From 334af0e29a950873a19f958b0e47d847808e8910 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Fri, 31 Jan 2020 22:43:11 +0100
Subject: Configure step: compiler checks done before basic settings

Until now, the project would first ask for the basic directories, then it
would start testing the compiler. But that was problematic because the
build directory can come from a previous setting (with `./project configure
-e'). Also, it could confuse users to first ask for details, then suddently
tell them that you don't have a working C library! We also need to store
the CPATH variable in the `LOCAL.conf' because in some cases, the compiler
won't work without it.

With this commit, the compiler checking has been moved at the start of the
configure script. Instead of putting the test program in the build
directory, we now make a temporary hidden directory in the source directory
and delete that directory as soon as the tests are done.

In the process, I also noticed that the copyright year of the two hidden
files weren't updated and corrected them.
---
 .dir-locals.el                                     |    4 +-
 .gitignore                                         |    3 +-
 reproduce/analysis/make/initialize.mk              |    6 +
 reproduce/software/bash/configure.sh               | 1443 ++++++++++----------
 .../software/config/installation/LOCAL.conf.in     |    1 +
 reproduce/software/make/high-level.mk              |    7 +-
 6 files changed, 728 insertions(+), 736 deletions(-)

diff --git a/.dir-locals.el b/.dir-locals.el
index 8c3e759..dae2993 100644
--- a/.dir-locals.el
+++ b/.dir-locals.el
@@ -9,8 +9,8 @@
 ;;
 ;; For more information see (info "(emacs) Directory Variables")
 ;;
-;; Copyright (C) 2017 Mosè Giordano <mose@gnu.org>
-;; Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+;; Copyright (C) 2017-2020 Mosè Giordano <mose@gnu.org>
+;; Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 ;;
 ;; Copying and distribution of this file, with or without modification,
 ;; are permitted in any medium without royalty provided the copyright
diff --git a/.gitignore b/.gitignore
index 379e704..9bce289 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,7 +9,7 @@
 # To help readability, please add new files based on the length of the
 # line you wish to add.
 #
-# Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification,
 # are permitted in any medium without royalty provided the copyright
@@ -43,3 +43,4 @@ tex/pipeline
 LOCAL_tmp.mk
 LOCAL_old.mk
 gnuastro-local.conf
+.compiler_test_dir_please_delete
\ No newline at end of file
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index fa39699..1137f28 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -140,6 +140,12 @@ export SHELL := $(installdir)/bin/bash
 export CPPFLAGS := -I$(installdir)/include
 export LD_LIBRARY_PATH := $(installdir)/lib
 
+# Until we build our own C library, without this, the project's GCC won't
+# be able to compile anything if the host C library isn't in a standard
+# place: in particular Debian-based operatings sytems. On other systems, it
+# will be empty.
+export CPATH := $(SYS_CPATH)
+
 # 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.
diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 96c4ad0..a6fbc4e 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -95,954 +95,933 @@ absolute_dir ()
 
 
 
-# Inform the user
-# ---------------
+# Check for C/C++ compilers
+# -------------------------
 #
-# 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
+# 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         !!!!!!!
 
------------------------------
-Project's local configuration
------------------------------
+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:
 
-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).
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 EOF
+    exit 1
+fi
 
 
 
 
 
-# What to do with possibly existing configuration file
-# ----------------------------------------------------
+# Special directory for compiler testing
+# --------------------------------------
 #
-# `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
-
+# This directory will be deleted when the compiler testing is finished.
+compilertestdir=.compiler_test_dir_please_delete
+if ! [ -d $compilertestdir ]; then mkdir $compilertestdir; 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
 
 
+# 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.
 
-# 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)
+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.
 
-        # 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)
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
 
-        # - 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
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
 
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
 
-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.
+   $ ./project configure -e
 
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 EOF
-        downloader="no-downloader-found"
-    fi;
+    exit 1
 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.
----------------
-
+# 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 > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void) {return EXIT_SUCCESS;}
 EOF
-    bdir=
-    currentdir=$(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 $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
 
-        # 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
+# 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
 
 
 
 
 
-# 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.
+# See if the C compiler can build static libraries
+# ------------------------------------------------
 
-EOF
-    read -p"(OPTIONAL) Input datasets directory ($indir): " inindir
-    if [ x$inindir != x ]; then
-        indir=$inindir
-        echo " -- Using '$indir'"
-    fi
-fi
+# 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
 
 
 
 
 
-# Dependency tarball directory
+# If we are on a Mac OS system
 # ----------------------------
-if [ x"$software_dir" = x ]; then
-    ddir=$optionaldir
+#
+# 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
-    ddir=$software_dir
+    host_cc=0
+    on_mac_os=no
 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
 
+# 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
 
 
-# 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}' $pconf)
+# See if a link-able static C library exists
+# ------------------------------------------
+#
+# After building GCC, we must use PatchELF to correct its RPATHs. However,
+# PatchELF links internally with `libstdc++'. So a dynamicly linked
+# PatchELF cannot be used to correct the links to `libstdc++' in general
+# (on some systems this causes no problem, but on others it doesn't!).
+#
+# However, to build a Static PatchELF, we need to be able to link with the
+# static C library, which is not always available on some GNU/Linux
+# systems. Therefore we need to check this here. If we can't build a static
+# PatchELF, we won't build any GCC either.
+if [ x"$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
 
-    # 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)
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-    # 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
+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.
 
-    # Make sure `bdir' is an absolute path and it exists.
-    berr=0
-    ierr=0
-    bdir=$(absolute_dir $inbdir)
+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.
 
-    if ! [ -d $bdir  ]; then if ! mkdir $bdir; then berr=1; err=1; fi; fi
-    if [ $err = 1 ]; then
-        cat <<EOF
+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:
 
-#################################################################
-########  ERORR reading existing configuration file  ############
-#################################################################
-EOF
-        if [ $verr = 1 ]; then
-            cat <<EOF
+    $ sudo yum install glibc-static
 
-These variables have no value: $novalue.
-EOF
-        fi
-        if [ $berr = 1 ]; then
-           cat <<EOF
+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.
 
-Couldn't create the build directory '$bdir' (value to 'BDIR') in
-'$pconf'.
-EOF
-        fi
+    $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
+    $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
 
-        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
 
+# 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
 
-# --------- 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
-# ------------------------------------------
+# 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.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-# 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
+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.
 
-# 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
+If you can't find a solution, please send the error message above to the
+link below and we'll try to help
 
-# Installed software
-instdir=$sdir/installed
-if ! [ -d $instdir ]; then mkdir $instdir; fi
+https://savannah.nongnu.org/support/?func=additem&group=reproduce
 
-# To record software versions and citation.
-verdir=$instdir/version-info
-if ! [ -d $verdir ]; then mkdir $verdir; fi
+TIP: Once you find the solution, you can use the '-e' option to use
+existing configuration:
 
-# Program and library versions and citation.
-ibidir=$verdir/proglib
-if ! [ -d $ibidir ]; then mkdir $ibidir; fi
+   $ ./project configure -e
 
-# 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
+EOF
+        exit 1
+    fi
+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
+# Delete the compiler testing directory
+# -------------------------------------
+#
+# This directory was made above to make sure the necessary compilers can be
+# run.
+rm -rf $compilertestdir
 
-# 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.
+# Inform the user
+# ---------------
 #
-# 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.
+# 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
 
-# Set the top-level shared memory location.
-if [ -d /dev/shm ]; then     shmdir=/dev/shm
-else                         shmdir=""
-fi
+-----------------------------
+Project's local configuration
+-----------------------------
 
-# 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
+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).
 
-# 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
+EOF
 
 
 
 
 
-# Check for C/C++ compilers
-# -------------------------
+# What to do with possibly existing configuration file
+# ----------------------------------------------------
 #
-# 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
+# `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
-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
+
+# 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
 
 
 
 
 
-# Check C compiler
-# ----------------
-gcc_works=0
-testprog=$tmpblddir/test-c
-testsource=$tmpblddir/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
-    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.
+# 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)
 
-If you can't find a solution, please send the error message above to the
-link below and we'll try to help
+        # 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)
 
-https://savannah.nongnu.org/support/?func=additem&group=reproduce
+        # - 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
 
-TIP: Once you find the solution, you can use the '-e' option to use
-existing configuration:
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-   $ ./project configure -e
+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
-    exit 1
+        downloader="no-downloader-found"
+    fi;
 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
-cat > $cprog <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void) {return EXIT_SUCCESS;}
-EOF
-if $CC $cprog -o$oprog -Wl,-rpath-link 2>/dev/null > /dev/null; then
-    export rpath_command="-Wl,-rpath-link=$instdir/lib"
-else
-    export rpath_command=""
-fi
-rm -f $oprog $cprog
+# 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.
+---------------
 
-# 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 $CC $cprog -o$oprog 2>/dev/null > /dev/null; then
-    needs_ldl=no;
-else
-    needs_ldl=yes;
-fi
-rm -f $oprog $cprog
-
-
+    bdir=
+    currentdir=$(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
 
-# See if the C compiler can build static libraries
-# ------------------------------------------------
+                # If it was newly created, it will be empty, so delete it.
+                if ! [ "$(ls -A $bdir)" ]; then rm --dir $bdir; fi
 
-# 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
+                # 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
 
-#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
+        # Reset `build_dir' to blank, so it continues asking when the
+        # previous value wasn't usable.
+        build_dir=
+    done
+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
+# Input directory
+# ---------------
+if [ x"$input_dir" = x ]; then
+    indir=$optionaldir
 else
-    host_cc=0
-    on_mac_os=no
+    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.
 
-# 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_cppflags=""
-sys_library_path=""
-if [ x"$$on_mac_os" != xyes ]; then
+NOTE II: This directory (if given) will only be read, nothing will be
+written into it, so no writing permissions are necessary.
 
-    # 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
+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.
 
-    # For a check:
-    #echo "sys_library_path: $sys_library_path"
-    #echo "sys_cpath: $sys_cpath"
+EOF
+    read -p"(OPTIONAL) Input datasets directory ($indir): " inindir
+    if [ x$inindir != x ]; then
+        indir=$inindir
+        echo " -- Using '$indir'"
+    fi
 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"$host_cc" = x0 ]; then
-    testprog=$tmpblddir/test-c
-    testsource=$tmpblddir/test.c
-    echo; echo; echo "Checking if static C library is available...";
-    cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/cdefs.h>
-int main(void){printf("...yes\n");
-               return EXIT_SUCCESS;}
+# Dependency tarball directory
+# ----------------------------
+if [ x"$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
-    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 $testsource
-        gccwarning=1
-        host_cc=1
-        cat <<EOF
+    read -p"(OPTIONAL) Directory of dependency tarballs ($ddir): " tmpddir
+    if [ x"$tmpddir" != x ]; then
+        ddir=$tmpddir
+        echo " -- Using '$ddir'"
+    fi
+fi
 
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         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
+# Write the parameters into the local configuration file.
+if [ $rewritepconfig = yes ]; then
 
-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.
+    # Add commented notice.
+    create_file_with_notice $pconf
 
-    $ export LDFLAGS="-L/PATH/TO/STATIC/LIBC \$LDFLAGS"
-    $ export CPPFLAGS="-I/PATH/TO/SYS/CDEFS_H \$LDFLAGS"
+    # 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)
 
-EOF
-    fi
-fi
+    # 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)
 
-# Print a warning if GCC is not meant to be built.
-if [ x"$gccwarning" = x1 ]; then
+    # Make sure all necessary variables have a value
+    err=0
+    verr=0
+    novalue=""
+    if [ x"$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
 
-PLEASE SEE THE WARNINGS ABOVE.
+#################################################################
+########  ERORR reading existing configuration file  ############
+#################################################################
+EOF
+        if [ $verr = 1 ]; then
+            cat <<EOF
 
-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'.
+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
-        sleep 5
+        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
 
 
 
 
 
-# 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 [ $host_cc = 1 ]; then
+# --------- Delete for no Gnuastro ---------
+# Get the version of Gnuastro that must be used.
+gversion=$(awk '$1=="gnuastro-version" {print $NF}' $depverfile)
 
-    # 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
+# 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
 ______________________________________________________
-!!!!!!!      Fortran Compiler NOT FOUND        !!!!!!!
+!!!!!!!!!!!!!!!!!!CONFIGURATION ERROR!!!!!!!!!!!!!!!!!
 
-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:
+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:
 
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+   $ rm $glconf
+   $ ./project configure
 
-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
+# ------------------------------------------
 
-    # See if the Fortran compiler works
-    testprog=$tmpblddir/test-f
-    testsource=$tmpblddir/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
+# 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
 
-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
+# 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
 
 
@@ -1185,7 +1164,6 @@ fi
 # 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.
-export CPPFLAGS="$CPPFLAGS $sys_cppflags"
 if [ x"$sys_library_path" != x ]; then
     if [ x"$LIBRARY_PATH" = x ]; then
         export LIBRARY_PATH="$sys_library_path"
@@ -1193,9 +1171,9 @@ if [ x"$sys_library_path" != x ]; then
         export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
     fi
     if [ x"$CPATH" = x ]; then
-        export LIBRARY_PATH="$sys_cpath"
+        export CPATH="$sys_cpath"
     else
-        export LIBRARY_PATH="$CPATH:$sys_cpath"
+        export CPATH="$CPATH:$sys_cpath"
     fi
 fi
 
@@ -1243,6 +1221,7 @@ fi
                     static_build=$static_build \
                     numthreads=$numthreads \
                     on_mac_os=$on_mac_os \
+                    sys_cpath=$sys_cpath \
                     host_cc=$host_cc \
                     -j$numthreads
 
diff --git a/reproduce/software/config/installation/LOCAL.conf.in b/reproduce/software/config/installation/LOCAL.conf.in
index 1045f72..0579218 100644
--- a/reproduce/software/config/installation/LOCAL.conf.in
+++ b/reproduce/software/config/installation/LOCAL.conf.in
@@ -12,5 +12,6 @@
 BDIR             = @bdir@
 INDIR            = @indir@
 DEPENDENCIES-DIR = @ddir@
+SYS_CPATH        = @sys_cpath@
 DOWNLOADER       = @downloader@
 GROUP-NAME       = @groupname@
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 0d05626..02ae1a5 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -70,8 +70,8 @@ all: $(foreach p, $(top-level-programs),  $(ibidir)/$(p)) \
 .SHELLFLAGS := --noprofile --norc -ec
 export CCACHE_DISABLE := 1
 export PATH := $(ibdir)
-export CXX := $(ibdir)/g++
 export CC := $(ibdir)/gcc
+export CXX := $(ibdir)/g++
 export SHELL := $(ibdir)/bash
 export F77 := $(ibdir)/gfortran
 export LD_RUN_PATH := $(ildir):$(il64dir)
@@ -79,6 +79,11 @@ export PKG_CONFIG_PATH := $(ildir)/pkgconfig
 export LD_LIBRARY_PATH := $(ildir):$(il64dir)
 export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
 
+# Until we build our own C library, without this, our GCC won't be able to
+# compile anything! Note that on most systems (in particular
+# non-Debian-based), `sys_cpath' will be empty.
+export CPATH := $(sys_cpath)
+
 # 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.
-- 
cgit v1.2.1