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, 106 insertions, 64 deletions

diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 7d4a3b5..3e4ec9a 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -20,17 +20,14 @@
 bash-version = 5.3.9
 binutils-version = 2.45.1
 bison-version = 3.8.2
-coreutils-version = 9.9
+coreutils-version = 9.11
 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 = 5.3.2
-gcc-version = 15.2.0
-gettext-version = 0.26
+gettext-version = 1.0
 git-version = 2.52.0
-gmp-version = 6.3.0
 grep-version = 3.12
 gzip-version = 1.14
 help2man-version = 1.49.3
@@ -38,17 +35,16 @@ isl-version = 0.27
 less-version = 685
 libiconv-version = 1.18
 libtool-version = 2.5.4
-libunistring-version = 1.4.1
+libunistring-version = 1.4.2
 libxml2-version = 2.15.1
 lzip-version = 1.25
-m4-version = 1.4.20
+m4-version = 1.4.21
 make-version = 4.4.1
 mpc-version = 1.3.1
 mpfr-version = 4.2.2
-nano-version = 8.7
+nano-version = 9.0
 openssl-version = 3.6.0
 perl-version = 5.42.0
-podlators-version = 6.0.2
 readline-version = 8.3.3
 sed-version = 4.9
 tar-version = 1.35
@@ -57,7 +53,6 @@ unzip-version = 6.0
 wget-version = 1.25.0
 which-version = 2.23
 xz-version = 5.6.3
-zip-version = 3.0
 zlib-version = 1.3.1
 
 # Version-dependent build
@@ -101,13 +96,23 @@ dash-version = 0.5.12
 #
 # As of GCC 15.1, the default C standard has been changed from C17 to C23
 # and the following software cannot be built with C23. So we have added
-# '-std=c17' to the CFLAGS environment variable in their build rules. After
-# updating their version (and if you have GCC 15.1 or later) first remove
-# '-std=c17' and then try the build. If it works, move the software back up
-# to the main list before the commit.
+# '-std=$(GNU_STD_OLD)' to the CFLAGS environment variable in their build
+# rules. A test is done in 'configure.sh' to see if the host compiler has
+# 'gnu17' and if not, to use 'gnu99'.  After updating a package's version
+# (and if you have GCC 15.1 or later) first remove '-std=$(GNU_STD_OLD)'
+# and then try the build. If it works, move the software package back up to
+# the main list before making a commit.
+gmp-version = 6.3.0
+file-version = 5.46
 ncurses-version = 6.5
 pkgconfig-version = 0.29.2
 
+# GCC
+# ---
+#
+# There is a version-specific 'sed -e' fix for a bug in this version of GCC
+# that should no longer be necessary in future versions.
+gcc-version = 15.2.0
 
 
 
@@ -138,6 +143,7 @@ emacs-version = 28.1
 expat-version = 2.6.4
 fftw-version = 3.3.10
 flex-version = 2.6.4-410-74a89fd
+framel-version = 8.47.3
 freetype-version = 2.13.3
 gdb-version = 11.1
 ghostscript-fonts-gnu-version = 6.0
@@ -146,6 +152,7 @@ ghostscript-version = 10.06.0
 gnuastro-version = 0.24
 gperf-version = 3.1
 gsl-version = 2.8
+healpix-version = 3.83-2024Nov13
 icu-version = 70.1
 imagemagick-version = 7.1.0-13
 imfit-version = 1.6.1
@@ -159,14 +166,17 @@ libpaper-version = 1.1.29
 libpng-version = 1.6.46
 libtiff-version = 4.7.0
 libtirpc-version = 1.2.6
+metaio-version = 8.5.0-a5da19d
 metastore-version = 1.1.2-23-fa9170b
 missfits-version = 2.8.0
-ninjabuild-version = 1.12.1
+ninjabuild-version = 1.13.2
 openblas-version = 0.3.29
-openmpi-version = 4.1.1
+openmpi-version = 5.0.10
 openssh-version = 8.0p1
+parallel-version = 20260322
 patch-version = 2.7.6
 pcre-version = 8.44
+pcre2-version = 10.45
 pixman-version = 0.40.0
 plplot-version = 5.15.0
 r-cran-version = 4.1.2
@@ -174,14 +184,19 @@ rpcsvc-proto-version = 1.4
 scamp-version = 2.10.0
 scons-version = 3.0.5
 sextractor-version = 2.25.0
+sqlite-version = 3.53.0
 swarp-version = 2.41.5
-swig-version = 4.0.2
+swig-version = 4.3.1
+tcl-version = 9.1a1
 tides-version = 2.0
+tk-version = 9.1a1
+tzdb-version = 2026a
 util-linux-version = 2.41.3
 valgrind-version = 3.18.1
 wcslib-version = 8.5
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5
+zip-version = 3.0-15
 
 # Xorg packages
 fontconfig-version = 2.16.0
@@ -224,6 +239,17 @@ minizip-version = $(zlib-version)
 # version 1.12.0.
 hdf5-version = 1.13.1
 
+# The lalsuite tarball within Maneage is based on the upstream commit
+# 678514ed of 21 May 2025 of https://git.ligo.org/lscsoft/lalsuite. But
+# instead of being a 950 Mb '.tar.gz' file including the '.git/' directory
+# (or a 320 Mb '.tar.gz' file without the '.git/' directory), our tarball
+# is a 25 Mb '.tar.lz' file (a factor of 30 to 10 times smaller). The main
+# difference (apart from the extra compression provided by lzip) is that
+# this light tarball does not include the big test data files. A
+# description of how this tarball was made and what files have been removed
+# is in the 'README-Maneage-LightWeight.md' file that is within the
+# tarball.
+lalsuite-version = v7.26-15-g1e4c5e5080
 
 
 
@@ -238,74 +264,77 @@ hdf5-version = 1.13.1
 # URL in 'reproduce/software/make/python.mk'.
 #
 # CLASS:PYTHON-START (important identifier for 'awk'; don't modify this line)
-asn1crypto-version = 0.24.0
-asteval-version = 0.9.16
-astropy-version = 7.0.1
+astropy-healpix-version = 1.1.2
 astropy-iers-data-version = 0.2025.2.24.0.34.4
+astropy-version = 7.1.0
 beautifulsoup4-version = 4.10.0
-beniget-version = 0.4.1
-certifi-version = 2018.11.29
 cffi-version = 1.15.0
-chardet-version = 3.0.4
+colorama-version = 0.4.6
 contourpy-version = 1.3.1
-corner-version = 2.0.1
+cosmodesi-mpytools-version = 1.0.0-04369fc9
 cppy-version = 1.3.1
 cycler-version = 0.12.1
 cython-version = 3.0.12
-eigency-version = 1.77
-emcee-version = 3.0.1
-entrypoints-version = 0.3
-esutil-version = 0.6.9
+exceptiongroup-version = 1.3.0
 extension-helpers-version = 1.2.0
 features-version = 0.5.12
 flake8-version = 3.7.8
 flit-core-version = 3.11.0
+flit-scm-version = 1.7.0
 fonttools-version = 4.56.0
-future-version = 0.18.1
 galsim-version = 2.3.5
-gast-version = 0.5.3
 gpep517-version = 16
 h5py-version = 2.10.0
+hatch-vcs-version = 0.5.0
+hatchling-version = 1.27.0
+healpy-version = 1.18.1
 html5lib-version = 1.0.1
-idna-version = 2.8
-jeepney-version = 0.4
+igwn-ligolw-version = 2.1.0
+igwn-segments-version = 2.1.0
+iniconfig-version = 2.1.0
 jinja2-version = 3.0.3
+joblib-version = 1.5.0
 kiwisolver-version = 1.4.8
+ligo-skymap-version = 2.4.0
 lmfit-version = 0.9.14
+lscsoft-glue-version = 4.1.0
 lsstdesccoord-version = 1.2.0
-markupsafe-version = 2.0.1
-meson-version = 1.7.0
 meson-python-version = 0.17.1
-mpi4py-version = 3.1.3
-mpmath-version = 1.1.0
+meson-version = 1.7.0
+mpi4py-version = 4.0.3
+networkx-version = 3.5
 numpy-version = 2.2.3
 packaging-version = 24.2
-pexpect-version = 4.7.0
+pandas-version = 2.2.3
+pathspec-version = 0.12.1
 pillow-version = 11.1.0
 pip-version = 19.0.2
-ply-version = 3.11
+pluggy-version = 1.6.0
 pybind11-version = 2.13.6
-pycodestyle-version = 2.5.0
-pycparser-version = 2.19
 pyerfa-version = 2.0.1.5
-pyflakes-version = 2.1.1
-pyproject-metadata-version = 0.9.0
+pyfftw-version = 0.15.1
+pygments-version = 2.19.2
 pyparsing-version = 3.2.1
-pypkgconfig-version = 1.5.1
+pyproject-metadata-version = 0.9.0
+pytest-version = 8.4.1
 python-dateutil-version = 2.9.0.post0
 python-installer-version = 0.7.0
+python3-fitsio-version = 1.3.0
 pythran-version = 0.11.0
+pytz-version = 2025.2
 pyyaml-version = 6.0.2
 requests-version = 2.21.0
-setuptools-version = 75.8.0
+scikit-base-version = 0.12.2
+scikit-learn-version = 1.6.1
 setuptools-scm-version = 8.2.0
+setuptools-version = 80.8.0
 sip_tpv-version = 1.1
 six-version = 1.17.0
-soupsieve-version = 1.8
 sympy-version = 1.4
-uncertainties-version = 3.1.6
-urllib3-version = 1.24.1
-webencodings-version = 0.5.1
+threadpoolctl-version = 3.6.0
+tqdm-version = 4.67.1
+trove-classifiers-version = 2025.5.9.12
+versioneer-version = 0.29
 wheel-version = 0.45.1
 
 # Matplotlib and Scipy are big packages that may have difficulty resolving
@@ -315,26 +344,11 @@ scipy-version = 1.15.2
 
 # CLASS:PYTHON-END (important identifier for 'awk'; don't modify this line)
 
-# Special Python modules:
-#
-# Healpy: When any Python module is requested, healpix will also build its
-#         Python module Healpy.
-#
-# Bug: Healpix 3.50 doesn't yet support Python 3.10, so we are commenting
-# it here. When future versions fix the problem, we'll un-comment it again.
-#healpy-version = xxxxx
-
 
 
 
 
-# Problematic software that are currently ignored:
-
-# Healpix 3.80 has different installation scheme that is not yet
-# implemented here, and unfortunately healpix 3.50 has conflicts with
-# CFITSIO's new version macro and Python 3.10. So for now, we are ignoring
-# it.
-#healpix-version = 3.50
+# Problematic software that is currently ignored:
 
 # Setuptools-rust crash (https://savannah.nongnu.org/bugs/index.php?61731),
 # so it and its dependencies are being ignored: 'cryptography', and thus
@@ -346,6 +360,34 @@ semantic-version-version = 2.10.0
 #keyring-version = 18.0.0
 #astroquery-version = 0.4
 
+# Not yet adated to the GPEP517 build method:
+#asn1crypto-version = 0.24.0
+#asteval-version = 0.9.16
+#beniget-version = 0.4.1
+#certifi-version = 2018.11.29
+#chardet-version = 3.0.4
+#corner-version = 2.0.1
+#eigency-version = 1.77
+#emcee-version = 3.0.1
+#entrypoints-version = 0.3
+#esutil-version = 0.6.9
+#future-version = 0.18.1
+#gast-version = 0.5.3
+#idna-version = 2.8
+#jeepney-version = 0.4
+#markupsafe-version = 2.0.1
+#mpmath-version = 1.1.0
+#pexpect-version = 4.7.0
+#ply-version = 3.11
+#pycodestyle-version = 2.5.0
+#pycparser-version = 2.19
+#pyflakes-version = 2.1.1
+#pypkgconfig-version = 1.5.1
+#soupsieve-version = 1.8
+#uncertainties-version = 3.1.6
+#urllib3-version = 1.24.1
+#webencodings-version = 0.5.1
+