Imported recent updates in Maneage, minor conflicts fixed

Some very minor conflicts came up and were easily corrected. They were
mostly in parts that are also shared with the demonstration in the core
Maneage branch.

2 files changed, 172 insertions, 156 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index fc34ca9..6ffb4ff 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -30,6 +30,20 @@ set -e
 
 
 
+# Project-specific settings
+# -------------------------
+#
+# The variables defined here may be different between different
+# projects. Ideally, they should be detected automatically, but we haven't
+# had the chance to implement it yet (please help if you can!). Until then,
+# please set them based on your project (if they differ from the core
+# branch).
+need_gfortran=0
+
+
+
+
+
 # Internal directories
 # --------------------
 #
@@ -44,9 +58,6 @@ ptconf=$cdir/LOCAL_tmp.conf
 poconf=$cdir/LOCAL_old.conf
 depverfile=$cdir/versions.conf
 depshafile=$cdir/checksums.conf
-# --------- Delete for no Gnuastro ---------
-glconf=$adir/gnuastro/gnuastro-local.conf
-# ------------------------------------------
 
 
 
@@ -186,35 +197,93 @@ free_space_warning()
 
 
 
+# See if we are on a Linux-based system
+# --------------------------------------
+#
+# Some features are tailored to GNU/Linux systems, while the BSD-based
+# behavior is different. Initially we only tested macOS (hence the name of
+# the variable), but as FreeBSD is also being inlucded in our tests. As
+# more systems get used, we need to tailor these kinds of things better.
+kernelname=$(uname -s)
+if [ x$kernelname = xLinux ]; then
+    on_mac_os=no
+
+    # Don't forget to add the respective C++ compiler below (leave 'cc' in
+    # the end).
+    c_compiler_list="gcc clang cc"
+else
+    host_cc=1
+    on_mac_os=yes
+
+    # Don't forget to add the respective C++ compiler below (leave 'cc' in
+    # the end).
+    c_compiler_list="clang gcc cc"
+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
+# To build the software, we'll need some basic tools (the C/C++ compilers
+# in particular) to be present.
+has_compilers=no
+for c in $c_compiler_list; do
+
+    # Set the respective C++ compiler.
+    if   [ x$c = xcc    ]; then cplus=c++;
+    elif [ x$c = xgcc   ]; then cplus=g++;
+    elif [ x$c = xclang ]; then cplus=clang++;
     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
+        cat <<EOF
+______________________________________________________
+!!!!!!!                   BUG                  !!!!!!!
+
+The respective C++ compiler executable name for the C compiler '$c' hasn't
+been set! You can add it in the 'reproduce/software/shell/configure.sh'
+script (just above this error message), or contact us with this web-form:
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+        exit 1
+    fi
+
+    # Check if they exist.
+    if type $c > /dev/null 2>/dev/null; then
+        export CC=$c;
+        if type $cplus > /dev/null 2>/dev/null; then
+            export CXX=$cplus
+            has_compilers=yes
+            break
         fi
     fi
-fi
-if [ $hascc = 0 ]; then
+done
+if [ x$has_compilers = xno ]; 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:
+To build this project's software, the host system needs to have both C and
+C++ compilers. The commands that were checked are listed below:
+
+    cc, c++            Generic C/C++ compiler (possibly links to below).
+    gcc, g++           Part of GNU Compiler Collection (GCC).
+    clang, clang++     Part of LLVM compiler infrastructure.
+
+If your compiler is not checked, please get in touch with the web-form
+below, so we add it. We will try our best to add it soon. Until then,
+please install at least one of these compilers on your system to proceed.
+
+    https://savannah.nongnu.org/support/?func=additem&group=reproduce
+
+NOTE: for macOS systems, the LLVM compilers that are provided in a native
+Xcode install are recommended. There are known problems with GCC on macOS.
 
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 EOF
@@ -238,10 +307,9 @@ 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...";
+echo; echo; echo "Checking host C compiler ('$CC')...";
 cat > $testsource <<EOF
 #include <stdio.h>
 #include <stdlib.h>
@@ -257,7 +325,7 @@ else
 ______________________________________________________
 !!!!!!!        C compiler doesn't work         !!!!!!!
 
-Host C compiler ('gcc') can't build a simple program.
+Host C compiler ('$CC') 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
@@ -268,11 +336,6 @@ 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
@@ -283,28 +346,6 @@ 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)
 # ----------------------------------------
 #
@@ -326,7 +367,7 @@ if $CC $testsource -o$testprog 2>/dev/null > /dev/null; then
 else
     needs_ldl=yes;
 fi
-rm -f $testprog $testsource
+
 
 
 
@@ -351,25 +392,6 @@ static_build=no
 
 
 
-# See if we are on a Linux-based system
-# --------------------------------------
-#
-# Some features are tailored to GNU/Linux systems, while the BSD-based
-# behavior is different. Initially we only tested macOS (hence the name of
-# the variable), but as FreeBSD is also being inlucded in our tests. As
-# more systems get used, we need to tailor these kinds of things better.
-kernelname=$(uname -s)
-if [ x$kernelname = xLinux ]; then
-    on_mac_os=no
-else
-    host_cc=1
-    on_mac_os=yes
-fi
-
-
-
-
-
 # Print warning if the host CC is to be used.
 if [ x$host_cc = x1 ]; then
     cat <<EOF
@@ -507,36 +529,40 @@ fi
 # ----------------
 #
 # 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.
+# have a fortran compiler: we'll build it internally for high-level
+# programs with GCC. 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 [ $hasfc = 0 ]; then
-        cat <<EOF
+    # If a Fortran compiler is necessary, see if 'gfortran' exists and can
+    # be used.
+    if [ "x$need_gfortran" = "x1" ]; then
+
+        # First, see if 'gfortran' 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        !!!!!!!
 
-The project won't be building its own GCC (which includes a Fortran
-compiler) on this system. If you need software that need a Fortran
-compiler, it will crash with an error. Fortran is necessary for many
-lower-level scientific programs, hence this warning. 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:
+This project requires a Fortran compiler. However, the project won't/can't
+build its own GCC on this system (GCC also builds the 'gfortran' Fortran
+compiler). Please install 'gfortran' using your operating system's package
+manager, then re-run this configure script to continue the configuration.
 
-  https://savannah.nongnu.org/support/?func=additem&group=reproduce
+Currently the only Fortran compiler we check is '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:
 
-Project's configuration will continue in 5 seconds.
+  https://savannah.nongnu.org/support/?func=additem&group=reproduce
 ______________________________________________________
 
 EOF
-        sleep 5
-    else
+            exit 1
+        fi
 
-        # See if the Fortran compiler works
+        # Then, see if the Fortran compiler works
         testsource=$compilertestdir/test.f
         echo; echo; echo "Checking host Fortran compiler...";
         echo "      PRINT *, \"... Fortran Compiler works.\""  > $testsource
@@ -552,25 +578,18 @@ ______________________________________________________
 
 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
+A working Fortran compiler is necessary for this project. Please use the
+error message above to find a good solution in your operating system 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
-
-Project's configuration will continue in 5 seconds.
 ______________________________________________________
 
 EOF
-            sleep 5
+            exit 1
         fi
     fi
 fi
@@ -579,17 +598,6 @@ 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
 # ---------------
 #
@@ -623,12 +631,10 @@ EOF
 # (for example the user might have ran `./project configure' by mistake).
 printnotice=yes
 rewritepconfig=yes
-rewritegconfig=yes
-if [ -f $pconf ] || [ -f $glconf ]; then
+if [ -f $pconf ]; then
     if [ $existing_conf = 1 ]; then
         printnotice=no
         if [ -f $pconf  ]; then rewritepconfig=no; fi
-        if [ -f $glconf ]; then rewritegconfig=no; fi
     fi
 fi
 
@@ -999,44 +1005,6 @@ 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 -e
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-EOF
-        exit 1
-    fi
-fi
-# ------------------------------------------
-
-
-
-
-
 # Delete final configuration target
 # ---------------------------------
 #
@@ -1150,12 +1118,15 @@ fi
 # 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 .gnuastro
+rm -f .build .local
+
 ln -s $bdir .build
 ln -s $instdir .local
 ln -s $texdir tex/build
 ln -s $tikzdir tex/tikz
+
 # --------- Delete for no Gnuastro ---------
+rm -f .gnuastro
 ln -s $topdir/reproduce/analysis/config/gnuastro .gnuastro
 # ------------------------------------------
 
@@ -1267,6 +1238,43 @@ 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.
+#
+# IMPORTANT NOTE: This test has to be done **AFTER** the definition of
+# 'instdir', otherwise, it is going to be used as an empty string.
+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
+
+
+
+
+
+# Delete the compiler testing directory
+# -------------------------------------
+#
+# This directory was made above to make sure the necessary compilers can be
+# run.
+rm -f $testprog $testsource
+rm -rf $compilertestdir
+
+
+
+
+
 # Paths needed by the host compiler (only for `basic.mk')
 # -------------------------------------------------------
 #
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 05a4143..9188fc9 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -104,9 +104,17 @@ download_tarball() {
         tarballurl=$url/$tarball
     fi
 
-    # See if it is in the input software directory.
+    # See if it is in the input-software directory, if so, make a link, if
+    # not copy it. The only issue is that the file in the input-software
+    # directory may actually be a link itself. So to avoid complications
+    # with many links, we'll use 'realpath' (if it exists) to parse the
+    # link and link to an actual file.
     if [ -f "$ddir/$tarball" ]; then
-      cp $ddir/$tarball $ucname
+      if type realpath > /dev/null 2> /dev/null; then
+        ln -sf "$(realpath $ddir/$tarball)" "$ucname"
+      else
+        cp $ddir/$tarball $ucname
+      fi
     else
       $downloadwrapper "$downloader" nolock $tarballurl $ucname \
                        "$bservers"
@@ -118,7 +126,7 @@ download_tarball() {
       expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' $checksumsfile)
       if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
       else
-        echo "ERROR: Non-matching checksum for '$tarball'."
+        echo "ERROR: Non-matching checksum: $tarball"
         echo "Checksum should be: $expectedchecksum"
         echo "Checksum is:        $checksum"
         exit 1