Summary: this will not affect your software or analysis.

Until now, Maneage's configuration was failing during the build of
util-linux on macOS.

With this commit, the issue is solved by avoiding the building of bits.o
(the problematic part). It was checked both on GNU/Linux and macOS that the
removal of this util-linux feature does not affect any of the subsequent
programs that need util-linux.

Summary: this commit will not affect your project's software or analysis.

Until now, the ending copyright years of all files in Maneage were
2025. But we have already entered 2026 so it is important to update them.

With this commit, the ending copyright year of all files is changed to
2026.

Summary: your project will only be affected if it uses Gnuastro and
depended on the FITS keywords that kept the information above (in the 0th
HDU).

Until now, there was no Maneage-specific configuration for Gnuastro, so as
in its default/manual operation, Gnuastro would keep all the metadata that
it keeps in manual/default mode. However, in a large pipeline that involves
the temporary creation of thousands of FITS files (which are usually
deleted shortly after), such metadata are just overhead. For the final
products of the pipeline, it is the responsibility of the pipeline designer
to only keep these in the final products of the pipeline, not all the
intermediate files.

With this commit, the default installation of Gnuastro in Maneage disables
all such metadata in its products in the output FITS files and provides
tips for users on the final metadata to include in their pipeline's
outputs.

Summary: The Apptainer script's option names have been renamed: '--sif' and
'--base-sif' are new names for the old '--project-name' and '--base-name'.

Until now the options that took SIF files in the Apptainer script were not
too clear (in their name): ending in '-name' (not clearly mentioning that
it needs a file name). Also, in the same script, we had forgot to add an
option to allow the user to choose a different base operating system!

With this commit, both the issues above have been fixed: the options end in
'-sif' (clearly informing the user that a SIF file is expected) and we now
have a new '--base-os' option. In the process, a few other parts of Maneage
were also polished:

  - README-hacking.md: the newly published J-PLUS PSF paper was added to
    the list of Maneage'd papers and the final journal information for the
    NASIM paper has been added. Some typos here and there were also fixed.

  - The curretnly used VIM needed the the '-std=gnu17': necessary now that
    the default Maneage GCC 15.2.0 for the high-level software which
    defaults to C23.

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'.

Summary: after merging this commit into your project, it should be
re-configured since the location of software installation files like
'LOCAL.conf' or the LaTeX macros of the software environment have
changed. But it should not affect the analysis phase of your project.

Until this commit, it was not possible to run a pre-built Maneage'd project
(in a container) on a newly cloned Maneage'd project source. This was
because the containers should be read-only, but during the various checks
of the configuration (to verify that we are using the same software
environment in the container and the source), we were writing/testing many
things in the build directory, and 'LOCAL.conf' which was actually in the
source directory!

Furthermore, the '.local' and '.build' were built at configure time, making
it hard to run the same container from a newly cloned Maneage'd project. To
make things harder for the scenario above, the 'configure.sh' script would
pause on every message and didn't have a quiet mode (making it practically
impossible to run './project configure' before './project make' on every
container run).

With this commit, all these issues have been addressed and it is now
possible to simply get a built container, clone a Maneage'd project and run
the analysis (using the built environment of the container that is verified
on every run). The respective changes/additions are described below:

 - The high-level container scripts ('apptainer.sh' and 'docker.sh', along
   with their READMEs) have been moved to the 'reproduce/software/shell'
   directory and the old 'reproduce/software/containers' directory has been
   deleted. This is because we have classified the software files by their
   language/format and the container scripts are scripts in the end.

 - The './project' script:

    - Now has two extra options: '--quiet' and '--no-pause'. Both are
      directly passed to the 'configure.sh' script. They will respectively
      disable any informative printed message or any pause after that
      message (if it is printed).

    - The '--build-dir' option is now also relevant for './project make':
      when it is given, it will re-create the two '.build' and '.local'
      symbolic links at the top source directory in all scenarios
      ('configure', 'make' or 'shell'). This will allow both the
      configuration, analysis and shell phases to safely assume they exist
      and match the user's desire at run-time.

    - The build/analysis directory's sub-directories that need to be built
      before 'top-make.mk' are now built in a separate function to help in
      readability.

 - The 'configure.sh' script:

    - For developers: a new 'check_elapsed' variable has been defined that
      will enable the newly added 'elapsed_time_from_prev_step'
      function. This function should be used from now on at the end of
      every major step to help find bottlenecks.

 - The targets of the software in 'pre-make-build.sh' now also have the
   version of the software in their file name. Until now, they didn't have
   the version, so there was no way to detect if the software has been
   updated or not in the source. For Lzip and Make (that also get built
   after GCC), the ones in this script have a '-pre-make' suffix also.

 - 'Local.conf.in' now has descriptions for every variable.

 - The '-std=gnu17' option is now used instead of '-std=c17' for basic
   software that cannot be built without specifying the C standard in GCC
   15.1 (described in previous commit: 2881fc0a6205). See [1] for more
   details; in summary: '-std=gnu17' is also supported on macOS's Clang and
   has some features that 'pkg-config' needs

 - Generally: some longer code lines have been broken or indentation
   decreased to fit the 75 character line length. This has not reduced
   readability however. For example the long 'echo' commands are now
   replaced by multiple 'printf's, or the indentation is still clearly
   visible.

The seeds of the work on this commit started by a branch containing three
commits by Giacomo Lorenzetti (133 insertions, 100 deletions). Upon merging
with the main 'maneage' branch, they were generalized and re-organized to
become this commit.

The following issues have also been addressed with this commit:

 - The LaTeX calls (during the building of 'paper.pdf') do not contain
   Maneage'd dynamic libraries. This is because we don't build the LaTeX
   binaries from source, an TeXLive manager uses the host environment.

 - The 'docker.sh' script:

    - Adds the '--project-name' option: its internal variable existed, but
      the option for the user to define it at run-time was not.

    - Ported to macOS: it does not check being a member of the 'docker'
      group, and finds the number of threads using macOS-specific tools.

 - The 'apptainer.sh' script:

    - Now installs 'wget' in the base container also (necessary when the
      user doesn't have the tarballs).

[1] https://savannah.nongnu.org/bugs/?67068#comment2

Summary: this will not affect already built/configured projects, only
improving the portability of future builds.

Until this commit, no specific C standard version was given during the
build of Basic software (which use the host's c compiler, culminating in
the building of GCC within Maneage). On the other hand, GCC 15.1 was
recentely released and made available on some operating systems. GCC 15.1
has made C23 its standard C version (from C17), as a result, some of the
basic software crashed and didn't allow Maneage to built on those operating
systems.

With this commit, the '-std=c17' flag has been added to software that
crashed when the host GCC was 15.1. Also, they have been grouped with a
description of this problem in 'versions.conf' so we check the need for
this option in future version updates.

In parallel, some minor edits/clarifications were made in the two
'README-apptainer.md' and 'README-docker.md' files to be more useful.

Summary: it is necessary to re-configure your project (just running
'./project configure -e', not deleting 'build/software' to re-build
software) after this commit, see "Affected files" item below).

Until now, we only had a relatively long set of manual instructions for
building Maneage within Docker in the top-level README. This was hard to
automate, focing Maneage users to write custom commands based on the
instructions and maintain those scripts outside of Maneage. As a result,
experience could not be shared between projects (or at most in the README
file!).

With this commit, a new 'reproduce/software/containers' directory has been
created within Maneage that contains two scripts (with a unified interface)
greatly simplifying the building of the project's software environment
within a container (one script for Apptainer and one for Docker). Two
READMEs have been added for each container to help in their first time
usage. Also, the old checklist within the main README has been replaced
with a short introduction on containers and points the interested readers
to the custom README of each container technology.

Since we wanted the containers to be read-only after build, we needed to
fully decouple the 'build/software' and 'build/analysis', such that
'./project configure' only writes to the former and './project make' only
writes the latter. The file and directories mentioned in the affected files
are cases that both project phases was writing to the 'build/software' and
'build/analysis' directories.

Affected files: 'preparation-done.mk' and 'lockdir' which were previously
in the 'build/software' directory are now made during the 'make' phase and
the 'configure' phase no longer builds the 'build/analysis' or anything
within it. Also, the software version LaTeX macros (which were previously
written during the 'configure' phase in the 'analysis' directory) are now
written in the software directory and copied into the analysis for usage in
LaTeX while building the paper.

Other minor additions in this commit:

  - The './project' script has a new '--timing' option to write the
    starting and ending times of the project in a file. It also builds the
    high-level analysis directories when './project make' is called (but
    before calling 'top-make.mk'.

  - The 'tar' calls in the custom build commands of the software building
    Makefiles now have the '--no-same-owner --no-same-permissions' options
    like the 'tar' call within the 'uncompress' function of
    'build-rules.mk'.

This commit was originally written by Giacomo Lorenzetti only for Apptainer
on the registered commit date. It was later re-implemented from scratch by
Mohammad Akhlaghi to have a unified interface for both Apptainer and Docker
and merged into Maneage on 2025-04-23.

Summary: this will not affect any analysis.

Until this commit, the old version of 'setuptools-rust' did not install
with the updated Python version (see [1]).

With this commit, 'setuptools-rust' is upgraded to version 1.10.2 (from
1.1.2) and 'semantic-version' 2.10.0 (needed by 'setuptools-rust') is
added. In addition this commit:
  - removes a duplicate rule for building 'cycler' in 'python.mk'.
  - comments all the un-commented '*-url' variables of 'urls.conf'.

[1] https://savannah.nongnu.org/bugs/?61731

Summary: this will not affect any analysis.

Until this commit, there were often fatal errors when re-installing a
python package in the Maneage system (after events such as: an error during
the install; a computer reboot; a modification of dependencies or build
rules in 'high-level.mk'; or a removal of the successful-install indicator
file '.local/version-info/python/PACKAGENAME-PACKAGEVERSION'). The reason
for this particular failure was that 'python-installer' considers file
clobbering - replacing an old existing file by a new file - to be a fatal
error; the python function 'FileExistsError' is used to report the error
and terminate execution.

With this commit, the build rule for 'python-installer' comments out the
'FileExistsError' line in 'src/installer/destinations.py'. Based on several
tests of interrupted installs of python packages, it appears that this
commit solves this bug, allowing convenient re-installs of python packages.