Summary: this commit has no effect on your project's analysis steps, just
check the list of changed Python software versions (if you used them).
Until now, the Python packages of Maneage had not been maintained for some
time, there were several portability issues: updates to the GNU C Library
needed an update to some of the basic software, and the latest macOS
features caused some crashes.
With this commit, along with the software version updates of [1], the
removed software of [2] and newly added software of [3], the following
issues in Maneage have been addressed:
- README-hacking:
- Published paper list: Added links to two published papers.
- Publication checklist: added tips on how to squash the full LaTeX
source of a Maneage'd projet (which includes many LaTeX files) into a
single LaTeX file for some journals.
- A new "Maneage Development Workflow" section has been added; see it
for details.
- paper.mk: empty macro files are not included in the built 'project.tex'
since they have no effect and because they can cause problems with
uploading to arXiv (which removes empty files).
- verify.mk: when verification is activated:
- When a macro file does not exist (can happen by mistake), an error is
printed to remind the author.
- Better dealing with empty macro files (no need to add their hash).
- versions.conf: 26 Python packages that cannot currently be built with
the new Python build system of Maneage have been separated and commented
to cause an early crash if they are required; and encourage volunteers
to help update them.
This commit is a git "squash" of contributions from the following people
- Boud Roukema: updated/added Python packages and fixed many portability
issues.
- Faezeh Bidjarchian: fixed some portability issues on macOS.
- Giacomo Lorenzetti: tested and fixed issues in newly added software.
- Khalid Masum: fixed issue with order of LD_LIBRARY_PATH in 'basic.mk'.
- Mohammad Akhlaghi: fixed basic software issues and reviewed edits for
the merge.
- Raul Infante-Sainz: fixed portability issues on macOS.
- Sepideh Eskandarlou: helped in finding the verification fixes.
[1] Updated software
Name Group Version (old -> new)
---- ----- --------------------
GNU Coreutils basic 9.9 -> 9.11
GNU Gettext basic 0.26 -> 1.0
GNU libunistring basic 1.4.1 -> 1.4.2
GNU M4 basic 1.4.20 -> 1.4.21
GNU Nano basic 8.7 -> 9.0
Ninja high-level 1.12.1 -> 1.13.2
OpenMPI high-level 4.1.1 -> 5.0.10
SWIG high-level 4.0.2 -> 4.3.1
Zip high-level 3.0 -> 3.0-15
Astropy python 7.0.1 -> 7.1.0
mpi4py python 3.1.3 -> 4.0.3
setuptools python 75.8.0 -> 80.8.0
[2] Removed software: 'podlators' has been removed from basic software
because the necessary scripts that it provided are included in Perl's
default installation.
[3] New software:
Name Group Version
---- ----- -------
framel high-level 8.47.3
GNU Parallel high-level 20260322
Healpix high-level 3.83-2024Nov13
Metaio high-level 8.5.0-a5da19d
PCRE2 high-level 10.45
SQLite high-level 3.53.0
TCL high-level 9.1a1
TK high-level 9.1a1
tzdb high-level 2026a
lalsuite high-level v7.26-15-g1e4c5e5080
astropy-healpix python 1.1.2
colorama python 0.4.6
cosmodesi-mpytools python 1.0.0-04369fc9
exceptiongroup python 1.3.0
filt-scm python 1.7.0
hatchling python 1.27.0
hatch-vcs python 0.5.0
healpy python 1.18.1
joblib python 1.5.0
igwn-ligolw python 2.1.0
igwn-segments python 2.1.0
iniconfig python 2.1.0
ligo-skymap python 2.4.0
lscsoft-glue python 4.1.0
networkx python 3.5
pandas python 2.2.3
pathspec python 0.12.1
pluggy python 1.6.0
pyfftw python 0.15.1
pygments python 2.19.2
pytest python 8.4.1
python3-fitsio python 1.3.0
pytz python 2025.2
scikit-base python 0.12.2
scikit-learn python 1.6.1
threadpoolctl python 3.6.0
tqdm python 4.67.1
trove-classifiers python 2025.5.9.12
versioneer python 0.29
Summary: this commit has no effect on your projects. Until now, the list of published papers with Maneage had some formatting inconsistencies and didn't mention the arXiv link for the paper. It also used the NASA ADS as the main link to the paper (while the ADS is being replaced with the ScienceExplorer; or SciX for short). With this commit, all the issues above have been addressed in that list.
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: will not affect existing configuration or analysis. Until this commit, there were two typos in the list of papers that were added in the previous commit. With this commit, they have been corrected.
Summary: will not affect existing configuration or analysis. Until this commit, the customization checklist did not contain any reference to the recently made branches of Maneage for customization on certain journals (currently just the American Astronomical Society journals and Astronomy and Astrophysics). Also, the list of papers published with Maneage had not been updated for a long time. With this commit, both have been added to 'README-hacking.md'.
Summary: will not affect existing configuration or analysis. Until this commit, if the Maneage readline library (used by the shell) did not match the local readline library, the 'pdflatex' command would crash when building the template Maneage branch. This was because PGFPlots uses the local shell and we do not build TeXLive from source within Maneage yet. Previously, we had added a modification to 'LD_LIBRARY_PATH' before the 'pdflatex' command to use 'sys_library_sh_path', but the variable was never initilized (because it was only available within the configuration phase)! With this commit, the problem is solved by adding that variable within 'LOCAL.conf' so it is available in the analysis phase of a Maneage'd project also. In order to do so, the set of commands that set the 'sys_library_sh_path' variable within 'configure.sh' was brought up before the creation of 'LOCAL.conf'. In case you have had this problem, the solution is to delete '.build/software/config/LOCAL.conf' and re-configure your project by manually setting the necessary directories. In this way, the 'LOCAL.conf' is created again with the new variable. This bug was found with the help of Faezeh Bidjarchian.