From 852d996f8f5f1e5e0114dc82aaf33d81c725fb20 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 19 Jan 2020 15:08:08 +0000
Subject: Better search for static C library at start of configuration

Until now, to see if a working static C library and `sys/cdefs.h' exist, we
were checking absolute locations like `/usr/include/sys/cdefs.h' or
`/usr/lib/libc.a' and `/usr/lib64/libc.a'. But this is not robust because
on different systems, they can be in different locations.

With this commit, we actually use `find' to find the location of `libc.a'
and use that to add elements to CPPFLAGS and LDFLAGS. This should fix the
problem on systems that have them on non-standard locations.
---
 reproduce/software/bash/configure.sh | 183 ++++++++++++++---------------------
 1 file changed, 75 insertions(+), 108 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 08f2609..0bb0917 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -819,42 +819,6 @@ static_build=no
 
 
 
-# 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`'):
-
-  $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done
-
--------------------------
-
-
-EOF
-    sleep $tsec
-fi
-
-
-
-
-
 # If we are on a Mac OS system
 # ----------------------------
 #
@@ -869,6 +833,7 @@ 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
 
@@ -876,74 +841,33 @@ fi
 
 
 
-# See if GCC can be built
-# -----------------------
-#
-# On some GNU/Linux distros, the C compiler is broken into `multilib' (for
-# 32-bit and 64-bit support, with their own headers). On these systems,
-# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by
-# default. So GCC will crash with different ugly errors! The only solution
-# is that user manually installs the `multilib' part as root, before
-# running the configure script.
+# Necessary C library element positions
+# -------------------------------------
 #
-# Note that `sys/cdefs.h' may be available in other directories (for
-# example `/usr/include/x86_64-linux-gnu/') that are automatically included
-# in an installed GCC. HOWEVER during the build of GCC, all those other
-# directories are ignored. So even if they exist, they are useless.
-gccwarning=0
-if [ $host_cc = 0 ]; then
-    if ! [ -f /usr/include/sys/cdefs.h ]; then
-        host_cc=1
-        gccwarning=1
-        cat <<EOF
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the
-project can't build its custom GCC to ensure better reproducibility. We
-strongly recommend installing the proper package (for your operating
-system) that installs this necessary file. For example on some Debian-based
-GNU/Linux distros, you need these two packages: 'gcc-multilib' and
-'g++-multilib'.
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-    fi
+# 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.
+if [ x"$$on_mac_os" = xyes ]; then
+    sys_libc_ldflags=;
+else
+    sys_libc_ldflags=$(find /lib* /usr/lib*/* -name "libc.a" \
+                           | sed -e's|/libc\.a||g' \
+                           | tr ' ' '\n' \
+                           | awk '{printf "-L%s ", $1}' );
+    sys_libc_cppflags=$(echo $sys_libc_ldflags \
+                            | tr ' ' '\n' \
+                            | sed -e's|-L|-I|' -e's|/lib/|/include/|' \
+                            | awk '!/\/lib/{printf "%s ", $1}' );
+    #echo "sys_libc_ldflags: $sys_libc_ldflags"
+    #echo "sys_libc_cppflags: $sys_libc_cppflags"
+    export LDFLAGS="$LDFLAGS $sys_libc_ldflags"
+    export CPPFLAGS="$CPPFLAGS $sys_libc_cppflags"
+fi
 
-    if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then
-        # This is just a place holder
-        host_cc=$host_cc
-    else
-        host_cc=1
-        gccwarning=1
-        cat <<EOF
 
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because
-of this, the project can't build its custom GCC to ensure better
-reproducibility. We recommend installing the proper package (for your
-operating system) that installs this necessary file.
-
-Some possible solutions:
-  1. On some Debian-based GNU/Linux distros, these two packages may fix the
-     problem: 'gcc-multilib' and 'g++-multilib'.
-  2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have
-     '/usr/lib64', then running the following command might fix this
-     particular problem by making a symbolic link.
-         $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
-     After the configure script is finished, delete the link with 'rm
-     /usr/lib64' (you won't need it any more as far as this project is
-     concerned).
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-EOF
-    fi
-fi
 
 # See if a link-able static C library exists
 # ------------------------------------------
@@ -957,18 +881,22 @@ fi
 # 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 [ $host_cc = 0 ]; then
+if [ x"$host_cc" = x0 ]; then
     testprog=$tmpblddir/test-c
     testsource=$tmpblddir/test.c
     echo; echo; echo "Checking if static C library is available...";
     echo "#include <stdio.h>"                       > $testsource
     echo "#include <stdlib.h>"                     >> $testsource
-    echo "int main(void){printf(\"...yes\");"      >> $testsource
+    echo "#include <sys/cdefs.h>"                  >> $testsource
+    echo "int main(void){printf(\"...yes\n\");"    >> $testsource
     echo "               return EXIT_SUCCESS;}"    >> $testsource
-    if gcc $testsource -o$testprog -static -lc && $testprog; then
+    cc_call="gcc $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
@@ -979,15 +907,18 @@ if [ $host_cc = 0 ]; then
 !!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-A usable static C library ('libc.a', in any directory) cannot be linked in
-the current settings of this system. Because of this we can't build a
-static PatchELF, hence we can't build GCC.
+A usable static C library ('libc.a', in any directory) cannot be linked,
+and 'sys/cdefs.h' cannot be included with the current settings of this
+system. Because of this we can't build a static PatchELF, hence we can't
+build GCC.
 
 If you have 'libc.a', but in a non-standard location (for example in
-'/PATH/TO/STATIC/LIBC/libc.a'), please run this command, then re-configure
-the project to fix this problem.
+'/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"
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
@@ -996,7 +927,7 @@ EOF
 fi
 
 # Print a warning if GCC is not meant to be built.
-if [ $gccwarning = 1 ]; then
+if [ x"$gccwarning" = x1 ]; then
         cat <<EOF
 
 PLEASE SEE THE WARNINGS ABOVE.
@@ -1090,6 +1021,42 @@ 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`'):
+
+  $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done
+
+-------------------------
+
+
+EOF
+    sleep $tsec
+fi
+
+
+
+
+
 # Number of threads for basic builds
 # ----------------------------------
 #
-- 
cgit v1.2.1


From be73ea496657099603cce7e20413b9c6ee993c94 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 19 Jan 2020 21:15:37 +0000
Subject: LIBRARY_PATH is set accordingly based on the host

Until now, GCC wouldn't build properly on Debian-based operating systems
because `ld' needed to link with several necessary C library features like
`crti.o' and `crtn.o' (this is an `ld' issue, not GCC). The solution is to
add the directory containing them to `LIBRARY_PATH'. In the previous
commit, I actually searched for these files, but while testing on another
system, I noticed that it can be problematic (other architectures may
exist).

With this commit, we are actually finding the build architecture of the
running GCC (which is the same as the `ld') and using that to fix a fixed
directory to `LIBRARY_PATH'.
---
 reproduce/software/bash/configure.sh | 56 +++++++++++++++++++++++++-----------
 1 file changed, 40 insertions(+), 16 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 0bb0917..c0f8025 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -848,21 +848,26 @@ fi
 # 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.
-if [ x"$$on_mac_os" = xyes ]; then
-    sys_libc_ldflags=;
-else
-    sys_libc_ldflags=$(find /lib* /usr/lib*/* -name "libc.a" \
-                           | sed -e's|/libc\.a||g' \
-                           | tr ' ' '\n' \
-                           | awk '{printf "-L%s ", $1}' );
-    sys_libc_cppflags=$(echo $sys_libc_ldflags \
-                            | tr ' ' '\n' \
-                            | sed -e's|-L|-I|' -e's|/lib/|/include/|' \
-                            | awk '!/\/lib/{printf "%s ", $1}' );
-    #echo "sys_libc_ldflags: $sys_libc_ldflags"
-    #echo "sys_libc_cppflags: $sys_libc_cppflags"
-    export LDFLAGS="$LDFLAGS $sys_libc_ldflags"
-    export CPPFLAGS="$CPPFLAGS $sys_libc_cppflags"
+sys_cppflags=""
+sys_library_path=""
+if [ x"$$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_cppflags=-I/usr/include/$gcctarget
+        fi
+    fi
+
+    # For a check:
+    #echo "sys_library_path: $sys_library_path"
+    #echo "sys_cppflags: $sys_cppflags"
 fi
 
 
@@ -1149,6 +1154,24 @@ fi
 
 
 
+# library_path (ONLY FOR BASIC)
+# -----------------------------
+#
+# During the basic build, we need to include possibly existing special C
+# compiler targets (if they exist).
+export CPPFLAGS="$CPPFLAGS $sys_cppflags"
+if [ x"$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
+fi
+
+
+
+
+
 # Build basic software
 # --------------------
 #
@@ -1160,9 +1183,9 @@ 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 \
-     numthreads=$numthreads \
      host_cc=$host_cc \
      -j$numthreads
 
@@ -1184,6 +1207,7 @@ else
 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 \
-- 
cgit v1.2.1


From 0ccea404bf994525a6f42ccea8ed7e325660627a Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 19 Jan 2020 22:21:34 +0000
Subject: Corrected typo in last commit (forgetting \ at end of line)

In the previous commmit, I had forgot to add a `\' after the newly added
`sys_library_path' variable to the `high-level.mk' call.
---
 reproduce/software/bash/configure.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index c0f8025..8cdd744 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -1207,7 +1207,7 @@ else
 fi
 .local/bin/env -i HOME=$bdir \
     .local/bin/make -f reproduce/software/make/high-level.mk \
-                    sys_library_path=$sys_library_path
+                    sys_library_path=$sys_library_path \
                     rpath_command=$rpath_command \
                     static_build=$static_build \
                     numthreads=$numthreads \
-- 
cgit v1.2.1


From 7ac86df891798fd1f0ef4d7a40aff43ec9621854 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Mon, 20 Jan 2020 00:05:41 +0000
Subject: IMPORTANT!!! Configuration Makefiles now have a .conf suffix

Until now, the configuration Makefiles (in
`reproduce/software/config/installation' and `reproduce/analysis/config')
had a `.mk' suffix, similar to the workhorse Makefiles. Although they are
indeed Makefiles, but given their nature (to only keep configuration
parameters), it is confusing (especially to early users) for them to also
have a `.mk' (similar to the analysis or software building Makefiles).

To address this issue, with this commit, all the configuration Makefiles
(in those directories) are now given a `.conf' suffix. This is also assumed
for all the files that are loaded.

The configuration (software building) and running of the template have been
checked with this change from scratch, but please report any error that may
not have been noticed.

THIS IS AN IMPORTANT CHANGE AND WILL CAUSE CRASHES OR UNEXPECTED BEHAVIORS
FOR PROJECTS THAT HAVE BRANCHED FROM THIS TEMPLATE. PLEASE CORRECT THE
SUFFIX OF ALL YOUR PROJECT'S CONFIGURATION MAKEFILES (IN THE DIRECTORIES
ABOVE), OTHERWISE THEY AREN'T AUTOMATICALLY LOADED ANYMORE.
---
 reproduce/software/bash/configure.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 8cdd744..c681298 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -38,11 +38,11 @@ cdir=reproduce/software/config
 
 sbdir=$cdir/installation
 
-pconf=$sbdir/LOCAL.mk
-ptconf=$sbdir/LOCAL_tmp.mk
-poconf=$sbdir/LOCAL_old.mk
-depverfile=$cdir/installation/versions.mk
-depshafile=$cdir/installation/checksums.mk
+pconf=$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=$cdir/gnuastro/gnuastro-local.conf
 # ------------------------------------------
@@ -117,7 +117,7 @@ EOF
 # What to do with possibly existing configuration file
 # ----------------------------------------------------
 #
-# `LOCAL.mk' is the top-most local configuration for the project. If it
+# `LOCAL.conf' is the top-most local configuration for the project. If it
 # already exists when this script is run, we'll make a copy of it as backup
 # (for example the user might have ran `./project configure' by mistake).
 printnotice=yes
@@ -299,10 +299,10 @@ if [ x"$input_dir" = x ]; then
 else
     indir=$input_dir
 fi
-wfpc2name=$(awk '!/^#/ && $1=="WFPC2IMAGE" {print $3}' $adir/INPUTS.mk)
-wfpc2md5=$(awk  '!/^#/ && $1=="WFPC2MD5"   {print $3}' $adir/INPUTS.mk)
-wfpc2size=$(awk '!/^#/ && $1=="WFPC2SIZE"  {print $3}' $adir/INPUTS.mk)
-wfpc2url=$(awk  '!/^#/ && $1=="WFPC2URL"   {print $3}' $adir/INPUTS.mk)
+wfpc2name=$(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
 
-- 
cgit v1.2.1


From cf0427009decbcad33a269898a428341e9c0ceff Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Wed, 22 Jan 2020 15:14:03 +0000
Subject: Better explanation for missing static C library

Until now, the explanation for a missing static C library didn't actually
guide the users to look above and see the error message! So with this
commit, I edited it a little to be more clear (and mention to look
above). Also, I noticed that on Amazon AWS systems, the static C library is
installed as a separate package, so to help the users, I added the
necessary command and some better explanation.
---
 reproduce/software/bash/configure.sh | 34 ++++++++++++++++++++++------------
 1 file changed, 22 insertions(+), 12 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index c681298..60f69b9 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -912,18 +912,28 @@ if [ x"$host_cc" = x0 ]; then
 !!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-A usable static C library ('libc.a', in any directory) cannot be linked,
-and 'sys/cdefs.h' cannot be included with the current settings of this
-system. Because of this we can't build a static PatchELF, hence we can't
-build GCC.
-
-If you have 'libc.a', 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"
+The 'sys/cdefs.h' headaer 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"
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-- 
cgit v1.2.1


From 2264c0fea5668cd8f827cdbd89004fd390b0b14f Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 23 Jan 2020 18:54:29 +0000
Subject: IMPORTANT: Project preparation is now also done with project make

Until now, the main commands to run the project were these: `./project
configure' (to build the software), `./project prepare' (to possibly
arrange input datasets and build special configuration Makefiles) and
finally `./project make' to run the project.

The main logic behind the "prepare" phase `top-prepare.mk' is to build
configuration files that can be fed into the "make" step and optimize its
operation. For example when the total number of necessary inputs for the
majority of the analysis is not as large as the total number of
inputs. With "prepare" (when necessary), you go through the raw inputs,
select the ones that are necessary for the rest of the project. The output
of `top-prepare.mk' is a configuration file (a Make variable) that keeps
the IDs (numbers, names, etc). That configuration file would then be used
in the `top-make.mk' to identify the lower level targets and allow optimal
project organization and management.

But the last two are both part of the analysis, and while they indeed need
different calls to Make to be executed, many projects don't actually need a
preparation phase: ultimately, its an implementation choice by the project
developers and doesn't concern the project users (or the developers when
they are running it).

To avoid confusing the users, or simply annoying them when a projet doesn't
need it, with this commit, the top-level `top-prepare.mk' and `top-make.mk'
Makefiles are called with the single `./project make' command and
`./project prepare' has been dropped. I noticed this while writing the
paper on this system.
---
 reproduce/software/bash/configure.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 60f69b9..17e3048 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -1387,9 +1387,9 @@ echo `.local/bin/date` > $finaltarget
 # The configuration is now complete, we can inform the user on the next
 # step(s) to take.
 if [ x$reproducible_paper_group_name = x ]; then
-    buildcommand="./project prepare -j8"
+    buildcommand="./project make -j8"
 else
-    buildcommand="./project prepare --group=$reproducible_paper_group_name -j8"
+    buildcommand="./project make --group=$reproducible_paper_group_name -j8"
 fi
 cat <<EOF
 
-- 
cgit v1.2.1


From cccf8782014beb85b8c8cb23d6ece56c849773f3 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Thu, 23 Jan 2020 19:17:16 +0000
Subject: Hashbangs of project and configure.sh set to /bin/sh

Until now, the hashbang of these two shell scripts was set to `/bin/bash',
hence assuming that GNU Bash exists on the host system! But this is an
extra requirement on the host operating system and these two scripts should
be written such that they operate on a POSIX shell (the generic `/bin/sh'
which can point to any shell program).

With this commit this has been implemented! We may confront some errors as
the system is run on other systems, but we should fix such errors and work
hard to make these two scripts as POSIX-compatible as possible (runnable on
any shell, so as not to force users to install Bash before running the
project).

This completes Task #15525.
---
 reproduce/software/bash/configure.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 17e3048..6e5abb8 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -1,4 +1,4 @@
-#! /bin/bash
+#! /bin/sh
 #
 # Necessary preparations/configurations for the reproducible project.
 #
-- 
cgit v1.2.1


From f37005b729065f0e4ff6bfa99e5410ebb210cd60 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Mon, 27 Jan 2020 15:15:40 +0000
Subject: Initial scripts compatible with Dash (minimalistic POSIX)

Until now, the initial project scripts were primarily tested with GNU
Bash. But Bash is not generally available on all systems (it has many
features beyond POSIX). Because of this, effectively we were imposing the
requirement on the user that they must have Bash installed. We recently
started this with setting the shebang of `project' and
`reproduce/software/bash/configure.sh' to `/bin/sh'. After doing so, Raul
and Gaspar reported an error on their systems.

To fix the problem, I installed Dash (a minimalist POSIX-compliant shell)
on my computer and temporarily set the shebangs to `/bin/dash', ran the
project configuration step and fixed all issues that came up. With this
commit, it can go all the way to building GCC on my system's Dash. After
this stage (when `high-level.mk' is called), there is no problem, because
we have our own version of GNU Bash and that installed version is used.
Probably some more issues still remain and will hopefully be found in the
future.

While doing this, I also noticed the following two minor issues:

 - The `./project configure' option `--input-dir' was not recognized
   because it was mistakenly checking `--inputdir'. It has been corrected.

 - The test C programs now use the `<<EOF' method instead of `echo'.

 - In `basic.mk', the extra space between `syspath' and `:=' was removed
   (it was an ancient relic!).
---
 reproduce/software/bash/configure.sh | 80 +++++++++++++++++++++---------------
 1 file changed, 46 insertions(+), 34 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index 6e5abb8..a4b3e64 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -57,7 +57,8 @@ glconf=$cdir/gnuastro/gnuastro-local.conf
 # In case someone opens the files output from the configuration scripts in
 # a text editor and wants to edit them, it is important to let them know
 # that their changes are not going to be permenant.
-function create_file_with_notice() {
+create_file_with_notice ()
+{
     if echo "# IMPORTANT: file can be RE-WRITTEN after './project configure'" > "$1"
     then
         echo "#"                                                      >> "$1"
@@ -81,7 +82,8 @@ function create_file_with_notice() {
 #
 # Since the build directory will go into a symbolic link, we want it to be
 # an absolute address. With this function we can make sure of that.
-function absolute_dir() {
+absolute_dir ()
+{
     if stat "$1" 1> /dev/null; then
         echo "$(cd "$(dirname "$1")" && pwd )/$(basename "$1")"
     else
@@ -239,7 +241,7 @@ EOF
     bdir=
     currentdir=$(pwd)
     junkname=pure-junk-974adfkj38
-    while [ x$bdir == x ]
+    while [ x$bdir = x ]
     do
         # Ask the user (if not already set on the command-line).
         if [ x"$build_dir" = x ]; then
@@ -264,10 +266,12 @@ EOF
             fi
         fi
 
-        # Make sure the given directory is not a subdirectory of the
-        # source directory.
+        # If its given, make sure it isn't a subdirectory of the source
+        # directory.
         if ! [ x"$bdir" = x ]; then
-            if [[ $bdir == $currentdir* ]]; 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 $bdir; fi
@@ -638,13 +642,13 @@ fi
 # particular) to be present.
 hascc=0;
 if type cc > /dev/null 2>/dev/null; then
-    if type c++ > /dev/null 2>/dev/null; then hascc=1; fi
+    if type c++ > /dev/null 2>/dev/null; then export CC=cc; hascc=1; fi
 else
     if type gcc > /dev/null 2>/dev/null; then
-        if type g++ > /dev/null 2>/dev/null; then hascc=1; fi
+        if type g++ > /dev/null 2>/dev/null; then export CC=gcc; hascc=1; fi
     else
         if type clang > /dev/null 2>/dev/null; then
-            if type clang++ > /dev/null 2>/dev/null; then hascc=1; fi
+            if type clang++ > /dev/null 2>/dev/null; then export CC=clang; hascc=1; fi
         fi
     fi
 fi
@@ -676,14 +680,15 @@ gcc_works=0
 testprog=$tmpblddir/test-c
 testsource=$tmpblddir/test.c
 echo; echo; echo "Checking host C compiler...";
-echo "#include <stdio.h>"                                  > $testsource
-echo "#include <stdlib.h>"                                >> $testsource
-echo "int main(void){printf(\"...C compiler works.\n\");" >> $testsource
-echo "               return EXIT_SUCCESS;}"               >> $testsource
-if gcc $testsource -o$testprog && $testprog; then
+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
 
 ______________________________________________________
@@ -723,10 +728,12 @@ fi
 # LLVM's linker don't accept it an can cause problems.
 oprog=$sdir/rpath-test
 cprog=$sdir/rpath-test.c
-echo "#include <stdio.h>"          > $cprog
-echo "int main(void) {return 0;}" >> $cprog
-if [ x$CC = x ]; then CC=gcc; fi;
-if $CC $cprog -o$oprog -Wl,-rpath-link &> /dev/null; then
+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=""
@@ -755,7 +762,11 @@ main(void) {
     return 0;
 }
 EOF
-if gcc $cprog -o$oprog &> /dev/null; then needs_ldl=no; else needs_ldl=yes; fi
+if $CC $cprog -o$oprog 2>/dev/null > /dev/null; then
+    needs_ldl=no;
+else
+    needs_ldl=yes;
+fi
 rm -f $oprog $cprog
 
 
@@ -782,7 +793,7 @@ static_build=no
 #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
+#if $CC $cprog -o$oprog -static > /dev/null; then
 #    export static_build="yes"
 #else
 #    export static_build="no"
@@ -890,12 +901,14 @@ if [ x"$host_cc" = x0 ]; then
     testprog=$tmpblddir/test-c
     testsource=$tmpblddir/test.c
     echo; echo; echo "Checking if static C library is available...";
-    echo "#include <stdio.h>"                       > $testsource
-    echo "#include <stdlib.h>"                     >> $testsource
-    echo "#include <sys/cdefs.h>"                  >> $testsource
-    echo "int main(void){printf(\"...yes\n\");"    >> $testsource
-    echo "               return EXIT_SUCCESS;}"    >> $testsource
-    cc_call="gcc $testsource $CPPFLAGS $LDFLAGS -o$testprog -static -lc"
+    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 && $testprog; then
         gccwarning=0
         good_static_libc=1
@@ -912,7 +925,7 @@ if [ x"$host_cc" = x0 ]; then
 !!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-The 'sys/cdefs.h' headaer cannot be included, or a usable static C library
+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.
 
@@ -927,7 +940,7 @@ 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
+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.
@@ -1057,13 +1070,12 @@ will be installed in:
 **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`'):
+configured (in another terminal, but on this same directory: 'pwd'):
 
-  $ while true; do echo; date; ls .build/software/build-tmp; sleep 1; done
+  $ ./project --check-config
 
 -------------------------
 
-
 EOF
     sleep $tsec
 fi
@@ -1281,8 +1293,8 @@ fi
 # After everything is installed, we'll put all the names and versions in a
 # human-readable paragraph and also prepare the BibTeX citation for the
 # software.
-function prepare_name_version() {
-
+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).
-- 
cgit v1.2.1


From 50832921ab5eac62350855955d3af3f6f0766bbf Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Fri, 31 Jan 2020 20:29:02 +0100
Subject: Architecture-specific C headers on Debian-based OSs now accounted

Rencely the building of GCC was allowed on Debian-based systems that have
their basic C library in architecture-specific directories, like
`/usr/lib/x86_64-linux-gnu'. However, these systems also have their headers
in non-standard locations, for example `/usr/include/x86_64-linux-gnu' and
this caused a crash on a new Ubuntu system.

/usr/include/stdio.h:27:10: fatal error: bits/libc-header-start.h: No
such file or directory
   27 | #include <bits/libc-header-start.h>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.

The reason it didn't cause problems on other Ubuntus that we tested before
was historic: In the old days, we would ask Ubuntu systems to install
multilib features to have GCC. Because they had installed those features,
this problem didn't show up! But this wasn't mandatory!

With this commit, the `CPATH' environment variable is set (similar to how
`LIBRARY_PATH' was set) and this fixed the problem on a clean Debian
virtual machine.

This bug was reported by Sebastian Luna Valero.
---
 reproduce/software/bash/configure.sh | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

diff --git a/reproduce/software/bash/configure.sh b/reproduce/software/bash/configure.sh
index a4b3e64..96c4ad0 100755
--- a/reproduce/software/bash/configure.sh
+++ b/reproduce/software/bash/configure.sh
@@ -872,13 +872,13 @@ if [ x"$$on_mac_os" != xyes ]; then
     if [ x"$gcctarget" != x ]; then
         if [ -f /usr/lib/$gcctarget/libc.a ]; then
             export sys_library_path=/usr/lib/$gcctarget
-            export sys_cppflags=-I/usr/include/$gcctarget
+            export sys_cpath=/usr/include/$gcctarget
         fi
     fi
 
     # For a check:
     #echo "sys_library_path: $sys_library_path"
-    #echo "sys_cppflags: $sys_cppflags"
+    #echo "sys_cpath: $sys_cpath"
 fi
 
 
@@ -1176,11 +1176,15 @@ fi
 
 
 
-# library_path (ONLY FOR BASIC)
-# -----------------------------
+# Paths needed by the host compiler (only for `basic.mk')
+# -------------------------------------------------------
 #
-# During the basic build, we need to include possibly existing special C
-# compiler targets (if they exist).
+# 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.
 export CPPFLAGS="$CPPFLAGS $sys_cppflags"
 if [ x"$sys_library_path" != x ]; then
     if [ x"$LIBRARY_PATH" = x ]; then
@@ -1188,6 +1192,11 @@ if [ x"$sys_library_path" != x ]; then
     else
         export LIBRARY_PATH="$LIBRARY_PATH:$sys_library_path"
     fi
+    if [ x"$CPATH" = x ]; then
+        export LIBRARY_PATH="$sys_cpath"
+    else
+        export LIBRARY_PATH="$CPATH:$sys_cpath"
+    fi
 fi
 
 
-- 
cgit v1.2.1


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.
---
 reproduce/software/bash/configure.sh | 1443 +++++++++++++++++-----------------
 1 file changed, 711 insertions(+), 732 deletions(-)

(limited to 'reproduce/software/bash/configure.sh')

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
 
-- 
cgit v1.2.1


From 35ed6cf0df743175688b49a4559793cb7f6e9d66 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sat, 1 Feb 2020 21:24:00 +0100
Subject: 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'.
---
 reproduce/software/bash/configure.sh | 1407 ----------------------------------
 1 file changed, 1407 deletions(-)
 delete mode 100755 reproduce/software/bash/configure.sh

(limited to 'reproduce/software/bash/configure.sh')

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
-- 
cgit v1.2.1