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, 477 insertions, 68 deletions

diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 83486dc..d059544 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -438,6 +438,23 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	tar cf $$customtar cfitsio-$(cfitsio-version)
 	cd $$topdir
 
+#       Add SSE2 optimization only when we are on a Linux kernel or using
+#       macOS on an Intel CPU.
+	arch=$$(uname -m)
+	unames=$$(uname -s)
+	if [ "$$unames" = "Linux" ]; then
+	  confopts="$$confopts --enable-sse2"
+	elif [ "$$unames" = "Darwin" ] && [ "$$arch" = "x86_64" ]; then
+	  confopts="$$confopts --enable-sse2"
+	fi
+
+#       On macOS, system libraries (e.g., libSystem) are inside the SDK,
+#       not standard paths. 'xcrun' provides the correct SDK path; use $$
+#       so it is evaluated by the shell (not Make).
+	if [ $(on_mac_os) = yes ]; then
+	  export SDKROOT=$$(xcrun --show-sdk-path)
+	fi
+
 #	Continue the standard build on the customized tarball. Note that
 #	with the installation of CFITSIO, 'fpack' and 'funpack' are not
 #	installed by default. Because of that, they are added explicity.
@@ -446,7 +463,10 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 #	specific 'shared' target for the building of the shared libraries.
 	export gbuild_tar=$(ddir)/$$customtar
 	$(call gbuild, cfitsio-$(cfitsio-version), , \
-	               --enable-sse2 --enable-reentrant \
+	               $$confopts \
+	               --disable-curl \
+	               --disable-fortran \
+	               --enable-reentrant \
 	               --with-bzip2=$(idir), , \
 	               make fpack funpack)
 	rm $$customtar
@@ -505,36 +525,62 @@ $(ibidir)/expat-$(expat-version):
 	$(call gbuild, expat-$(expat-version), static)
 	echo "Expat $(expat-version)" > $@
 
+# FFTW manual customizations:
+#
+# - To activate the OpenMPI features of FFTW, add OpenMPI as a dependency
+#   of FFTW: the necessary flags are automatically added if OpenMPI was
+#   installed before FFTW.
+#
+# - There are Intel-specific optimizations that can be enabled by adding
+#   the following two options to 'opts'
+#
+#     --enable-avx --enable-sse2
+#
+#   However, they cause crashes on non-Intel processors (has been confirmed
+#   in ARM's aarch64). So in the generic scenario they are
+#   removed. Checking how these optimizations affect the numerical accuracy
+#   of the result (and thus optionally adding them for Intel-based
+#   processors) should be studied before they are optionally added for
+#   Intel-based CPUs (and ignored for others).
 $(ibidir)/fftw-$(fftw-version):
 
 #	Prepare the source tarball.
 	tarball=fftw-$(fftw-version).tar.lz
 	$(call import-source, $(fftw-url), $(fftw-checksum))
 
-#	FFTW's single and double precision libraries must be built
-#	independently: for the the single-precision library, we need to add
-#	the '--enable-float' option. We will build this first, then the
-#	default double-precision library.
-#
-#	There are Intel-specific optimizations that can be enabled by
-#	adding the following two options to 'confop'
-#
-#           --enable-avx --enable-sse2
-#
-#	However, they cause crashs on non-Intel processors (has been
-#	confirmed in ARM's aarch64). So in the generic scenario they are
-#	removed. Checking how these optimizations affect the numeric
-#	accuracy of the result (and thus optionally adding them for
-#	Intel-based processors) should be studied before they are
-#	optionally added for Intel-based CPUs (and ignored for others).
-	confop="--enable-shared --enable-threads"
-	$(call gbuild, fftw-$(fftw-version), static, \
-	               $$confop --enable-float)
-	$(call gbuild, fftw-$(fftw-version), static, \
-	               $$confop)
-	cp $(dtexdir)/fftw.tex $(ictdir)/
+#	Specific customizations: you can add the options mentioned above
+#	after the 'if' statements, for example: "opts=$$opts EXTRA".
+	opts="--enable-shared --enable-threads"
+	if [ x$(on_mac_os) = xyes ]; then opts="$$opts --disable-fortran"
+	else
+	  if [ -f $(ibidir)/openmpi-$(openmpi-version) ]; then
+	    opts="$$opts --enable-openmp --enable-mpi"
+	  fi
+	fi
+
+#	FFTW's single, double and long-double precision libraries must be
+#	built separately (fully independent builds and installs).
+	$(call gbuild, fftw-$(fftw-version), static, $$opts)
+	$(call gbuild, fftw-$(fftw-version), static, $$opts \
+	                                             --enable-float)
+	$(call gbuild, fftw-$(fftw-version), static, $$opts \
+	                                             --enable-long-double)
+	cp -pv $(dtexdir)/fftw.tex $(ictdir)/
 	echo "FFTW $(fftw-version) \citep{fftw}" > $@
 
+# 2026-02-20 'framel' is needed by the python package lalsuite, which is
+# needed by ligo-skymap; currently the compile of 'framel' 8.49.0 fails with
+#
+#    error: initialization of 'void (*)(void)' from incompatible
+#     pointer type 'void (*)(int,  char *)' [-Wincompatible-pointer-types]
+#
+# Hints: try using gcc -std=gnu99 or -std=gnu11 (default is -std=gnu17).
+$(ibidir)/framel-$(framel-version): $(ibidir)/cmake-$(cmake-version)
+	tarball=framel-$(framel-version).tar.lz
+	$(call import-source, $(framel-url), $(framel-checksum))
+	$(call cbuild, framel-$(framel-version), static)
+	echo "Framel $(framel-version)" > $@
+
 $(ibidir)/freetype-$(freetype-version): $(ibidir)/libpng-$(libpng-version)
 #	As of version 2.13.2, FreeType doesn't account for the 'SHELL'
 #	environment variable. The issue has been reported to the
@@ -571,64 +617,114 @@ $(ibidir)/hdf5-$(hdf5-version): $(ibidir)/openmpi-$(openmpi-version)
 	echo "HDF5 library $(hdf5-version)" > $@
 
 # HEALPix includes the source of its C, C++, Python (and several other
-# languages) libraries within one tarball. We will include the Python
-# installation only when any other Python module is requested (in
-# 'TARGETS.conf').
+# languages) libraries within one tarball. However, we do not build the
+# python version here; instead we provide 'healpy' as a separate package;
+# see 'python.mk' for the build rule.
 #
 # Note that the default './configure' script is an interactive script which
 # is hard to automate. So we need to go into the 'autotools' directory of
 # the 'C' and 'cxx' directories and configure the GNU Build System (with
 # 'autoreconf', which uses 'autoconf' and 'automake') to easily build the
 # HEALPix C/C++ libraries in batch mode.
-ifeq ($(strip $(targets-python)),)
-healpix-python-dep =
-else
-healpix-python-dep = $(ipydir)/matplotlib-$(matplotlib-version) \
-                     $(ipydir)/astropy-$(astropy-version)
-endif
-$(ibidir)/healpix-$(healpix-version): $(healpix-python-dep) \
+$(ibidir)/healpix-$(healpix-version): \
                   $(ibidir)/cfitsio-$(cfitsio-version) \
                   $(ibidir)/autoconf-$(autoconf-version) \
                   $(ibidir)/automake-$(automake-version)
+
+#	Import the tarball.
 	tarball=healpix-$(healpix-version).tar.lz
 	$(call import-source, $(healpix-url), $(healpix-checksum))
-	if [ x"$(healpix-python-dep)" = x ]; then
-	   pycommand1="echo no-healpy-because-no-other-python"
-	   pycommand2="echo no-healpy-because-no-other-python"
-	else
-	   pycommand1="python setup.py build"
-	   pycommand2="python setup.py install"
-	fi
-	rm -rf $(ddir)/Healpix_$(healpix-version)
+
+#	Setup the build directory
+	rm -rf $(ddir)/healpix-$(healpix-version)
 	topdir=$(pwd); cd $(ddir);
 	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
-	cd Healpix_$(healpix-version)
+	cd healpix-$(healpix-version)
 	$(shsrcdir)/prep-source.sh $(ibdir)
-	cd src/C/autotools
+
+#	Compile and install libsharp:
+	cd src/common_libraries/libsharp
 	autoreconf --install
 	./configure --prefix=$(idir)
 	make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
 	make install
-	cd ../../cxx/autotools/
+
+#	Compile and install the C version:
+	cd ../../C/autotools
+	printf "\n\nDEBUG ONLY\n\n"; /bin/pwd; printf "\nGUBED\n\n\n"
+	autoreconf --install
+	./configure --prefix=$(idir)
+	make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
+	make install
+
+#	Compile and install the C++ version:
+	cd ../../cxx/
+	printf "\n\nDEBUG.BBBB ONLY\n\n"; /bin/pwd; printf "\nBBB.GUBED\n\n\n"
 	autoreconf --install
 	./configure --prefix=$(idir)
 
 #	With CFITSIO 4.0, the 'CFITSIO_VERSION' macro has three
-#	components. But this version of Healpix doesn't yet account for
-#	this.
+#	components. But this (which?) version of Healpix doesn't yet
+#	account for this.
 	sed -i -e's/CFITSIO_VERSION/fitsversion/' cxxsupport/fitshandle.cc
 
 #	Continue with the building.
 	make V=1 -j$(numthreads) SHELL=$(ibdir)/bash
 	make install
-	cd ../../healpy
-	$$pycommand1
-	$$pycommand2
+
+#	Finalize the build
 	cd $$topdir
-	rm -rf $(ddir)/Healpix_$(healpix-version)
+	rm -rf $(ddir)/healpix-$(healpix-version)
 	cp $(dtexdir)/healpix.tex $(ictdir)/
 	echo "HEALPix $(healpix-version) \citep{healpix}" > $@
 
+# 2025-05-24 The build rules here for 'lalsuite' include git initialisation
+# with a dummy commit of all the source files since this is required for an
+# install unless the .git/ directory (currently 650 Mb) is included in the
+# tarball. Our lalsuite tarball also has many big data test files removed,
+# since these are unlikely to be needed in typically astronomy usage; this
+# brings the .tar.lz file down to 25 Mb from the default of about 950 Mb
+# (tar.gz) or 740 Mb (tar.lz).
+#
+# If you need to do full gravitational wave work with 'lalsuite', then you
+# should provide an alternative tarball and edit the three files
+# reproduce/software/config/{versions,checksums,urls}.conf in order to use
+# your preferred tarball.
+$(ipydir)/lalsuite-$(lalsuite-version): \
+                   $(ibidir)/automake-$(automake-version) \
+                   $(ibidir)/swig-$(swig-version) \
+                   $(ibidir)/metaio-$(metaio-version) \
+                   $(ibidir)/framel-$(framel-version) \
+                   $(ipydir)/astropy-$(astropy-version) \
+                   $(ipydir)/igwn-segments-$(igwn-segments-version) \
+                   $(ipydir)/lscsoft-glue-$(lscsoft-glue-version) \
+                   $(ipydir)/python-dateutil-$(python-dateutil-version)
+	tarball=lalsuite-$(lalsuite-version).tar.lz
+	$(call import-source, $(lalsuite-url), \
+	         $(lalsuite-checksum))
+
+#	First: build from source as if it's a C source only.
+	cd $(ddir)
+	unpackdir=lalsuite-$(lalsuite-version)
+	rm -rf $$unpackdir
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd $$unpackdir
+	$(shsrcdir)/prep-source.sh $(ibdir)
+
+#	A git commit is needed to generate version-control files; the
+#	strings in these will be rather arbitrary and should be ignored.
+	git init && git add .
+	git commit -a --no-edit -m "Dummy commit" \
+	           --author "Tarball <tar@ball.only>"
+	autoreconf
+	./configure --prefix="$(idir)" --enable-swig-python
+	make
+	make install
+
+#	Clean up and build final tarball
+	cd $(ddir); rm -fr $$unpackdir
+	echo "LALSuite $(lalsuite-version)" > $@
+
 $(ibidir)/libbsd-$(libbsd-version): $(ibidir)/libmd-$(libmd-version)
 	tarball=libbsd-$(libbsd-version).tar.lz
 	$(call import-source, $(libbsd-url), $(libbsd-checksum))
@@ -840,9 +936,52 @@ $(ibidir)/ninjabuild-$(ninjabuild-version): $(ibidir)/cmake-$(cmake-version)
 	echo "Ninja build system $(ninjabuild-version)" > $@
 
 $(ibidir)/openblas-$(openblas-version):
+
+#	Import the tarball.
 	tarball=openblas-$(openblas-version).tar.lz
 	$(call import-source, $(openblas-url), $(openblas-checksum))
-	if [ x$(on_mac_os) = xyes ]; then export CC=clang; fi
+
+#	If 'gcc' is actually a symbolic link to 'clang', then print the
+#	following message to guide the user on how to prepare their
+#	environment.
+	if $$CC --version | grep clang &> /dev/null; then
+
+#	  Print message.
+	  echo; echo
+	  printf "*********************************************\n"
+	  printf "OpenBlas could not be installed with Clang!\n\n"
+	  printf "In order to install OpenBLAS, GCC and Gfortran are "
+	  printf "needed. You can take the following steps to fix "
+	  printf "this:\n\n"
+	  printf "1. Install GCC with Homebrew.\n"
+	  printf "2. Get the full path of 'gcc', 'g++', and 'gfortran' "
+	  printf "(for example with 'which gcc').\n"
+	  printf "3. Comment the 'exit 1' and un-comment (and edit) the "
+	  printf "'export's that are below this message (in the "
+	  printf "'openblas' rule of "
+	  printf "'reproduce/software/make/high-level.mk', within the "
+	  printf "'openblas' rule):\n\n"
+	  printf "   exit 1\n"
+	  printf "   #export CC=/opt/homebrew/bin/gcc-XX\n"
+	  printf "   #export CXX=/opt/homebrew/bin/g++-XX\n"
+	  printf "   #export FC=/opt/homebrew/bin/gfortran-XX\n\n"
+	  printf "   with the lines:\n\n"
+	  printf "   #exit 1\n"
+	  printf "   export CC=/opt/homebrew/bin/gcc-15\n"
+	  printf "   export CXX=/opt/homebrew/bin/g++-15\n"
+	  printf "   export FC=/opt/homebrew/bin/gfortran-15\n\n"
+	  printf "5. Re-configure Maneage.\n"
+	  printf "*********************************************\n"
+	  echo; echo
+
+#	  Parts to modify when the message above is printed.
+	  exit 1
+	  #export CC=/opt/homebrew/bin/gcc-XX
+	  #export CXX=/opt/homebrew/bin/g++-XX
+	  #export FC=/opt/homebrew/bin/gfortran-XX
+	fi
+
+#	Do the build.
 	cd $(ddir)
 	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
 	cd openblas-$(openblas-version)
@@ -909,6 +1048,209 @@ $(ibidir)/tides-$(tides-version):
 	cp $(dtexdir)/tides.tex $(ictdir)/
 	echo "TIDES $(tides-version) \citep{tides}" > $@
 
+$(ibidir)/sqlite-$(sqlite-version): $(ibidir)/tcl-$(tcl-version)
+	tarball=sqlite-$(sqlite-version).tar.lz
+	$(call import-source, $(sqlite-url), $(sqlite-checksum))
+	$(call gbuild, sqlite-$(sqlite-version),, \
+	      --enable-all --enable-static --enable-shared)
+	echo "Sqlite $(sqlite-version)" > $@
+
+$(ibidir)/tcl-$(tcl-version): $(ibidir)/zlib-$(zlib-version) \
+                              $(ibidir)/tzdb-$(tzdb-version)
+
+#	If both the tcl and tk packages are needed, then they must be built
+#	together, with identical version numbers. Thus, for simplicity in
+#	the build system, whether or not we build only tcl, or both tcl and
+#	tk, we must check that the versions are identical.
+	if [ "x$(tcl-version)" != "x$(tk-version)" ]; then
+	    printf "Error: This build system requires identical tcl and "
+	    printf "tk versions to be selected **even if** tk is not "
+	    printf "going to be built. However, tcl-version=$(tcl-version) "
+	    printf "while tk-version=$(tk-version)\n"
+	    exit 1
+	fi
+
+#	Prepare the input tarball.
+	tarball=tcl-$(tcl-version).tar.lz
+	$(call import-source, $(tcl-url), $(tcl-checksum))
+
+#	Setup the build directory
+	cd $(ddir)
+	unpackdir_tcl=tcl-$(tcl-version)
+	rm -rf $${unpackdir_tcl}
+
+#	Install TCL
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd - # return to the top maneage directory
+	cd $(ddir)/$${unpackdir_tcl}/unix
+	$(shsrcdir)/prep-source.sh $(ibdir)
+	./configure --prefix="$(idir)"
+	make -j$(numthreads)
+	make install
+	cd - # return to the top maneage directory
+
+#	Setup the 'tclsh' symbolic link.
+	maj_min_version=$$(printf $(tcl-version)| \
+	      sed -e "s;^\([0-9]*\.[0-9]*\).*\';\1;")
+	printf "Will symlink tclsh$${maj_min_version} as tclsh ...\n"
+	cd $(ibdir)
+	rm -fv tclsh && ln -sv tclsh$${maj_min_version} tclsh
+	cd -
+	cd $(ddir)
+
+#	Finalize.
+	if (printf "$$unpackdir_tcl" | grep "[a-z][a-z]"); then \
+	     rm -fr $$unpackdir_tcl
+	fi
+	echo "Tcl $(tcl-version)" > $(ibidir)/tcl-$(tcl-version)
+
+
+# The tk library needs the X11 library for building GUIs, and should not
+# normally be needed for a non-interactive project. However, GUIs built
+# with tk might be convenient during development of a project, since visual
+# checks within the maneage shell may be useful.
+#
+# We need to rebuild tcl temporarily in the temporary build area in order
+# to build tk. However, we want the tk target to be dependent on tcl as a
+# prerequisite to avoid the possibility of parallel builds that risk
+# conflicting within the build area because of duplicate use of the same
+# tcl package directory after untarring the archive.
+$(ibidir)/tk-$(tk-version): $(ibidir)/zip-$(zip-version) \
+                            $(ibidir)/tcl-$(tcl-version) \
+                            $(ibidir)/libx11-$(libx11-version) \
+
+#	Prepare the tarball.
+	tarball=tk-$(tk-version).tar.lz
+	$(call import-source, $(tk-url), $(tk-checksum))
+
+#	If both the tcl and tk packages are needed, then they must be built
+#	together, with identical version numbers. Thus, for simplicity in
+#	the build system, whether or not we build only tcl, or both tcl and
+#	tk, we must check that the versions are identical.
+	if [ "x$(tcl-version)" != "x$(tk-version)" ]; then
+	    printf "Error: This build system requires identical tcl and "
+	    printf "tk versions to be selected **even if** tk is not "
+	    printf "going to be built. However, tcl-version=$(tcl-version) "
+	    printf "while tk-version=$(tk-version)\n"
+	    exit 1
+	fi
+
+#	Make sure no temporary directory exists.
+	cd $(ddir)
+	unpackdir=tk-$(tk-version)
+	if (printf "$$unpackdir" | grep "[a-z][a-z]"); then
+	  rm -rf $$unpackdir
+	fi
+
+#	Install TK: zipfs is being disabled because of the problem with
+#	installing zip (see the comments above zip).
+	cd $(ddir)
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd $$unpackdir/unix
+	$(shsrcdir)/prep-source.sh $(ibdir)
+	./configure  --prefix="$(idir)" --with-tcl=$(ildir)
+	make -j$(numthreads)
+	make install
+
+#	Finalize.
+	cd $(ddir)
+	if (printf "$$unpackdir" | grep "[a-z][a-z]"); then \
+	     rm -fr $$unpackdir; fi
+	echo "Tk $(tk-version)" > $(ibidir)/tk-$(tk-version)
+
+
+
+# WARNING: Dependence on glibc: tzdb (time zone data base) uses the 'zic'
+# program from the GNU C library. Until Maneage builds its own glibc, it is
+# imported from the host operating system in the 'low-level-links' step of
+# 'basic.mk'.
+$(ibidir)/tzdb-$(tzdb-version):
+
+#	Import the tarball
+	tarball=tzdb-$(tzdb-version).tar.lz
+	$(call import-source, $(tzdb-url), $(tzdb-checksum))
+
+#	Unpack the tarball.
+	cd $(ddir)
+	unpackdir=tzdb-$(tzdb-version)
+	rm -rf $$unpackdir
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd $$unpackdir
+
+#	Make necessary corrections.
+	TZGEN=$(strip $(ddir))/$$unpackdir/tzgen
+	printf "\n\n\n_____TZGEN=$${TZGEN}_____\n\n\n"
+	make AWK=gawk BACKWARD="backward" PACKRATDATA=backzone \
+	      PACKRATLIST=zone.tab VERSION_DEPS= tzdata.zi leapseconds
+
+#	Build the timezone data
+#
+#	The '-b fat' option was created in glibc by around 2020, when
+#	'-b slim' became the default. Allowing the default of '-b slim'
+#	could potentially lead to a #Y2038 bug [3].
+#
+#	Some other hacks are also needed for older glibc.
+#
+#	[1] https://mm.icann.org/pipermail/tz-announce/2020-October/000059.html
+#	[2] https://github.com/stub42/pytz/issues/48
+#	[3] https://en.wikipedia.org/wiki/Year_2038_problem
+	BFAT_OPTION=$$(if (zic -b fat 2>/dev/null); then \
+	                 printf "%sb fat" "-"; else printf ""; fi)
+	if [ "x$${BFAT_OPTION}" = "x" ]; then \
+	   sed -e 's/Sa\([^a-zA-Z]\)/Sat\1/g' \
+	       -e 's/Su\([^a-zA-Z]\)/Sun\1/g' \
+	       -e 's/^\(.\|..\) Sat/\1 Sa/' \
+	       -e "s/lastSu\'/lastSun/" tzdata.zi \
+	       | grep -v "^L" \
+	       > tzdata.zi.3letter.days
+	   zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null \
+	       tzdata.zi.3letter.days
+	   zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \
+	       tzdata.zi.3letter.days
+	else
+	   zic $${BFAT_OPTION} -d $${TZGEN} -L /dev/null tzdata.zi
+	   zic $${BFAT_OPTION} -d $${TZGEN}/right -L leapseconds \
+	       tzdata.zi
+	fi
+
+#	Replace hardlinks by symlinks
+	if [ "x$${BFAT_OPTION}" = "x" ]; then
+
+#	    Older method of creating symbolic links:
+	    grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \
+	      | while read L target name ; do
+	          absolute_name="$${TZGEN}/$$name"
+	          relative_target=$$(realpath -m -s \
+	                             --relative-to="$${absolute_name%/*}" \
+	                             "$${TZGEN}/$$target")
+	          maybe_newdir=$$(printf $$name | sed -e "s;/[^/]*\';;")
+	          mkdir -p $${TZGEN}/$${maybe_newdir}
+	          mkdir -p $${TZGEN}/right/$${maybe_newdir}
+	          ln -sf "$$relative_target" "$${TZGEN}/$$name"
+	          ln -sf "$$relative_target" "$${TZGEN}/right/$$name"
+	        done
+
+	else
+
+#	    More recent (2025-05-25) method of creating symbolic links:
+	    grep '^L ' $(ddir)/$$unpackdir/tzdata.zi \
+	      | while read L target name ; do
+	          absolute_name="$${TZGEN}/$$name"
+	          relative_target=$$(realpath -m -s \
+	                              --relative-to="$${absolute_name%/*}" \
+	                              "$${TZGEN}/$$target")
+	          ln -sf "$$relative_target" "$${TZGEN}/$$name"
+	          ln -sf "$$relative_target" "$${TZGEN}/right/$$name"
+	        done
+	fi
+
+#	Generate a posixrules file (with a UTC timezone) and install.
+	ln -s Etc/UTC $${TZGEN}/posixrules
+	mkdir -p $(idir)/share/zoneinfo
+	cp -rv $${TZGEN}/* $(idir)/share/zoneinfo/
+	cd $(ddir); rm -rf $$unpackdir
+	echo "IANA Time Zone Database (tzdb) $(tzdb-version)" > $@
+
 $(ibidir)/valgrind-$(valgrind-version):
 	tarball=valgrind-$(valgrind-version).tar.lz
 	$(call import-source, $(valgrind-url), $(valgrind-checksum))
@@ -964,7 +1306,19 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
 	tarball=wcslib-$(wcslib-version).tar.lz
 	$(call import-source, $(wcslib-url), $(wcslib-checksum))
 
+#	macOS arm64 fix: reserve extra space in binary headers so
+# 	install_name_tool (called bellow, after installation) can safely
+# 	update library paths. Without this, we get the following error:
+# 	"larger updated load commands do not fit". SDKROOT is also
+# 	necessary for system libraries.
+	if [ x$(on_mac_os) = xyes ]; then
+	  sdk=$$(xcrun --show-sdk-path)
+	  LDFLAGS="$$LDFLAGS -isysroot $$sdk"
+	  export LDFLAGS="$$LDFLAGS -Wl,-headerpad_max_install_names"
+	fi
+
 #	Build WCSLIB while disabling some features:
+#
 #	- Fortran is disabled because as of May 2023, on macOS systems
 #	  where we do not install GCC (and thus a standard 'gfortran'), the
 #	  LLVM Fortran compiler is not complete and will cause a crash. If
@@ -973,11 +1327,18 @@ $(ibidir)/wcslib-$(wcslib-version): $(ibidir)/cfitsio-$(cfitsio-version)
 #	  systems. Hopefully some time in the future, GCC will also be
 #	  install-able on macOS within Maneage or LLVM's 'gfortran' will
 #	  also be complete and will not cause a crash.
+#
 #	- PGPLOT is disabled because it has many manual steps in its
 #	  installation. Therefore, we currently do not build PGPlots in
 #	  Maneage. Once (if) it is added, we can remove '--without-pgplot'.
+#
+#	- Flex is disabled because we have not made it a prerequisite for
+#	  the 'wcslib' target, and we don't want the behaviour to differ
+#	  between host OSes that may or may not have 'flex', or may have
+#	  different versions of 'flex'.
 	$(call gbuild, wcslib-$(wcslib-version), , \
 	               LIBS="-pthread -lcurl -lm" \
+	               --disable-flex \
 	               --without-pgplot \
 	               --disable-fortran \
                        --with-cfitsiolib=$(ildir) \
@@ -1190,9 +1551,8 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 #	On macOS we use the system compiler and linker. The system linker
 #	there doesn't support '--copy-dt-needed-entries', while the one on
 #	Linux crashes if we remove it. So we only activate it on macOS.
-	ldflags=""
 	if [ x$(on_mac_os) = xno ]; then
-	     ldflags="LDFLAGS=-Wl,--copy-dt-needed-entries"
+	  export LDFLAGS="$$LDFLAGS -Wl,--copy-dt-needed-entries"
 	fi
 
 #	Unpack it and configure Ghostscript. The option
@@ -1202,8 +1562,7 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
 	cd ghostscript-$(ghostscript-version)
 	$(shsrcdir)/prep-source.sh $(ibdir)
-	./configure $$ldflags \
-	            --disable-cups \
+	./configure --disable-cups \
 	            --prefix=$(idir) \
 	            --enable-dynamic \
 	            --disable-compile-inits \
@@ -1405,6 +1764,16 @@ $(ibidir)/imfit-$(imfit-version): \
 	rm -rf $$unpackdir
 	echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
 
+# This is the LIGO lscsoft package 'metaio' [1] (to be distinguished from
+# some other packages with the same name).
+#
+# [1] https://git.ligo.org/lscsoft/metaio
+$(ibidir)/metaio-$(metaio-version):
+	tarball=metaio-$(metaio-version).tar.lz
+	$(call import-source, $(metaio-url), $(metaio-checksum))
+	$(call gbuild, metaio-$(metaio-version), static)
+	echo "Lscsoft Metaio $(metaio-version)" > $@
+
 # Minizip 1.x is actually distributed within zlib. It doesn't have its own
 # independent tarball. So we need a custom build, which include the GNU
 # Autotools (Autoconf and Automake). Note that Minizip 2.x isn't like this
@@ -1511,6 +1880,25 @@ $(ibidir)/netpbm-$(netpbm-version): \
 	rm -rf $$unpackdir
 	echo "Netpbm $(netpbm-version)" > $@
 
+$(ibidir)/parallel-$(parallel-version):
+
+#	Prepare the tarball and build it.
+	tarball=parallel-$(parallel-version).tar.lz
+	$(call import-source, $(parallel-url), $(parallel-checksum))
+	$(call gbuild, parallel-$(parallel-version), static)
+
+#	GNU Parallel requires the users to acknowledge that they will cite
+#	it. Otherwise, it prints a warning on every run: reminding the user
+#	to cite it. In Maneage, we make sure that all software that request
+#	citation are cited automatically, so there is no need for a
+#	Maneager to get this warning and we can automatically ensure the
+#	developer that it will be cited.
+	echo "will cite" | $(ibdir)/parallel --citation
+
+#	Copy the BibTeX source of the citation and finish.
+	cp -pv $(dtexdir)/parallel.tex $(ictdir)/
+	echo "GNU Parallel $(parallel-version) \citep{parallel}" > $@
+
 $(ibidir)/patch-$(patch-version):
 	tarball=patch-$(patch-version).tar.gz
 	$(call import-source, $(patch-url), $(patch-checksum))
@@ -1529,6 +1917,13 @@ $(ibidir)/pcre-$(pcre-version):
 	               , V=1 -j$(numthreads))
 	echo "Perl Compatible Regular Expressions $(pcre-version)" > $@
 
+$(ibidir)/pcre2-$(pcre2-version):
+	tarball=pcre2-$(pcre2-version).tar.lz
+	$(call import-source, $(pcre2-url), $(pcre2-checksum))
+	$(call gbuild, pcre2-$(pcre2-version), static)
+	echo "Perl Compatible Regular Expressions 2 $(pcre2-version)" > $@
+
+
 # On macOS 12.3 Monterey with AppleClang 13.1.6.13160021, Plplot 5.15.0
 # needs the 'finite' function of 'math.h' which has been deprecated in
 # macOS. By manually adding "#define finite isfinite" in 'math.h' like
@@ -1695,15 +2090,13 @@ $(ibidir)/swarp-$(swarp-version): $(ibidir)/fftw-$(fftw-version)
 	cp $(dtexdir)/swarp.tex $(ictdir)/
 	echo "SWarp $(swarp-version) \citep{swarp}" > $@
 
-$(ibidir)/swig-$(swig-version):
-
-#	Option --without-pcre was a suggestion once the configure step was
-#	tried and it failed. It was not recommended but it works!  pcr is a
-#	dependency of swig
+$(ibidir)/swig-$(swig-version): \
+                          $(ibidir)/pcre2-$(pcre2-version)
+#	Not disabling pcre, since PCRE is needed for lalsuite (python).
 	tarball=swig-$(swig-version).tar.lz
 	$(call import-source, $(swig-url), $(swig-checksum))
 	$(call gbuild, swig-$(swig-version), static, \
-	               --without-pcre --without-tcl)
+	               --without-tcl)
 	echo "Swig $(swig-version)" > $@
 
 # The disables:
@@ -1779,6 +2172,10 @@ $(ibidir)/util-linux-$(util-linux-version): \
 	sed -i '/flex/d' autogen.sh
 	./autogen.sh
 
+#	The 'autogen.sh' call resets the 'SHELL' (that was corrected in
+#	'prep-source.sh') to '/bin/sh'. Therefore, we need to correct it.
+	sed -i -e's|SHELL = /bin/sh|SHELL = $(SHELL)|' po/Makefile.in.in
+
 #	Having updated 'configure.ac', we need to re-generate the
 #	'./configure' script with 'autoreconf' (which is part of Autoconf
 #	and needs Automake; hence why they are dependencies.
@@ -1892,16 +2289,28 @@ $(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
 	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
 	echo "Unzip $(unzip-version)" > $@
 
-$(ibidir)/zip-$(zip-version): $(ibidir)/gzip-$(gzip-version)
+$(ibidir)/zip-$(zip-version):
+
+#	Prepare the tarball and build directory.
 	tarball=zip-$(zip-version).tar.lz
 	$(call import-source, $(zip-url), $(zip-checksum))
-	$(call gbuild, zip-$(zip-version), static,, \
-	               -f unix/Makefile generic \
-	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-	               -f unix/Makefile generic \
-	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
-	echo "Zip $(zip-version)" > $@
 
+#	Unpack and go into the directory.
+	export LDFLAGS="$$LDFLAGS -static"
+	cd $(ddir)
+	rm -fr zip-$(zip-version)/
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd zip-$(zip-version)/
+
+#	Build and install
+	make SHELL=$(ibdir)/bash -f unix/Makefile generic
+	make SHELL=$(ibdir)/bash install -f unix/Makefile \
+	     generic BINDIR=$(ibdir) MANDIR=$(idir)/man/man1
+
+#	Go back to the top build directory, clean up and finalize.
+	cd $(ddir)
+	rm -rf zip-$(zip-version)/
+	echo "Zip $(zip-version)" > $@