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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'.
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SUMMARY: no change necessary in your project, this commit only involves
changes in how already-existing software are built. Some handy options have
also been added to the top-level project script and the copyright years
have been updated.
Until now, if the host's '/bin/sh' had conflicts with the Maneage
environment, the configuration of Maneage would crash as soon as we entered
the building of high-level software. The full scenario is described in the
comments of the newly added 'reproduce/software/shell/prep-source.sh'. This
is most relevant when building older Maneage'd project in newer
environments.
With this commit, the following changes were made to avoid the problem
above:
- Maneage edits the source code of all installed software to replace
'/bin/sh' with Maneage's own shell before the programs are
built. Through this, we were able to solve the problem described
above.
- The portable '#!/usr/bin/env sh' shebangs are now used at the start of
the scripts that run during configure time so it uses the first
available shell that it finds in its PATH (the system's before Dash is
built), then Dash, and after Dash is built, Bash.
- For TeXLive, since we don't install it from source, it was necessary to
add the libraries necessary for the local '/bin/sh' in LD_LIBRARY_PATH.
Some high-level options have been added to the './project' script to
simplify certain operations:
--keep-going: do not stop upon the first crash, but keep going on to
build targets until all build-able targets have been built. This is
very useful for debugging large pipelines and allows you to isolate the
problematic part of your project.
--highlight-all: equivalent to calling both '--highlight-new' &
'--highlight-notes'.
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