IMPORTANT: Python and some basic software updated, improved portabilityHEADmaneage

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

1 files changed, 120 insertions, 20 deletions

diff --git a/README-hacking.md b/README-hacking.md
index a86581c..6d02976 100644
--- a/README-hacking.md
+++ b/README-hacking.md
@@ -185,12 +185,23 @@ Library](https://scixplorer.org) (successor to the [NASA
 ADS](https://ui.adsabs.harvard.edu)) which contains further bibliographic
 information like title, DOI and etc, in a unified format (independent of
 which journal the paper is published in).
+
+ - Eskandarlou et
+   al. ([2026](https://scixplorer.org/abs/2026arXiv260322166E), A&A
+   accepted;
+   arXiv:[2603.22166](https://arxiv.org/abs/2510.2603.22166)). The
+   project's version controlled source is on
+   [Gitlab](https://gitlab.com/sepideh.esk/alba), necessary software,
+   outputs and backup of history are available at
+   [zenodo.17674805](http://doi.org/10.5281/zenodo.17674805); and the
+   archived git history is available at
+   [swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99](https://archive.softwareheritage.org/swh:1:dir:7c203a565ec6ef40d8419dbdf70e8639b78f4b99;origin=https://gitlab.com/Sepideh.Esk/alba;visit=swh:1:snp:adc584ff3540ea3151de6ebc8462805e8818b1f4;anchor=swh:1:rev:f9d0f9cb25c80415107c962cc53d369a650e9b82).
  - Eskandarlou et
    al. ([2026](https://scixplorer.org/abs/2026A%26A...705A..67E), A&A,
    Volume 705, id.A67, 14 pp;
    arXiv:[2510.12940](https://arxiv.org/abs/2510.12940)). The project's
    version controlled source is on
-   [Gitlab](https://gitlab.com/Sepideh.Esk/psf-j-plus), necessary software,
+   [Gitlab](https://gitlab.com/sepideh.esk/psf-j-plus), necessary software,
    outputs and backup of history are available at
    [zenodo.17348653](http://doi.org/10.5281/zenodo.17348653); and the
    archived git history is available at
@@ -234,6 +245,17 @@ which journal the paper is published in).
    at [zenodo.10058165](https://doi.org/10.5281/zenodo.10058165); and the
    archived git history is available at
    [swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d](https://archive.softwareheritage.org/swh:1:dir:1064a48d4bb58d6684c3df33c6633a04d4141d2d;origin=https://codeberg.org/gnuastro/papers;visit=swh:1:snp:a083ff647c571f895d1ccc9f7432fa1b9a1d03a8;anchor=swh:1:rev:ff77b619daa50b05ddd83206d979d1f8a53d040b).
+ - Peper, Roukema & Bolejko
+   ([2023](https://scixplorer.org/abs/2023MNRAS.525...91P), MNRAS, 525, 91,
+   DOI:10.1093/mnras/stad2246,
+   arXiv:[2304.00591](https://arxiv.org/abs/2304.00591)): The live version
+   of the controlled source is [at
+   Codeberg](https://codeberg.org/mpeper/lensing); the main input
+   dataset, a software snapshot, the software tarballs, the project outputs
+   and editing history are available at
+   [zenodo.8103985](https://zenodo.org/record/8103985); and the archived
+   git history is available at
+   [swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914](https://archive.softwareheritage.org/swh:1:dir:f57fd0e254bcb976c1ab34b6c9c9708e891f7914;origin=https://codeberg.org/mpeper/lensing;visit=swh:1:snp:984413c49bb02ee0eec88c3ac01614808d57beb7;anchor=swh:1:rev:185c36f1b6263588526be3881078626869041882).
  - Eskandarlou et
    al. ([2023](https://scixplorer.org/abs/2023RNAAS...7..269E), RNAAS,
    Volume 7, Issue 12, id.269;
@@ -557,26 +579,25 @@ project files. However, file dates are important in the current design of
 Maneage: Make checks the dates of the prerequisite files and target files
 to see if the target should be re-built.
 
-To fix this problem, for Maneage we use a forked version of
-[Metastore](https://github.com/mohammad-akhlaghi/metastore). Metastore use
-a binary database file (which is called `.file-metadata`) to keep the
-modification dates of all the files under version control. This file is
-also under version control, but is hidden (because it shouldn't be modified
-by hand). During the project's configuration, Maneage installs to Git hooks
-to run Metastore 1) before making a commit to update its database with the
-file dates in a branch, and 2) after doing a checkout, to reset the
-file-dates after the checkout is complete and re-set the file dates back to
-what they were.
+This is relevant, for example, in the `analysis/` side of calculations when
+a rule in a `reproduce/analysis/make/SOMETHING.mk` is dependent on
+`reproduce/analysis/conf/SOMETHING.conf` (where `SOMETHING` is one of the
+science pipeline steps that you have prepared). Switching back and forth
+between git branches will update the timestamp on `SOMETHING.conf`,
+incorrectly implying, according to the Make rules, that a rule in
+SOMETHING.mk has to be run again.
 
-In practice, Metastore should work almost fully invisibly within your
-project. The only place you might notice its presence is that you'll see
-`.file-metadata` in the list of modified/staged files (commonly after
-merging your branches). Since its a binary file, Git also won't show you
-the changed contents. In a merge, you can simply accept any changes with
-`git add -u`. But if Git is telling you that it has changed without a merge
-(for example if you started a commit, but canceled it in the middle), you
-can just do `git checkout .file-metadata` and set it back to its original
-state.
+To address this problem, you can use the `touch` command to backdate the
+timestamp of files that you want to be considered to be old. For example
+with the command below:
+
+```shell
+$ touch --date=2000-01-01 reproduce/analysis/conf/SOMETHING.conf
+$ ls -l reproduce/analysis/conf/SOMETHING.conf # to check
+```
+
+You may want to use a date that is obviously (to you) fake, so that you
+don't accidentally believe the date later on.
 
 
 
@@ -1434,6 +1455,50 @@ future.
    are public). If not, you can mention that everything is ready for such a
    submission after acceptance.
 
+     * Some journals (like the "Astronomy and Astrophysics" journal)
+       require that only a single LaTeX file be submitted without any
+       commens (along with all the figures). In other words, they do not
+       want any sub-directories: only a single LaTeX file, one `.bbl` file
+       and one PDF per figure. Here is how you can do this:
+       ```shell
+       # If you don't already have 'latexpand' in your OS, install it:
+       $ tlmgr install latexpand
+
+       # Unpack the tarball and make a directory for a single-LaTeX source.
+       $ tar -xf maneaged-XXXXXXX.tar.gz
+       $ cd maneaged-XXXXXXX.tar.gz
+       $ mkdir one-latex
+
+       ## The '--empty-comments' and subsequent call to AWK (that removes
+       ## lines starting with '%') is because we need the lines ending in a
+       ## '%' for some LaTeX macros).
+       $ latexpand paper.tex --output=one-latex/paper-0.tex \
+                   --empty-comments
+       $ awk '!/^%/' one-latex/paper-0.tex > one-latex/paper.tex
+       $ rm one-latex/paper-0.tex
+
+       ## Copy the other necessary files (if you are using specific journal
+       ## style files, also copy them).
+       $ cp paper.bbl one-latex/
+       $ cp tex/tikz/*.pdf one-latex/
+
+       ## Correct the location of the images.
+       $ sed -i -e's|tex/tikz/|./|' one-latex/paper.tex
+       ```
+
+        * You can confirm the contents of the `one-latex` directory made
+          above by running `pdflatex paper` inside that directory. Your
+          operating system's LaTeX may not have all the necessary packages,
+          in that case run `tlmgr install XXXXX` (where `XXXXX` is the
+          value of `texlive-packages` in
+          `reproduce/software/config/texlive-packages.conf`. Afterwards,
+          clean up all the temporary files with this command:
+          ```shell
+          $ rm *.log *.aux *.auxlock *.bcf *.out *.xml
+          ```
+
+        * Upload the contents of this `one-latex` directory to the journal.
+
  - **Future versions**: Both Zenodo and arXiv allow uploading new versions
    after your first publication. So it is recommended to put more recent
    versions of your published projects later (for example after applying
@@ -1793,6 +1858,41 @@ for the benefit of others.
 
 
 
+Maneage Development Workflow
+============================
+
+Maneage users can only use it by developing it, therefore Maneage is a very
+unique software: the boundary between a user and developer is very blurry
+by design/philosophy. We hope that all users can contribute to the
+`maneage` branch for project-agnostic bugs/features that they fix/add. In
+this section, the development workflow is described:
+
+ - At any point that you find a bug or want to share a fix, anyone is
+   welcome to open a "Bug" or "Task" on GNU Savannah (which is the main
+   project management interface of Maneage). In case the submitter already
+   has a commit to merge, they can fork Maneage (similar to [this forking
+   tutorial](https://www.gnu.org/software/gnuastro/manual/html_node/Forking-tutorial.html))
+   and share their commit in the Savannah post.
+
+ - The review of bugs and merge requests will happen at the earliest
+   possible time for the maintainer. At this point, the maintainer will
+   create a new development branch over the `maneage` branch in a
+   development repository (not the main Maneage repository) and all
+   separate merge requests will be rebased over that branch. Finally, all
+   the commits in that branch will be `squash`ed into a single commit that
+   will be merged over the `maneage` branch. Of course, every contributor
+   will be acknowledged in the squashed commit for their contribution.
+
+   - The `squash`ing into a single commit is intentionally done because the
+     `maneage` branch is shared between all projects that use Maneage and
+     we do not want to introduce complexity in their history by preserving
+     all the various development commits that were done before the
+     merge.
+
+   - After the merge, the development branch may be deleted from the
+     development repository: any historically relevant point that you find
+     when making a commit should be written as comments within the source
+     (to be preserved during the squash) and not in the commit message.