IMPORTANT: version updates and improved portability

Summary: this commit involves a major version update of many basic software
and Gnuastro's major dependencies. So it may affect your configuration and
analysis.

Until now, the most recent software updates weren't properly tested on
MacOS, causing the software configuration step to fail. In particular, the
'prep-source.sh' (that corrects any hard-coded '/bin/sh' within the
unpacked tarballs of all software) as well as some issues in the 'tar',
'util-linux' and 'ghostscript' programs. These portability issues were
found and fixed by Raul Infante-Sainz and Giacomo Lorenzetti.

With this commit, those portability issues have been addressed while
updating the following software. Also see notes below the list.

   High-level software:
     CFITSIO             4.5.0       -->     4.6.3
     Ghostscript         10.04.0     -->     10.06.0
     Gnuastro            0.23        -->     0.24
     Util-linux          2.40.4      -->     2.41.3
     WCSLIB              8.4         -->     8.5

   Basic software:
     cURL                8.11.1      -->     8.17.0
     GNU Bash            5.2.37      -->     5.3.9
     GNU Binutils        2.43.1      -->     2.45.1
     GNU Coreutils       9.6         -->     9.9
     GNU Diffutils       3.10        -->     3.12
     GNU AWK             5.3.1       -->     5.3.2
     GNU GCC             14.2.0      -->     15.2.0
     GNU Gettext         0.23.1      -->     0.26
     GNU Grep            3.11        -->     3.12
     GNU Gzip            1.13        -->     1.14
     GNU Libunistring    1.3         -->     1.4.1
     GNU M4              1.4.19      -->     1.4.20
     GNU MPFR            4.2.1       -->     4.2.2
     GNU Nano            8.3         -->     8.7
     GNU Readline        8.2.13      -->     8.3.3
     Git                 2.48.1      -->     2.52.0
     Less                668         -->     685
     Libxml2             2.13.1      -->     2.15.1
     OpenSSL             3.4.0       -->     3.6.0
     Perl                5.40.1      -->     5.42.0

The latest versions of Bash and M4 were prepared for the new default C
standard of GCC 15.*, so the '-std=gnu17' was removed for them. Also, while
a new version of Dash was available, it would cause an issue when building
in Apptainer, so it has been described in 'versions.conf' to be aware in
the future updates.

Libgit2 has been removed as a dependency of Gnuastro. The reason is fully
described in the comment on top of Gnuastro's build rule in
'high-level.mk'.

1 files changed, 34 insertions, 26 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 166e8ff..db5ac8e 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -17,38 +17,39 @@
 # --------------------------------------------------------------
 #
 # CLASS:BASIC (important identifier for 'awk'; don't modify this line)
-binutils-version = 2.43.1
+bash-version = 5.3.9
+binutils-version = 2.45.1
 bison-version = 3.8.2
-coreutils-version = 9.6
-curl-version = 8.11.1
-dash-version = 0.5.12
-diffutils-version = 3.10
+coreutils-version = 9.9
+curl-version = 8.17.0
+diffutils-version = 3.12
 file-version = 5.46
 findutils-version = 4.10.0
 flock-version = 0.4.0
-gawk-version = 5.3.1
-gcc-version = 14.2.0
-gettext-version = 0.23.1
-git-version = 2.48.1
+gawk-version = 5.3.2
+gcc-version = 15.2.0
+gettext-version = 0.26
+git-version = 2.52.0
 gmp-version = 6.3.0
-grep-version = 3.11
-gzip-version = 1.13
+grep-version = 3.12
+gzip-version = 1.14
 help2man-version = 1.49.3
 isl-version = 0.27
-less-version = 668
+less-version = 685
 libiconv-version = 1.18
 libtool-version = 2.5.4
-libunistring-version = 1.3
-libxml2-version = 2.13.5
+libunistring-version = 1.4.1
+libxml2-version = 2.15.1
 lzip-version = 1.25
+m4-version = 1.4.20
 make-version = 4.4.1
 mpc-version = 1.3.1
-mpfr-version = 4.2.1
-nano-version = 8.3
-openssl-version = 3.4.0
-perl-version = 5.40.1
+mpfr-version = 4.2.2
+nano-version = 8.7
+openssl-version = 3.6.0
+perl-version = 5.42.0
 podlators-version = 6.0.2
-readline-version = 8.2.13
+readline-version = 8.3.3
 sed-version = 4.9
 tar-version = 1.35
 texinfo-version = 7.2
@@ -86,6 +87,15 @@ certpem-version = 2025-02-10
 # supported.
 patchelf-version = 0.13
 
+# Dash
+# ----
+#
+# Dash 0.5.13.1 causes the build of pkg-config to put the building of
+# Maneage within apptainer to go into the background! Forcing the user to
+# run 'fg' to continue the build. When updating to a later version, be
+# careful about this: that it does not cause this issue.
+dash-version = 0.5.12
+
 # Not working with C23
 # --------------------
 #
@@ -96,8 +106,6 @@ patchelf-version = 0.13
 # '-std=c17' and then try the build. If it works, move the software back up
 # to the main list before the commit.
 ncurses-version = 6.5
-bash-version = 5.2.37
-m4-version = 1.4.19
 pkgconfig-version = 0.29.2
 
 
@@ -123,7 +131,7 @@ automake-version = 1.17
 boost-version = 1.87.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 4.5.0
+cfitsio-version = 4.6.3
 cmake-version = 3.31.5
 eigen-version = 3.4.0
 emacs-version = 28.1
@@ -134,8 +142,8 @@ freetype-version = 2.13.3
 gdb-version = 11.1
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-ghostscript-version = 10.04.0
-gnuastro-version = 0.23
+ghostscript-version = 10.06.0
+gnuastro-version = 0.24
 gperf-version = 3.1
 gsl-version = 2.8
 icu-version = 70.1
@@ -169,10 +177,10 @@ sextractor-version = 2.25.0
 swarp-version = 2.41.5
 swig-version = 4.0.2
 tides-version = 2.0
-util-linux-version = 2.40.4
+util-linux-version = 2.41.3
 valgrind-version = 3.18.1
 vim-version = 9.0
-wcslib-version = 8.4
+wcslib-version = 8.5
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5