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, 64 insertions, 32 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index ca3bf6e..3e0163e 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -228,7 +228,7 @@ empty_build_tmp() {
     # accidentally delete the whole root partition (or a least the '/home'
     # partition of the user).
     if ! [ x"$( ls -A $tmpblddir )" = x ]; then
-        rm -r "$tmpblddir"/*
+        rm -rf "$tmpblddir"/*
     fi
     rm -r "$tmpblddir"
 }
@@ -378,7 +378,11 @@ if [ $built_container = 0 ]; then
         # between Intel or Apple M1 CPUs. Here we disinguish between Apple
         # M1 or others.
         maccputype=$(sysctl -n machdep.cpu.brand_string)
-        if [ x"$maccputype" = x"Apple M1" ]; then
+        if    [ x"$maccputype" = x"Apple M1" ] \
+           || [ x"$maccputype" = x"Apple M2" ] \
+           || [ x"$maccputype" = x"Apple M3" ] \
+           || [ x"$maccputype" = x"Apple M4" ] \
+           || [ x"$maccputype" = x"Apple M5" ] ; then
             address_size_physical=$(sysctl -n machdep.cpu.thread_count)
             address_size_virtual=$(sysctl -n machdep.cpu.logical_per_package)
         else
@@ -781,6 +785,25 @@ fi
 
 
 
+# Older C standard versions
+# -------------------------
+#
+# Some basic packages require an old standard of C compilation; for their
+# list, see the 'Not working with C23' list in '../config/versions.conf'.
+# Here, we first try 'gnu17', but if that fails on the host compiler, we
+# fall back to 'gnu99'.
+if [ $built_container = 0 ]; then
+   printf "int main(void){; return 0;}\n" > $testsource
+   if gcc -std=gnu17 $testsource -o $testprog 2> /dev/null; then
+       std_c_old="gnu17"
+   else std_c_old="gnu99"
+   fi
+   rm $testsource $testprog
+fi
+
+
+
+
 # Fortran compiler
 # ----------------
 #
@@ -856,33 +879,6 @@ fi
 
 
 
-# See if the linker accepts -Wl,-rpath-link
-# -----------------------------------------
-#
-# '-rpath-link' is used to write the information of the linked shared
-# library into the shared object (library or program). But some versions of
-# LLVM's linker don't accept it an can cause problems.
-#
-# IMPORTANT NOTE: This test has to be done **AFTER** the definition of
-# 'instdir', otherwise, it is going to be used as an empty string.
-if [ $built_container = 0 ]; then
-   cat > $testsource <<EOF
-#include <stdio.h>
-#include <stdlib.h>
-int main(void) {return EXIT_SUCCESS;}
-EOF
-   if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \
-          > /dev/null; then
-       export rpath_command="-Wl,-rpath-link=$instdir/lib"
-   else
-       export rpath_command=""
-   fi
-
-   # Delete the temporary directory for compiler checking.
-   rm -f $testprog $testsource
-   rm -r $compilertestdir
-   elapsed_time_from_prev_step compiler-rpath
-fi
 
 
 
@@ -1426,9 +1422,9 @@ elapsed_time_from_prev_step downloader
 # by the algorithm in 'configure.sh' when evaluating the variable
 # 'sys_library_sh_path'. This leads to a fatal syntax error in (at least)
 # 'ncurses', because the option using 'sys_library_sh_path' contains an
-# unquoted RAM address in parentheses.  Even if the address were quoted, it
-# would still be incorrect. This 'grep command excludes candidate host path
-# strings that look like RAM addresses to address the problem.
+# unquoted RAM address in parentheses. Even if the address were quoted, it
+# would still be incorrect. This 'grep' command excludes candidate host
+# path strings that look like RAM addresses to address the problem.
 #
 # [1] https://savannah.nongnu.org/bugs/index.php?66847
 # [2] https://stackoverflow.com/questions/34428037/how-to-interpret-the-output-of-the-ldd-program
@@ -1550,6 +1546,41 @@ fi
 
 
 
+# See if the linker accepts -Wl,-rpath-link
+# -----------------------------------------
+#
+# '-rpath-link' is used to write the information of the linked shared
+# library into the shared object (library or program). But some versions of
+# LLVM's linker don't accept it an can cause problems.
+#
+# IMPORTANT NOTE: This test has to be done **AFTER** the definition of
+# 'instdir'. Otherwise, the rpath-link value set within rpath_command in
+# the case of a successful test compile (if $CC ...) will be "/lib",
+# i.e. the host system root /lib directory, instead of the maneage library
+# directory.
+if [ $built_container = 0 ]; then
+   cat > $testsource <<EOF
+#include <stdio.h>
+#include <stdlib.h>
+int main(void) {return EXIT_SUCCESS;}
+EOF
+   if $CC $testsource -o$testprog -Wl,-rpath-link 2>/dev/null \
+          > /dev/null; then
+       export rpath_command="-Wl,-rpath-link=$instdir/lib"
+   else
+       export rpath_command=""
+   fi
+
+   # Delete the temporary directory for compiler checking.
+   rm -f $testprog $testsource
+   rm -r $compilertestdir
+   elapsed_time_from_prev_step compiler-rpath
+fi
+
+
+
+
+
 # Software building directory (possibly in RAM)
 # ---------------------------------------------
 #
@@ -1833,6 +1864,7 @@ if [ $quiet = 0 ]; then echo "Building/validating software: basic"; fi
      numthreads=$numthreads \
      needs_ldl=$needs_ldl \
      on_mac_os=$on_mac_os \
+     std_c_old=$std_c_old \
      host_cc=$host_cc \
      -j$numthreads
 elapsed_time_from_prev_step make-software-basic