Configuration: Imported recent updates from Maneageaas-journals

Until this commit, the AAS journals branch was based on Maneage commit
8161194 (dated 2022-05-22). However, maneage has been updated recently so
it is necessary to also update this branch.

With this commit, the merge has been done (and tested).

8 files changed, 213 insertions, 37 deletions

diff --git a/reproduce/software/shell/bashrc.sh b/reproduce/software/shell/bashrc.sh
index 814de2c..6bbd774 100755
--- a/reproduce/software/shell/bashrc.sh
+++ b/reproduce/software/shell/bashrc.sh
@@ -34,7 +34,7 @@
 #       shell').
 #
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 4f71bee..d58a829 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -2,9 +2,9 @@
 #
 # Necessary preparations/configurations for the reproducible project.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2021-2023 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2025 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # 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
@@ -1252,6 +1252,14 @@ instlibdir="$instdir"/lib
 if ! [ -d "$instlibdir" ]; then mkdir "$instlibdir"; fi
 ln -fs "$instlibdir" "$instdir"/lib64
 
+# Wrapper over Make as a single command so it does not default to '/bin/sh'
+# during installation (needed by some programs like CMake).
+instbindir=$instdir/bin
+if ! [ -d $instbindir ]; then mkdir $instbindir; fi
+makewshell="$instbindir/make-with-shell"
+echo "$instbindir/make SHELL=$instbindir/bash \$@" > $makewshell
+chmod +x $makewshell
+
 
 
 
@@ -1431,6 +1439,15 @@ fi
 
 
 
+# Make sure the temporary build directory is empty (un-finished
+# source/build files from previous builds can remain there during debugging
+# or software updates).
+rm -rf $tmpblddir/*
+
+
+
+
+
 # Inform the user that the build process is starting
 # -------------------------------------------------
 #
@@ -1558,6 +1575,35 @@ fi
 
 
 
+# Libraries necessary for the system's shell
+# ------------------------------------------
+#
+# In some cases (mostly the programs that Maneage doesn't yet build by
+# itself), the programs may call the system's shell, not Maneage's
+# shell. After we close-off the system environment from Maneage, this will
+# cause a crash! To avoid such cases, we need to find the locations of the
+# libraries that the shell needs and temporarily add them to the library
+# search path.
+if [ x"$on_mac_os" != xyes ]; then
+    sys_library_sh_path=$(otool -L /bin/sh \
+                              | awk '/\/lib/{print $1}' \
+                              | sed 's#/[^/]*$##' \
+                              | sort \
+                              | uniq \
+                              | awk '{printf "%s:", $1}END{printf "\b"}')
+else
+    sys_library_sh_path=$(ldd /bin/sh \
+                              | awk '{if($3!="") print $3}' \
+                              | sed 's#/[^/]*$##' \
+                              | sort \
+                              | uniq \
+                              | awk '{printf "%s:", $1}END{printf "\b"}')
+fi
+
+
+
+
+
 # Find Zenodo URL for software downloading
 # ----------------------------------------
 #
@@ -1575,11 +1621,11 @@ fi
 # which will download the DOI-resolved webpage, and extract the Zenodo-URL
 # of the most recent version from there (using the 'coreutils' tarball as
 # an example, the directory part of the URL for all the other software are
-# the same). This is not done if the option '--debug' is used.
+# the same). This is not done if the options '--debug' or `--offline` are used.
 zenodourl=""
 user_backup_urls=""
 zenodocheck=.build/software/zenodo-check.html
-if [ x$debug = x ]; then
+if [ x$debug = x ] && [ x$offline = x ]; then
   if $downloader $zenodocheck https://doi.org/10.5281/zenodo.3883409; then
       zenodourl=$(sed -n -e'/coreutils/p' $zenodocheck \
                       | sed -n -e'/http/p' \
@@ -1646,6 +1692,7 @@ fi
 # tools, but we have to be very portable (and use minimal features in all).
 echo; echo "Building necessary software (if necessary)..."
 .local/bin/make $keepgoing -f reproduce/software/make/basic.mk \
+     sys_library_sh_path=$sys_library_sh_path \
      user_backup_urls="$user_backup_urls" \
      sys_library_path=$sys_library_path \
      rpath_command=$rpath_command \
@@ -1673,17 +1720,30 @@ else
     numthreads=$jobs
 fi
 .local/bin/env -i HOME=$bdir \
-     .local/bin/make $keepgoing -f reproduce/software/make/high-level.mk \
-          user_backup_urls="$user_backup_urls" \
-          sys_library_path=$sys_library_path \
-          rpath_command=$rpath_command \
-          all_highlevel=$all_highlevel \
-          static_build=$static_build \
-          numthreads=$numthreads \
-          on_mac_os=$on_mac_os \
-          sys_cpath=$sys_cpath \
-          host_cc=$host_cc \
-          -j$numthreads
+               .local/bin/make $keepgoing \
+               -f reproduce/software/make/high-level.mk \
+               sys_library_sh_path=$sys_library_sh_path \
+               user_backup_urls="$user_backup_urls" \
+               sys_library_path=$sys_library_path \
+               rpath_command=$rpath_command \
+               all_highlevel=$all_highlevel \
+               static_build=$static_build \
+               numthreads=$numthreads \
+               on_mac_os=$on_mac_os \
+               sys_cpath=$sys_cpath \
+               host_cc=$host_cc \
+               offline=$offline \
+               -j$numthreads
+
+
+
+
+
+# Delete the temporary Make wrapper
+# ---------------------------------
+#
+# See above for its description.
+rm $makewshell
 
 
 
diff --git a/reproduce/software/shell/git-post-checkout b/reproduce/software/shell/git-post-checkout
index a1340d7..7b521a3 100755
--- a/reproduce/software/shell/git-post-checkout
+++ b/reproduce/software/shell/git-post-checkout
@@ -4,7 +4,7 @@
 # controlled files (with each commit) using the 'metastore' program.
 #
 # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This script is taken from the 'examples/hooks/pre-commit' file of the
 # 'metastore' package (installed within the project, with an MIT license
diff --git a/reproduce/software/shell/git-pre-commit b/reproduce/software/shell/git-pre-commit
index 02ba488..7b98ad0 100755
--- a/reproduce/software/shell/git-pre-commit
+++ b/reproduce/software/shell/git-pre-commit
@@ -4,7 +4,7 @@
 # controlled files (with each commit) using the 'metastore' program.
 #
 # Copyright (C) 2016 Przemyslaw Pawelczyk <przemoc@gmail.com>
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # WARNING:
 #
diff --git a/reproduce/software/shell/pre-make-build.sh b/reproduce/software/shell/pre-make-build.sh
index 808429b..93d3266 100755
--- a/reproduce/software/shell/pre-make-build.sh
+++ b/reproduce/software/shell/pre-make-build.sh
@@ -2,7 +2,7 @@
 #
 # Very basic tools necessary to start Maneage's default building.
 #
-# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 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
@@ -48,7 +48,7 @@ instdir="$sdir"/installed
 tmpblddir="$sdir"/build-tmp
 confdir=reproduce/software/config
 ibidir="$instdir"/version-info/proglib
-downloadwrapper=reproduce/analysis/bash/download-multi-try
+downloadwrapper=reproduce/analysis/bash/download-multi-try.sh
 
 # Derived directories
 bindir="$instdir"/bin
@@ -123,7 +123,8 @@ download_tarball() {
     # Make sure this is the correct tarball.
     if type sha512sum > /dev/null 2> /dev/null; then
       checksum=$(sha512sum "$ucname" | awk '{print $1}')
-      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' "$checksumsfile")
+      expectedchecksum=$(awk '/^'$progname'-checksum/{print $3}' \
+                             "$checksumsfile")
       if [ x$checksum = x$expectedchecksum ]; then mv "$ucname" "$maneagetar"
       else
         echo "ERROR: Non-matching checksum: $tarball"
@@ -135,8 +136,10 @@ download_tarball() {
     fi
   fi
 
-  # If the tarball is newer than the (possibly existing) program (the version
-  # has changed), then delete the program.
+  # If the tarball is newer than the (possibly existing) program (the
+  # version has changed), then delete the program. When the LaTeX name is
+  # not given here, the software is re-built later (close to the end of
+  # 'basic.mk') and the name is properly placed there.
   if [ -f "$ibidir/$progname" ]; then
       if [ "$maneagetar" -nt "$ibidir/$progname" ]; then
           rm "$ibidir/$progname"
@@ -210,10 +213,15 @@ build_program() {
         fi
     fi
 
-    # Clean up the source directory
+    # Clean up the source directory and write the LaTeX name of the
+    # software (if necessary: otherwise, just make an empty file).
     cd "$topdir"
     rm -rf "$tmpblddir/$unpackdir"
-    echo "$progname_tex $version" > "$ibidir/$progname"
+    if [ x"$progname_tex" = x ]; then
+        echo "" > "$ibidir/$progname"
+    else
+        echo "$progname_tex $version" > "$ibidir/$progname"
+    fi
   fi
 }
 
@@ -256,7 +264,7 @@ build_program
 # Make that has a different executable name (using the '--program-prefix='
 # configure option) from the "default" make (which is this one!).
 progname="make"
-progname_tex="GNU Make"
+progname_tex="" # Make re-built after GCC (empty string to avoid repetition)
 url=$(awk '/^'$progname'-url/{print $3}' $urlfile)
 version=$(awk '/^'$progname'-version/{print $3}' $versionsfile)
 tarball=$progname-$version.tar.lz
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
new file mode 100755
index 0000000..dcdc472
--- /dev/null
+++ b/reproduce/software/shell/prep-source.sh
@@ -0,0 +1,94 @@
+#!/usr/bin/env sh
+#
+# Necessary corrections in the un-packed source of programs to make them
+# portable (for example to not use '/bin/sh').
+#
+# Usage: Run in top source directory (will work on all files within the
+#        directory that it is run in ):
+#   ./prep-source.sh /FULL/ADDRESS/TO/DESIRED/BIN
+#
+# Copyright (C) 2024-2025 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.
+#
+# You should have received a copy of the GNU General Public License along
+# with this script.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Abort the script in case of an error
+set -e
+
+
+
+
+# Read the first argument.
+bindir="$1"
+if [ x"$bindir" = x ]; then
+    printf "$0: no argument (location of the 'bin/' directory "
+    printf "containing the 'bash' executable)\n"
+    exit 1
+elif ! [ -d "$bindir" ]; then
+    printf "$0: the directory given as the first argument ('$bindir')"
+    printf "does not exist"
+fi
+
+
+
+
+
+# Find all the files that contain the '/bin/sh' string and correct them to
+# Maneage's own Bash. We are using 'while read' to read the file names line
+# by line. This is necessary to account file names that include the 'SPACE'
+# character (happens in CMake for example!).
+#
+# Note that dates are important in the source directory (files depend on
+# each other), so we should read the original date and after making. We are
+# also not using GNU SED's '-i' ('--in-place') option because the host OS
+# may not have GNU SED.
+#
+# Actual situation which prompted the addition of this step: a Maneage'd
+# project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a
+# system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The
+# newer version of Bash needed the newer Readline library function(s) that
+# were not available in Maneage's Readline library. Therefore, as soon as
+# the basic software were built and Maneage entered the creation of
+# high-level software (where we completely close-off the host environment),
+# Maneage crashed with the following '/bin/sh' error:
+#
+#   /bin/sh: symbol lookup error: /bin/sh: undefined symbol: rl_trim_arg_from_keyseq
+#
+# This lead to the discovery that through '/bin/sh' the host operating
+# system was leaking into our closed Maneage environment which needs to be
+# closed. This needs a source-level correction because '/bin/sh' is
+# hard-coded in the source code of almost all programs (their build
+# scripts); and in special programs like GNU Make, GNU M4 or CMake it is
+# actually hardcoded in the source code (not just build scripts).
+if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash
+else                           shpath="$bindir"/dash
+fi
+grep -I -r -e'/bin/sh' $(pwd)/* \
+    | sed -e's|:|\t|' \
+    | awk 'BEGIN{FS="\t"}{print $1}' \
+    | sort \
+    | uniq \
+    | while read filename; do \
+         tmp="$filename".tmp; \
+         origtime="$(date -R -r "$filename")"; \
+         origperm=$(stat -c '%a' "$filename"); \
+         sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \
+         mv "$tmp" "$filename"; \
+         chmod $origperm "$filename"; \
+         touch -d"$origtime" "$filename"; \
+         echo "Corrected /bin/sh in $filename"; \
+      done
diff --git a/reproduce/software/shell/run-parts.in b/reproduce/software/shell/run-parts.in
index a7b7705..053f5f3 100755
--- a/reproduce/software/shell/run-parts.in
+++ b/reproduce/software/shell/run-parts.in
@@ -10,8 +10,8 @@
 # However, it didn't have a copyright statement. So one is being added
 # here.
 #
-# Copyright (C) 2023 Authors mentioned above.
-# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2025 Authors mentioned above.
+# Copyright (C) 2025-2024 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
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index 472b4c0..09e1c89 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -15,8 +15,8 @@
 #
 # Discussion: https://savannah.nongnu.org/task/?15699
 #
-# Copyright (C) 2022-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2022-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 # Released under GNU GPLv3+
 
 # Abort the script in case of an error.
@@ -159,12 +159,19 @@ for f in $allfiles; do
     name=$(echo $(basename $f) \
 	       | sed -e 's/.tar.*//' -e's/_/-/')
 
+    # Lzip will not be available to unpack Lzip itself, so just use Tar.
+    if [[ $name =~ ^lzip ]]; then
+      outname=$name.tar
+    else
+      outname=$name.tar.lz
+    fi
+
     # Skip previously packed files
-    if [ -f $odir/$name.tar.lz ]; then
+    if [ -f $odir/$outname ]; then
 
         # Print the info message if not in quiet mode
         if [ -z $quiet ]; then
-            echo "$scriptname: $odir/$name.tar.lz: already present in output directory"
+            echo "$scriptname: $odir/$outname: already present in output directory"
         fi
 
         # skip this file
@@ -206,19 +213,26 @@ for f in $allfiles; do
     # Put the current date on all the files because some packagers will not
     # add dates to their release tarballs, resulting in dates of the
     # Unix-time zero'th second (1970-01-01 at 00:00:00)!
-    touch $(find "$name"/ -type f)
+    # -print0 is needed for those tarballs that has paths with spaces. For
+    # the same reason it's needed also `xargs -0`. (`xargs` is needed also
+    # for large tarballs such as gcc's)
+    find "$name"/ -type f -print0 | xargs -0 touch
 
     # Pack with recommended options
     tar -c -Hustar --owner=root --group=root \
         -f $name.tar $name/
-    lzip -9 $name.tar
+
+    # Lzip will not be available when unpacking Lzip, so we just use Tar.
+    if [[ ! $name =~ ^lzip ]]; then
+        lzip -9 $name.tar
+    fi
 
     # Move the compressed file from the temporary directory to the target
     # output directory
-    mv $name.tar.lz $odir/
+    mv $outname $odir/
 
     # Print the sha512sum along with the filename for a quick reference
-    echo $(sha512sum $odir/$name.tar.lz)
+    echo $(sha512sum $odir/$outname)
 
     # Clean up the temporary directory
     rm -rf $tmpdir