IMPORTANT: 73 software upgrades and added offline mode

Summary: This is a software update to make Maneage more portable and up to
date. It does not involve any Maneage infrastructure changes. You should
just re-build your project to make sure the updated software haven't
removed/changed any of their features that you were using.

Until now, the software in Maneage had not been updated for almost 2.5
years (since August 2022) and were starting to get dated! Also, when no
internet is available (for example in a HPC), the Zenodo check would always
cause a crash and needed to be commented manually.

With this commit, all the basic software that had been updated as well as
the dependencies of Gnuastro (which we commit to maintaining) have been
updated after a check of their webpage (see the full list below). To fix
the offline issue, a new '--offline' option has been added to the project
script. The other following changes were made:

 - tarball-prepare: has become more resilient (for dealing with file name
   with spaces or Lzip, which should not be compressed).

 - Readme: improve documentation when used in Docker.

Below you can see the list of basic software that have been updated. The
only basic software that have not been updated upstream since the previous
Maneage software update are 'bison', 'flock', 'm4', 'pkgconfig', 'unzip'
and 'zip'.

    bash                5.2-rc2            5.2.37
    binutils            2.39               2.43.1
    coreutils           9.1                9.6
    curl                7.84.0             8.11.1
    dash                0.5.11-057cd65     0.5.12
    diffutils           3.8                3.10
    file                5.42               5.46
    findutils           4.9.0              4.10.0
    gawk                5.1.1              5.3.1
    gcc                 12.1.0             14.2.0
    gettext             0.21               0.23.1
    git                 2.37.1             2.48.1
    gmp                 6.2.1              6.3.0
    grep                3.7                3.11
    gzip                1.12               1.13
    help2man            1.49.2             1.49.3
    isl                 0.24               0.27
    less                590                668
    libiconv            1.17               1.18
    libtool             2.4.7              2.5.4
    libunistring        1.0                1.3
    libxml2             2.9.12             2.13.5
    lzip                1.23               1.25
    make                4.3                4.4.1
    mpc                 1.2.1              1.3.1
    mpfr                4.1.0              4.2.1
    nano                6.4                8.3
    ncurses             6.3                6.5
    openssl             3.0.5              3.4.0
    perl                5.36.0             5.40.1
    podlators           4.14               6.0.2
    readline            8.2-rc2            8.2.13
    sed                 4.8                4.9
    tar                 1.34               1.35
    texinfo             6.8                7.2
    wget                1.21.2             1.25.0
    which               2.21               2.23
    xz                  5.2.5              5.6.3
    zlib                1.2.11             1.3.1

The high-level software that have been updated.

    autoconf            2.71               2.72
    automake            1.16.5             1.17
    cfitsio             4.1.0              4.5.0
    cmake               3.24.0             3.31.5
    expat               2.4.1              2.6.4
    fontconfig          2.14.0             2.16.0
    freetype            2.11.0             2.13.3
    ghostscript         9.56.1             10.04.0
    gnuastro            0.18               0.23
    gsl                 2.7                2.8
    libffi              3.4.2              3.4.7
    libgit2             1.3.0              1.9.0
    libice              1.0.10             1.1.2
    libidn              1.38               1.42
    libjpeg             9e                 9f
    libpaper            1.1.28             1.1.29
    libpng              1.6.37             1.6.46
    libpthread-stubs    0.4                0.5
    libsm               1.2.3              1.2.5
    libtiff             4.4.0              4.7.0
    libxau              1.0.9              1.0.12
    libxcb              1.15               1.17
    libxdmcp            1.1.3              1.1.5
    libxext             1.3.4              1.3.6
    libxt               1.2.1              1.3.1
    python              3.10.6             3.13.12
    util-macros         1.19.3             1.20.2
    wcslib              7.11               8.4
    xcb-proto           1.15               1.17
    xorgproto           2022.1             2024.1
    xtrans              1.4.0              1.5.2

2 files changed, 23 insertions, 8 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 857f3b5..f226ced 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1612,11 +1612,11 @@ 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' $zenodocheck \
                       | sed -n -e'/http/p' \
@@ -1723,6 +1723,7 @@ fi
                on_mac_os=$on_mac_os \
                sys_cpath=$sys_cpath \
                host_cc=$host_cc \
+               offline=$offline \
                -j$numthreads
 
 
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index e12ff98..09e1c89 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -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