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, 17 insertions, 16 deletions

diff --git a/reproduce/software/shell/docker.sh b/reproduce/software/shell/docker.sh
index ab454aa..5cd8f11 100755
--- a/reproduce/software/shell/docker.sh
+++ b/reproduce/software/shell/docker.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/usr/bin/env bash
 #
 # Create a Docker container from an existing image of the built software
 # environment, but with the source, data and build (analysis) directories
@@ -409,22 +409,25 @@ else
         # that the user gave there.
         mkdir $tmp_dir/$tsdir
         cp -r "$software_dir"/* $tmp_dir/$tsdir/
-        printf "    --mount=type=bind,source=$tsdir,target=$dts \x5C\n" >> $df
+        printf "    --mount=type=bind,source=$tsdir,target=$dts \x5C\n" \
+               >> $df
     fi
 
     # Construct the rest of the 'RUN' command.
     printf "    cp -r $dsr /home/maneager/source; \x5C\n"          >> $df
     printf "    cd /home/maneager/source; \x5C\n"                  >> $df
-    printf "    ./project configure --jobs=$jobs \x5C\n"           >> $df
+    printf "    ./project configure \x5C\n"                        >> $df
+    printf "              --no-pause \x5C\n"                       >> $df
+    printf "              --jobs=$jobs \x5C\n"                     >> $df
     printf "              --build-dir=$intbuild \x5C\n"            >> $df
     printf "              --input-dir=/home/maneager/input \x5C\n" >> $df
-    printf "              --software-dir=$dts; \x5C\n"             >> $df
+    printf "              --software-dir=$dts; \x5C\n"  >> $df
 
-    # We are deleting the '.build/software/tarballs' directory because this
-    # directory is not relevant for the analysis of the project. But in
-    # case any tarball was downloaded, it will consume space within the
-    # container.
-    printf "    rm -rf .build/software/tarballs; \x5C\n" >> $df
+    # We are deleting the contents of the '.build/software/tarballs'
+    # directory (tarballs of the sources of the software) because they are
+    # not relevant to the execution of the project and will consume space
+    # within the container.
+    printf "    rm -rf .build/software/tarballs/*; \x5C\n" >> $df
 
     # We are deleting the source directory becaues later (at 'docker run'
     # time), the 'source' will be mounted directly from the host operating
@@ -432,12 +435,9 @@ else
     printf "    cd /home/maneager; \x5C\n" >> $df
     printf "    rm -rf source\n" >> $df
 
-    # Build the Maneage container and delete the temporary directory. The
-    # '--progress plain' option is for Docker to print all the outputs
-    # (otherwise, it will only print a very small part!).
+    # Build the Maneage container and delete the temporary directory.
     cd $tmp_dir
     docker build ./ -t $project_name \
-           --progress=plain \
            --shm-size=$shm_size \
            --no-cache \
            2>&1 | tee build.log
@@ -453,14 +453,15 @@ if ! [ x"$image_file" = x ] && ! [ -f "$image_file" ]; then
     # Save the image into a tarball
     tarname=$(echo $image_file | sed -e's|.gz$||')
     if [ $quiet = 0 ]; then
-        printf "$scriptname: info: saving docker image to '$tarname'"
+        printf "$scriptname: info: saving docker image to '$tarname'\n"
     fi
     docker save -o $tarname $project_name
 
     # Compress the saved image
     if [ $quiet = 0 ]; then
         printf "$scriptname: info: compressing to '$image_file' (can "
-        printf "take +10 minutes, but volume decreases by more than half!)"
+        printf "take +10 minutes, but volume decreases by more than "
+        printf "half!)\n"
     fi
     gzip --best $tarname
 fi
@@ -470,7 +471,7 @@ fi
 if ! [ x"$build_only" = x ]; then
     if [ $quiet = 0 ]; then
         printf "$scriptname: info: Maneaged project has been configured "
-        printf "successfully in the '$project_name' image"
+        printf "successfully in the '$project_name' image\n"
     fi
     exit 0
 fi