(absolute_dir $build_dir)
-                rm -rf $build_dir/$junkname
-            else
-                echo " -- Can't write in '$build_dir'"; echo
-            fi
-        else
-            if mkdir $build_dir 2> /dev/null; then
-                instring="the newly created"
-                bdir=$(absolute_dir $build_dir)
-            else
-                echo " -- Can't create '$build_dir'"; echo
-            fi
-        fi
-
-        # If its given, make sure it isn't a subdirectory of the source
-        # directory.
-        if ! [ x"$bdir" = x ]; then
-            echo "Given build directory: $bdir"
-            if echo "$bdir/" \
-                    | grep '^'$currentdir 2> /dev/null > /dev/null; then
-
-                # If it was newly created, it will be empty, so delete it.
-                if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
-
-                # Inform the user that this is not acceptable and reset `bdir'.
-                bdir=
-                echo " -- The build-directory cannot be under the source-directory."
-                echo "    Please specify another build-directory that is outside of the source."
-                echo ""
-            else
-                echo " -- Build directory set to ($instring): '$bdir'"
-            fi
-        fi
-
-        # Reset `build_dir' to blank, so it continues asking when the
-        # previous value wasn't usable.
-        build_dir=
-    done
-fi
-
-
-
-
-
-# Input directory
-# ---------------
-if [ x"$input_dir" = x ]; then
-    indir=$optionaldir
-else
-    indir=$input_dir
-fi
-wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.conf)
-wfpc2md5=$(awk  '!/^#/ && $1=="WFPC2MD5"   {print $3}' $adir/INPUTS.conf)
-wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE"  {print $3}' $adir/INPUTS.conf)
-wfpc2url=$(awk  '!/^#/ && $1=="WFPC2URL"   {print $3}' $adir/INPUTS.conf)
-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|@sys_cpath[@]|'"$sys_cpath"'|' \
-        -e's|@downloader[@]|'"$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
-
-
-
-
-
-# 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
-
-**TIP**: you can see which software is being installed at every moment with
-the following command. See "Inspecting status" section of
-'README-hacking.md' for more. In short, run it while the project is being
-configured (in another terminal, but on this same directory: 'pwd'):
-
-  $ ./project --check-config
-
--------------------------
-
-EOF
-    sleep $tsec
-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=$jobs
-    fi
-else
-    numthreads=1;
-fi
-
-
-
-
-
-# Build `flock' before other program
-# ----------------------------------
-#
-# Flock (or file-lock) is a unique program that is necessary to serialize
-# the (generally parallel) processing of make when necessary. GNU/Linux
-# machines have it as part of their `util-linux' programs. But to be
-# consistent in non-GNU/Linux systems, we will be using our own build.
-#
-# The reason that `flock' is sepecial is that we need it to serialize the
-# download process of the software tarballs.
-flockversion=$(awk '/flock-version/{print $3}' $depverfile)
-flockchecksum=$(awk '/flock-checksum/{print $3}' $depshafile)
-flocktar=flock-$flockversion.tar.gz
-flockurl=http://github.com/discoteq/flock/releases/download/v$flockversion/
-
-# Prepare/download the tarball.
-if ! [ -f $tardir/$flocktar ]; then
-    flocktarname=$tardir/$flocktar
-    ucname=$flocktarname.unchecked
-    if [ -f $ddir/$flocktar ]; then
-        cp $ddir/$flocktar $ucname
-    else
-        if ! $downloader $ucname $flockurl/$flocktar; then
-            rm -f $ucname;
-            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
-
-    # Make sure this is the correct tarball.
-    if type sha512sum > /dev/null 2>/dev/null; then
-        checksum=$(sha512sum "$ucname" | awk '{print $1}')
-        if [ x$checksum = x$flockchecksum ]; then mv "$ucname" "$flocktarname"
-        else echo "ERROR: Non-matching checksum for '$flocktar'."; exit 1
-        fi;
-    else mv "$ucname" "$flocktarname"
-    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" > $ibidir/flock
-fi
-
-
-
-
-
-# Paths needed by the host compiler (only for `basic.mk')
-# -------------------------------------------------------
-#
-# At the end of the basic build, we need to build GCC. But GCC will build
-# in multiple phases, making its own simple compiler in order to build
-# itself completely. The intermediate/simple compiler doesn't recognize
-# some system specific locations like `/usr/lib/ARCHITECTURE' that some
-# operating systems use. We thus need to tell the intermediate compiler
-# where its necessary libraries and headers are.
-if [ x"$sys_library_path" != x ]; then
-    if [ x"$LIBRARY_PATH" = x ]; then
-        export LIBRARY_PATH="$sys_library_path"
-    else
-        export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
-    fi
-    if [ x"$CPATH" = x ]; then
-        export CPATH="$sys_cpath"
-    else
-        export CPATH="$CPATH:$sys_cpath"
-    fi
-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).
-echo; echo "Building necessary software (if necessary)..."
-make -f reproduce/software/make/basic.mk \
-     good_static_libc=$good_static_libc \
-     rpath_command=$rpath_command \
-     static_build=$static_build \
-     numthreads=$numthreads \
-     needs_ldl=$needs_ldl \
-     on_mac_os=$on_mac_os \
-     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=$bdir \
-    .local/bin/make -f reproduce/software/make/high-level.mk \
-                    sys_library_path=$sys_library_path \
-                    rpath_command=$rpath_command \
-                    static_build=$static_build \
-                    numthreads=$numthreads \
-                    on_mac_os=$on_mac_os \
-                    sys_cpath=$sys_cpath \
-                    host_cc=$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.
-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 $@ \
-            | .local/bin/sort \
-            | .local/bin/awk 'NF>0 { \
-                  c++; \
-                  if(c==1) \
-                    { \
-                      if('$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 on your system)
-
-    $buildcommand
-
-To change the configuration later, please re-run './project configure', DO
-NOT manually edit the relevant files.
-
-EOF
diff --git a/reproduce/software/bash/git-post-checkout b/reproduce/software/bash/git-post-checkout
deleted file mode 100755
index f6366dc..0000000
--- a/reproduce/software/bash/git-post-checkout
+++ /dev/null
@@ -1,66 +0,0 @@
-#!@BINDIR@/bash
-#
-# The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
-#
-# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). We have just changed the name of the `MSFILE' and also
-# set special characters for the installation location of meta-store so our
-# own installation is found by Git.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to permit
-# persons to whom the Software is furnished to do so, subject to the
-# following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
-# NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
-# USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-
-# File containig the metadata and metastore executable.
-MSFILE=".file-metadata"
-MSBIN=@BINDIR@/metastore
-
-# If metastore is not installed, then ignore this script (exit with a
-# status of 0).
-if [ ! -f $MSBIN ]; then exit 0; fi
-
-# Delete all temporary files
-find @TOP_PROJECT_DIR@/ -name "*~" -type f -delete
-
-# Function to help in reporting a crash.
-exit_on_fail() {
-	"$@"
-	if [ $? -ne 0 ]; then
-		echo "Failed to execute: $@" >&2
-		exit 1
-	fi
-}
-
-# Check if the metadata file exists.
-if [ ! -e "$MSFILE" ]; then
-	echo "\"$MSFILE\" missing" >&2
-	exit 1
-fi
-
-# Run metastore.
-exit_on_fail \
-       $MSBIN -a -m -e -E -q -O @USER@ -G @GROUP@ -f "$MSFILE"
-
-# Return with a success code (0).
-exit 0
diff --git a/reproduce/software/bash/git-pre-commit b/reproduce/software/bash/git-pre-commit
deleted file mode 100755
index 9d550db..0000000
--- a/reproduce/software/bash/git-pre-commit
+++ /dev/null
@@ -1,83 +0,0 @@
-#!@BINDIR@/bash
-#
-# The example hook script to store the metadata information of version
-# controlled files (with each commit) using the `metastore' program.
-#
-# Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-#
-# WARNING:
-#
-# If the commit is aborted (e.g. by not entering any synopsis),
-# then updated metastore file (.metadata by default) is not reverted,
-# so its new version remains in the index.
-# To undo any changes in metastore file written since HEAD commit,
-# you may want to reset and checkout HEAD version of the file:
-#
-#     git reset HEAD -- .metadata
-#     git checkout HEAD -- .metadata
-#
-# This script is taken from the `examples/hooks/pre-commit' file of the
-# `metastore' package (installed within the project, with an MIT license
-# for copyright). Here, the name of the `MSFILE' and also set special
-# characters for the installation location of meta-store so our own
-# installation is found by Git.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a
-# copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to permit
-# persons to whom the Software is furnished to do so, subject to the
-# following conditions:
-#
-# The above copyright notice and this permission notice shall be included
-# in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
-# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN
-# NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-# OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
-# USE OR OTHER DEALINGS IN THE SOFTWARE.
-
-# File containig the metadata and metastore executable.
-MSFILE=".file-metadata"
-MSBIN=@BINDIR@/metastore
-
-# If metastore is not installed, then ignore this script (exit with a
-# status of 0).
-if [ ! -f $MSBIN ]; then exit 0; fi
-
-# Function to help in reporting a crash.
-exit_on_fail() {
-	"$@"
-	if [ $? -ne 0 ]; then
-		echo "Failed to execute: $@" >&2
-		exit 1
-	fi
-}
-
-# Run metastore.
-exit_on_fail \
-	$MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
-
-# If it's first metastore commit, store again to include $MSFILE in $MSFILE.
-if ! git-ls-tree --name-only HEAD 2>/dev/null | grep -Fqx "$MSFILE"; then
-	exit_on_fail \
-	        $MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
-fi
-
-# Check if the metadata file exists.
-if [ ! -e "$MSFILE" ]; then
-	echo "\"$MSFILE\" missing" >&2
-	exit 1
-fi
-
-# Add the metadata file to the Git repository.
-exit_on_fail \
-	git-add "$MSFILE"
-
-# Return with a success code (0).
-exit 0