IMPORTANT: Python and some basic software updated, improved portabilityHEAD maneage

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
author: Boud Roukema <boud@cosmo.torun.pl> 2026-01-18 22:50:48 +0600
committer: Mohammad Akhlaghi <mohammad@akhlaghi.org> 2026-05-03 03:00:18 +0200
commit: d99b69fdb52f2fd522f53bba29a42d3ba8af5361 (patch)
tree: c99e3b167a6af946f268a8f597de059b2a2c7dc2 /reproduce
parent: d7264f9cfd6dd17fa2b5a60a8696dfde08ee18de (diff)
16 files changed, 1313 insertions, 376 deletions
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index d2db4d3..c218cdd 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -19,6 +19,21 @@
 
 
 
+# Software info in TeX
+# --------------------
+#
+# The information of the installed software is placed in the
+# '.build/software' directory (which the TeX build should not depend
+# on). Therefore, we should copy those macros here in the LaTeX build
+# directory, so the TeX directory is completely independent from each
+# other.
+$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
+	cp $(bsdir)/config/*.tex $(mtexdir)/
+
+
+
+
+
 # LaTeX macros for paper
 # ----------------------
 #
@@ -40,19 +55,36 @@
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can give any value other than 'yes' to
 # 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
-$(mtexdir)/project.tex: $(mtexdir)/verify.tex
+$(mtexdir)/project.tex: $(mtexdir)/verify.tex $(mtexdir)/dependencies.tex
 
 #	If no PDF is requested, or if LaTeX isn't available, don't continue
 #	to building the final PDF. Otherwise, merge all the TeX macros into
 #	one for building the PDF.
-	@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then
+	@if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ];
+	  then
 
 #	  Put a LaTeX input command for all the necessary macro files.
-#	  'hardware-parameters.tex' is created in 'configure.sh'.
+#	  Note that 'hardware-parameters.tex' is created in 'configure.sh'
+#	  (which is why it is first in the list).
 	  projecttex=$(mtexdir)/project.tex
 	  rm -f $$projecttex
-	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
-	    echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
+	  for t in hardware-parameters $(subst paper,,$(makesrc)); do
+
+#	    Only add the macro file to 'project.tex' if the macro file is
+#	    not empty. Empty macro files are not a bug in Maneage alone: 1)
+#	    the processing of a sub-Makefile may not need to produce any
+#	    written macro for the PDF, and that is perfectly fine. 2) LaTeX
+#	    can also '\input' an empty file. However, it is important for
+#	    for publication servers (like arXiv) that do not allow
+#	    uploading empty files. Therefore, when 'project.tex' contains
+#	    empty files, such severs will not be able compile the PDF
+#	    because the file name is mentioned in 'project.tex', but cannot
+#	    be found in the uploaded files.
+	    tfile=tex/build/macros/$$t.tex
+	    if [ -s $$tfile ]; then
+	      echo "\input{$$tfile}" >> $$projecttex
+	    fi
+
 	  done
 
 #	  Possibly highlight the '\new' parts of the text.
@@ -110,21 +142,6 @@ tikzdir:=$(texbdir)/tikz
 
 
 
-# Software info in TeX
-# --------------------
-#
-# The information of the installed software is placed in the
-# '.build/software' directory (which the TeX build should not depend
-# on). Therefore, we should copy those macros here in the LaTeX build
-# directory, so the TeX directory is completely independent from each
-# other.
-$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
-	cp $(bsdir)/config/*.tex $(mtexdir)/
-
-
-
-
-
 # The bibliography
 # ----------------
 #
@@ -137,8 +154,7 @@ $(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
 # recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \
-                      | $(mtexdir)/project.tex
+$(texbdir)/paper.bbl: tex/src/references.tex | $(mtexdir)/project.tex
 
 #	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 4fedefd..91c4b77 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -138,11 +138,44 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
 
 #	  Verify TeX macros (the values that go into the PDF text).
 	  for m in $(verify-check); do
-	    file=$(mtexdir)/$$m.tex
-	    if [ $$m == delete-me ]; then s=711e2f7fa1f16ecbeeb3df6bcb4ec705
-	    else echo; echo "'$$m' not recognized."; exit 1
+
+#	    Set the macro file name, make sure it exists (the user may have
+#	    forgot to create it in the respective sub-Makefile).
+	    tfile=$(mtexdir)/$$m.tex
+	    if ! [ -f $$tfile ]; then
+	      printf "$$tfile: ERROR: does not exist! If you do not "
+	      printf "(currently) plan macros to be added to the final "
+	      printf "PDF from that sub-Makefile, do the following to "
+	      printf "avoid this error: put a 'touch \$$@' as the recipe "
+	      printf "of the '\$$(mtexdir)/$$m.tex' target (at the bottom "
+	      printf "of 'reproduce/analysis/make/$$m.mk'). If you later "
+	      printf "decide to define macros there, simply replace the "
+	      printf "temporary 'touch \$$@' command with the command(s) "
+	      printf "to prepare/write the macro (see 'initialize.mk' "
+	      printf "as an example)\n";
+	      exit 1
 	    fi
-	    $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
+
+#	    Check the hash for this file and verify it.
+	    case $$m in
+	      delete-me) s=711e2f7fa1f16ecbeeb3df6bcb4ec705;;
+	      *) # This file's hash is not in the list above.
+
+#	         If the file is empty, we can skip it (with the 'continue'
+#	         command). Otherwise, the user should be informed with an
+#	         error.
+	         if [ -s $$tfile ]; then
+	            printf "$$tfile: ERROR: please add the hash of this "
+	            printf "macro file to the list of hashes above this "
+	            printf "error message (in "
+	            printf "'reproduce/analysis/make/verify.mk')\n"; exit 1
+	         else
+	            continue
+	         fi
+	         ;;
+	    esac
+	    $(call verify-txt-no-comments-no-space, $$tfile, $$s, $@.tmp)
+
 	  done
 
 #	  Move temporary file to final target.
diff --git a/reproduce/software/bibtex/parallel.tex b/reproduce/software/bibtex/parallel.tex
new file mode 100644
index 0000000..1ba1018
--- /dev/null
+++ b/reproduce/software/bibtex/parallel.tex
@@ -0,0 +1,15 @@
+%% Copyright (C) 2026-2026 Boud Roukema <boud@cosmo.torun.pl>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{parallel,
+       author = {{Tange}, Ole},
+        title = "{GNU Parallel 20260322, https://doi.org/10.5281/zenodo.19321428}",
+      journal = {Zenodo.19321428},
+         year = 2026,
+        month = mar,
+          doi = {10.5281/zenodo.19321428},
+}
diff --git a/reproduce/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf
index 4e76b13..51791a5 100644
--- a/reproduce/software/config/TARGETS.conf
+++ b/reproduce/software/config/TARGETS.conf
@@ -42,5 +42,7 @@ top-level-programs = gnuastro
 top-level-python =
 
 # R libraries/modules
-# [For developers 2022-01-02: 'r-cran-cowplot r-cran-gridExtra' for all]
+#
+# As of 2022-01-02: to have all of the R packages, select 'r-cran-cowplot
+# r-cran-gridExtra'.
 top-level-r-cran =
diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 81f325f..9e1c437 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -19,7 +19,7 @@ bash-checksum = b905e107403ceb25ad92f26ab71d6a7f12b1cadbcb27de9f5fefa7da31e96de0
 binutils-checksum = ad7bbebc0c4e537c15d7537027246e2c1c0d355efcd6a369c7ef91c6491ec6a6e9af24c60b7df7508213abeedbd2e53c41549889073ac1f629b0746b78ee894b
 bzip2-checksum = 929cb1b2d0db8a505e2bafe3ce2c893c8f132dd617c0110e86e19f116b570a85de3c8a635483b530456fc8f8b6698c8190d21313e47607f442807b10489ac86e
 certpem-checksum = d1198511bf1f61a624691c182ecdd57ff468030a4af8b0f0ef248a5ce1f42ed883c684fc5aafdd791d5d3aa24504fbfbab11043231594b1c4e21fdb7247e5a33
-coreutils-checksum = 1aa2775ef67ed9ddf30e527fd7b813ba83b43e921e1493d44c016bf2750ccb1478ea08a2cd000a619fb22f800f7f84bb03fff5acdcfad7a45d5aef833fdbf041
+coreutils-checksum = 6f761311e673ded32c0b8d29605630bc703920718b305937a057f992fb344106e57ea96b51bba5ac674a815acc592fb127eb38a4fba6c40f07ff6b123c432e87
 curl-checksum = 5b0213eb1d1c2146c591a72ba0d763c40cf707c7fcc43f4807cccec12ddd3cc63127da0f18f96c2450efc8607812519dbccbc924b5b629712fbc7b02b4976aee
 dash-checksum = f21a2ac71606a5ae8dbda5639d111f385cc44c357c580a83e453b33faa32c92fd83f8ca6c5d2cf720343f8ab1cfec247ca499596f78ee19f62d67cd1d7ae0c69
 diffutils-checksum = 9d42c57a5ae4770b6d84b76f324c7c09c62792cac063048793037281972983dd4c409868545f2460c281f761adba6c49fab3fa227ab5231397809474cedbdfc1
@@ -28,7 +28,7 @@ findutils-checksum = 826c643e7f5c5d6976a47eabcd9807e51350d09ee8fc7dc931f2d9276f9
 flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9
 gawk-checksum = 9013f5cb4c08aa13029ecf0c6b5e02ac93a3b500683b07ae8d34d698f0451dd5146a0a5aef96a249112834e27b379869d8e541f6a1b99accf701ba6a48f58f33
 gcc-checksum = f7386218e0993e19da1092bf625791cb9ec269667f7bdf378fef359a304aa08e4d79cb7b9f56d5d7028b53b29071005707a1cad0fd1b770884ab02310ed7b028
-gettext-checksum = ec0aaf00e5ccfd5c0c51be2239590cf9f7f9105b072081c8374caa75c08611e4c1ebfd6ac6a487f7b54f57c2d8b493fe6ab4ca8d62592dba4db5715e67855f3d
+gettext-checksum = dbdc5016a776f12feb7134c05e2568ba9134bfa66b824967b4cc81d2093328c0f3bbcf269ad5a60ff2257625c763ac96c071685ee2b1d397730b06a058f565aa
 git-checksum = e2a3d2cf272554c0e9fa2abc4cf7b1eff17884911859f17567b76f170996802caa01675a42dbf29af7fc283a07e8dc4a11382ffbd2a03d7d62238e8c598f0b56
 gmp-checksum = ad65de00ecb46cf454ed6c40d2a57ce2528f5fa64df1284dfa15036f1e8cf27760a09a4ecdfcc39048faffb71339bba30d99dd365c54173dbc2ba629bee2fad9
 grep-checksum = 4e39935e26a0d742c0e854135940693166ea142673f50dfd589eedc96dded0e8dcad425e6519ee85d59fdf9d418381ba775a7c560cbeebcdf8a1848339243145
@@ -37,20 +37,19 @@ isl-checksum = 615827a86e809c9645e090786008f8b37d7efc7fee6501ff81e937a299a5a72e7
 less-checksum = f02557d9b85d4144e530ef8f2e95329b7bd2eba1be2513558cd7359cf520e1e6723c4d62b6dd42082084003ac9cb23c3d1d9ad7ca73d58597f7fedf31e9d08fd
 libiconv-checksum = 1f33fcf7f617990812a26e15092dbb2f9e81400cee117eefd40ade813f7ca17c0b9a50a7a9881b4ab0b9c0be8475528204c347d940cbc667a918570e0bde051a
 libtool-checksum = 2aa6d535b4d644393d7ca5c8f174b09923dbdb50d947ba40917aad75c8cecf957fec7a54717bd3670c44130331b1f08fae3694e32c79c8e187c31e909b3d401b
-libunistring-checksum = 3e79a3f5a1c13ce9554071ffecafa24a95ba36e2c1087940aa1ba93957ed14290779d1603b401431eda20c3da5f345a0b8842191a3e65f03fb2667e2a1443e30
+libunistring-checksum = 6621b23b89e68f38a88bd0f0d017c1f20c0b81aa35901ce0e2620054de41a89194c71e55c27de5b9aa0dbbffdb9479c2411b9069cdad09ed67ecf4b1611af525
 libxml2-checksum = aee3946beba88dba0a4ba573704da0c48de3233e5a1717ac6d8e647f3c8b65131c1b4d320604adedd8eff3364af11a3489a2c26b57b8151b59fca60da3f2a1c3
 lzip-checksum = 513b7ecdee1d6f12298cbbb025286c887c5e6588e1268b489735955f822a8e305e7a8d4d06054a77b2f4c40f8d82e9e6d779cd73d4227ca3cdfe4002b9e42a98
-m4-checksum = f24f0a0f71bb5241f8bbf5cb75e260a546ee9206b80478544944053768fae77f322839e78d5524a2bc5cdc06fa921ca88b1d366ed3c67b745cf55df3a30de158
+m4-checksum = 3025f1bc2f645d0fb7ea3be4788d4670c8aa7901c8afcd90f3f04454b80fe855ce5bb036061ea3d6e800f58cb3721efd72cbf00a7598ecf931377c43e41d1508
 make-checksum = 154a0247297a7b0131ff63fa8636d651b33aacc8f4a0dad1db176995b20c2039f4fd58eeb2ec27cc0ca7a95c1853199a4ee35a14afc5084995ecc1d694203412
 mpc-checksum = 76e0720e6287d8b7a3eaa09dc5baa5a2b61dde88198c9e1bc9c458a268a44035d11fbab1c8019501a7ee2d5745c7eddfb0bb3c7297110a0fd9e027acb42d0fc3
 mpfr-checksum = 40066bbbfb394ad4fc2efcbf633542c43fc6e31e3503d0f8f425649c95cfd6aeed78e889852bdfe23f783b5b13766ebdada9c92e6a921d84c6a8703123e9c165
-nano-checksum = baac691afb7e1c956fa0be16a4857cda9513180e5b5b08d55745f5c5f53ada954301e8ab0aa12c46aeed8f984ad3cb77ea3029ec8ede9dcc76d1c84a9e640a58
+nano-checksum = 964ffb246e186ed865898fa29c4d39e869092c84685312dc00feeb4bc72ad019053384a79d7155a6fc396fb5f8a5d16fb894d1dd35fbc71563d3a52e79351f27
 ncurses-checksum = c94eccc1b23a9c6ca9b27881674b19802942802cf21084bd80e45e0b9e50a2d99e0e18a1ecd5cf3e686949982ca93132a7fe2f117a7c4307283db5012b11a2d5
 openssl-checksum = 7cf3cfa3a190a8944366393942faab0813c8443dce5bdb8bdf11b7cae3627f9a3ed2698c6785ef4688c42df12983c2a9ce932e58f2e3691e752589dbae5ea363
 patchelf-checksum = f74409c00e7e50a88590267fa0c173f71239f1471985792f7bcdab750d202a9a25383c015987608bbcd6ace5b3642645d46dba63199ba54fabbcb51ae7fca8f6
 perl-checksum = d5c782948b97b706fe9650f6a9995591d9b90da3a98866d1db4d20025262d5606f4133222be4b96cc06578323db03759910e96012d8931033feaddca0e156e31
 pkgconfig-checksum = c37ab9336ac15a73bf5a23101f3fd8a04810f39b0679634e420e5d7bbd60a80cfc919122694cf83965beb071d2780681efc8d954ce99d77eb235a4dc7497e250
-podlators-checksum = 2e1e8547b0c890101a9fb8d80807b164a0a708820617a6826127930f85115285a0e4d62ddf8ce2401df14c021521a1b3ce0cad0d308e08f7b3d0c49d1b0dd36f
 readline-checksum = 349248d78cfc1deebdaaefc70a044835139cb8775d74bb33ae2a2600d9daef2b169608a8f706fc803a8d95fe9b309da1db0c6d19fa78eaa67430aff5b13feaa2
 sed-checksum = e801dacce45a08671e65897f85be0a37a29d97f61e846ca17ff870d3ab9f5a639dba73457491087ff637df4a81099b864d2496d59acf17a07916b43bfe0ae480
 tar-checksum = f8d0b543dc4a2a57d61d8a183d7a64d611d11f033c64683f022a7f1f956d352d364a959903a2549ab1256c1a068de51052960cf34a70f355b80e237f654bfac7
@@ -60,7 +59,6 @@ valgrind-checksum = a99e09e6d957ce435e64f4ce7b1a14e7e266282578171ce4e3bb3f405ce3
 wget-checksum = 75ba60150baf673def8ff5f2688af57d89d699f1b5105cb1a6bc0ce88778be191c74757665d773ac84fdab975851ca9015b30f12f31877fd752500efb49e0034
 which-checksum = cbda59450d35c2fa04f9072db43584ff745844cdb129bce1a382eb50bcd19815f0bbf12f2b03f748cb3f585acf0a16eb2e661b71f9066469236d28e9fa40f168
 xz-checksum = d897a55ae5ee7d778c68edff83c53e6624619f233acd529439fade305681d07b7665ba1d370cf84abb38c7f3f8f88c3d127974c4f59667843814211802501080
-zip-checksum = 433eda6a27074746a960952fa3b08028d5ba43fe976a1306dbace9209be5f89aa0554b17bba5815cd00984c0f64559c5fa0b754b620f6d646a2b145a8b599acc
 zlib-checksum = 8f0b28c7d0d5d1906c2c03586f4ad3188a7c7eb73d25295a7acaa88cdf87b7c82ac609282b9b12d2b4d5a368169e4bb5f88ba3b840b57e1cf32c78f2ee3ecd86
 
 
@@ -92,6 +90,7 @@ emacs-checksum = 91313dced8cd74f9e4a996eef42806aad00fb2576fc77b3694bb7b670624b6a
 expat-checksum = c006dff4ee90ee3722df94ef227cfaab3ee4ebf7ee8193a65b904798b4d185e89c863c75a1e8eae9c120bfbf79336c1e31a8b6aa3042f4131b9a1eb0e97c6643
 fftw-checksum = 28bd2f620399a415181027d30d7ea193aa487c7a277c9943d0051488908fd87e2731de0dfc3bebd22a6121d1deaa46037be8296a8a9cdb711f9fde4510c3d368
 flex-checksum = a18e0dcdd21bd51779fd70e5efc2d77fa7b2a56d4d0e929d8abb437f86d7fcfa2cd09b8268185698200866dac8bec4444c5a7cff3140c515eaa49fc77c5aea66
+framel-checksum = f93203bc7cebb35f2ef356fef7190ae6874345643ec35ebe7db22228fb1f0182656fa03339c1f749381ff875e7955f9b98240bc5b55889f0d97cb5db48ac5456
 freetype-checksum = fb2d89421633a56d4276b192106d930c9f29cf2b70c52d9e13ba0c6a2679b6f69c20ab9f14480522992c263b493f198f24593bdeddb5806a4d801ab7604a5926
 gdb-checksum = 4afd6660d2bbc4c48ce726062fb42217bdaa5974774407358b2624036a2ace48ed853746e4d6b83b9a409cd8fefc622b0727c79da8826e28e3d1444fa3a9d148
 ghostscript-checksum = 516f7f3bf8650ff5cf5a913ac1d69c196dbf62de97b77fba75fad7cfbace5c978a4aff7da0ede3590f56d68b240398ee17a1a504bd8e8ee76a4879b0b3b6a8df
@@ -101,11 +100,12 @@ gnuastro-checksum = f777f84d03cc106a12373416ec3617e4c598f7642f6ebf881fd59a3068c8
 gperf-checksum = 854cdb24337f14b0d4199cc97c4a1d2ec7f953ad8125a47a932d93f79bdc067e2de231859ac0e842f14b1a8d80c5606fdc2c295a370df5e85ea15023b478805b
 gsl-checksum = 9a46b431eed536182f31e1ecad781ade214ac8bd885ac88bbfd02b6e08482c294775a529e561d358c1f0211d8d20db4ec99b448b9006c3bf7599c076d3fbbcc3
 hdf5-checksum = 58d6d9a1c201efa0863d9c31d189b4d40b1a9b1fb1ab9cb3fdeb4463f508c043e467aa4d44484c2af111d4e2fb775223286da69568774e6edef285208290c67b
-healpix-checksum = c11949e92aae9919fd41de91cbab72beffe2519c1203ab153ba217c6b6c81f2c10ceb07b683da0d04fb53ef5c80a9b208bdbb5379f379b7da9d0611d2430cc8e
+healpix-checksum = eae764ede6b540d661619f4a1eacfb3cb4c6e3115bf696fdf45734ffa5c78bac1469dba7ad960bc6f082952dce8bbad54bc630ee7674afee1647cab400a750fb
 help2man-checksum = 83dca38c2020c85a66da882cd994b4e291eb6a0584149b7b3a74fec1444399ec5ecfc6296080fbc34071cd9f8ec5c931e249fde1f755c7f40930cecafb3efab0
 icu-checksum = ab14b52a3fdf2dcde6b5160ab7218eac381b850d3c278324379741c49d71fa6040fbacca94c6937e6c9fc15843761121deff302ca6854da5ca1cd5b26a34e839
 imagemagick-checksum = 2132614540b7422c9772fcebe7e8e358994efcfb53d8e48fa52992313b09b191847e395bad305322c377a4697014353bb8c15adc4edfd712e038504fc7f17c5e
 imfit-checksum = 15edd2349232c1c8e611b31d3a46b0700112d274515f54d0a0085bb4bfa6d3d5f8a15cd926516e043a29ce841accf3534ae58dbfb952d858dc9445199c957096
+lalsuite-checksum = 330f2576698bd3107621d49596da66c7629d314e5744b3a267b3fa346e7926bb255979506627abaeeba62ff9a776c6091e9150ab5c471c3b4a43bec40a1a5de1
 lapack-checksum = ff670e194a1d8c998f05e6143e01a09e6b43176c511217ea3c77742afd9f2566251c50fc23aeb916442401f7118c1d1fe21f0172382a7f4f2c516c1d7d873e24
 libbsd-checksum = 5c7d98474000af1271a36ab769e54aba41578e0b0f06e47af2986d6821b6586ac430ec04cc51b7836823834dd9d0aec9f4ab3af088b94f963b89729fa2cc95d8
 libffi-checksum = 027416da7066bd36ac0c9ed8228693e5eeeb5e11dc17afcd7ed7faa66a9e57f505e94dffaf18f8978e6b40964938d4289aa3b5fe8778abe8fb97a68138b8b120
@@ -118,15 +118,18 @@ libpaper-checksum = 8532e5e95b53e0dcb2b2c4c161d3840a34087b5870d449950a853dc312a4
 libpng-checksum = c4eff9a427302c6f228b93a5a6b74d1e667439ce77f20c086d91ec6efa932a0e7f5752b976f4af5cd07574c5e4999c86e2b9cae3e82cc448ee61f3d0dde9253d
 libtiff-checksum = 72ce12ce317ab2a5c188d3aeb575004eacf890dcb2729e9cb46f73c15cde2132624b4e229539af01626e59ea6a4a7380b4b5f90d5fecad787197b8b901615d20
 libtirpc-checksum = bcb6b5c062c1301aa1246ec93ae0a5c1d221b8421126d020863517cb814b43ed038fb6c0c2faf4e68ff133b69abefe4f4d42bfc870671da6c27ca941a30b155a
+metaio-checksum = efc7f052c550d1566123a8842d5f6237b330d8fa7b012b276117bb2587e4df08a603cdbf22149cad70e7725bacef57f5f396ab3a2965446b940a0665c12763fa
 metastore-checksum = ac1230686535a652e95024abaf6c5585bdab36f4e092bee5fa4deff2a913cd60f3a6bd8020c6887ccab97f0da3a284a0d4619fad5464a269e7b2040d6f7e6aaf
 missfits-checksum = 32727f5eb30573a1cedacb8900e2536867e4815059eee32e64e3db65be9291b8a91b9f45b2c9f3cf6fc2a8cc448012ea3d502bdd9dee516008e17d5086aee795
 netpbm-checksum = aef81d2e46850fae1fb34a38fa9f634be3c47c7c4e80f300c61aadd5532bcbccdec636e6c701e54caca67ac2d6ce3a7b6a9f090deb00cd4db718439986f89d8e
-ninjabuild-checksum = 3a6bfeef3ff1143d427a658d2d4119e4c9d85ebba37393760dd7a6dcce1c4a9e217009b6600b5a72338edb34680f0c45dc07b6b09afe1b0a9eb163993f2bc41a
+ninjabuild-checksum = 381f63e6b9d2b6863a35ceedc3d07b81a6b41d7539af9b4c3fae859c34a0f4b68340e5579193abfc221b0e4f413dc20c7caaf70480147d93ca7ade497bd01571
 openblas-checksum = c87485bb2b74cee175a6e631c63cb52fab174a2275d375c00680c4cbcd8d12a116223fda0349fc677cc9fe49794ce7b0342740855840df491b6141c8f2f4784a
-openmpi-checksum = 88c73fd708dd5fe3a893d5517425a8a4c3e252fae4715df9a9b0f2311abe94cf5f71be92f153820fbaeb32c7d0ac0175d5165bdadcadc731427309102182c1bd
+openmpi-checksum = 8480402a75c27e73ef51ca8410c6b527fccd62029aa45f36468e0c4dc0e5281f161a8a56237a1cc7e107ba7561c47acd63630e7bf8560e87bfd357c83c614607
 openssh-checksum = e280fa2d56f550efd37c5d2477670326261aa8b94d991f9eb17aad90e0c6c9c939efa90fe87d33260d0f709485cb05c379f0fd1bd44fc0d5190298b6398c9982
+parallel-checksum = 612adb4da6304eebf303d40f620c5ffcdea57c7e67ef9616efecdc4fce28041257c955a5d3a35135eeebfa0446514731716e729be865038d4eee7262179d56e8
 patch-checksum = 75d4e1544484da12185418cd4a1571994398140a91ac606fa08dd067004187dad77d1413f0eb3319b3fe4df076714615c98b29df06af052bb65960fa8b0c86bf
 pcre-checksum = abac4c4f9df9e61d7d7761a9c50843882611752e1df0842a54318f358c28f5953025eba2d78997d21ee690756b56cc9f1c04a5ed591dd60654cc78ba16d9ecfb
+pcre2-checksum = f6c7b59fe0195411eb25c63ed67b8921845ba5d9ce56fe538f654d8030132073f2ad8b166d3014d1c78951339c7553203e22c6aa1c92a0751a88c9757a208f52
 pixman-checksum = 333732b99994f7ea636d647e0b6123075351b27601b5b6370c9bc821a1ab3921386ddb92b51e015f3fc35104ba09be1e0d7bef47f0b4f73036b01d1d70396dd9
 plplot-checksum = 2c5a36d84ebd948402c924d304427b5702bc75bdd22753c9b3b910b382dfdcc26910382aae452f02d86b25c1c813bbe1f40c9305de1d2809d575975f610fdf10
 python-checksum = de940d7eceee69b8a04f12c613753f61db53ddac1c5cde5388dd342e88a09bae8da1f56b71b96f20997f6203d169e92e9e2558c43b38dbc323221d7bb362abfc
@@ -135,14 +138,19 @@ rpcsvc-proto-checksum = c3011d7d7ef97a4a751f6921df1a23e1dd8ac50fb0690c759d37010e
 scamp-checksum = c7a192f357c6808acd16d1c5d2657c5c8c2f61e4fecb8a4b18d39b07f4c444f85d5029c21571d41ec3ba9c8d075de8bd660b0e029bf5dd63e3819e963430a938
 scons-checksum = 0477038b014674049f12899b64584d44a85283d521b2422561e42020a5ae296a5af005684087c3ff410ed3fcbdcc5ff61998bc429eb29513f2a864138ffc4945
 sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a772944ea189bfce89fd791d316a790fc4b2cb15a62633b19d1d5331b1803dec2e70af7
+sqlite-checksum = f27d1fc39d3505ce85892bd9d5ef284c7f6235a1ad473a2fb0ab8c221a3a450aa572d1a9e37eeea66ad615a7957e3326400eff5f51854a389e0f008d33879276
 swarp-checksum = 810af6ea0a2dfc7b78b0f6aaa486b80c29f517b90c29f5037d05f31f761e96a55c8b5dcc259e1b435b25f45f01dac45ddba61da84000a69676cce119880bb05d
-swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d
+swig-checksum = 7db62945be0514e1196750f6e00f48edfbad1524501f72d646706a6b3149bceeb904ba28dce73f8a98a8d9b9a91814492482aa88b996366b411e8723a9f4bf4d
+tcl-checksum = e7e40a07d6c7d0a4c6a0055c36c12c1303167680768706f53f981aace063c802486d39a715dd393cdca0371757c34df2600642472ae36e7991d9bb70674da8d2
 tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
+tk-checksum = 87d431e4d995e78839fc5cf23ab8bebdd783adcf0c8ee1169cd7166aaf4884185ca3e72dd7c7ba6c55a3018d3529b036fde4dbde1c076a767fa5eb2668db5283
+tzdb-checksum = 6c0f7f24f08dae63900499ff55dca5775fb687d76451bfdb82ec24aa4bd29263fed5e0cc3efc32ea54eb2dde80cc17e4becdeb3d70b1f63646dd52a5538dc632
 util-linux-checksum = 3053377ca3e399a12ea86ba96ac38749ff15a42e76742ab4346eb2f96c8b24564077db44c5b173e8474c8770846dc355b1281a697ef5a168e239b1b6d693469c
 vim-checksum = 85d083fcf3638f2c3a049b88da46d569d6a250ae132f3821d440c07c4792befffc09e4235241ca96d7b0307a1bb96cd2222ac8a63fb41c6add8c2bdc6c17aabb
 wcslib-checksum = 68f40f268d4a4d6d052e444859070138f90f17fb1723cba2da88293b5f7a372885461a09da1ca0ba1686d08e7d731cae52e305b65a6f5edf13586f48a61dca55
 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
 yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
+zip-checksum = 74966fda50ea18b28a3bd03e91be3a75a9034cd923149a321e4cff3f233d696c4079181a996f81fa62ba121c4beb6588c31dea682e174b18b858121b72409ea4
 
 # Xorg related packages
 fontconfig-checksum = e71c684ffcc75015b1aa13918d6598a213b926630317e4babf876fc503e0444ed3211277080a08505cc26da033ee8e673bf5e246cb9d75d2fbe18a43160a0dad
@@ -172,7 +180,8 @@ xtrans-checksum = 84f1142994f93882c9c68a4a85a218290c1c979162dbd4c5ee6b6becf0f96b
 # hash here.
 asn1crypto-checksum = 44d442a6ddfa971e31e24712fe084368356deb5e1c4c3b3e813e0910931860215bc1c4f9eb2c4bd4fdef607c324086c096e9357068646efd28c97f2d4f85c62f
 asteval-checksum = 4d64900b2f7dfdd098d6c8c102f9d9fd46f9ec265a54330e7d94479ba41f0ee0698855658e18b8b32b9c255159eb9a085af5f0306eb6508663d3fea7d2e00b4a
-astropy-checksum = a91e327784a6ce0bb55119639e52037db0d802305dafedd46f27d9de96db819b43e336a4d43558a57e57459c4d1b7d6d3fe290771006e061d3779034f089aa9b
+astropy-checksum = 9c32139b880934f6fd82c47cbdd201b2c934bcb93216136bf24d7d676f2acfbc81e08f35e7290fc1fb9c49ed2c0f4632f0b5182b86bffe6d26abe16b52f2783c
+astropy-healpix-checksum = 685ec136eff28fd25ce67403f932297a8297e2de84d527890a81ddaa9a6bbbc70922a204c08225840b03d3c6be8af7476e01d4f87285ffa71b6d7d19493fb332
 astropy-iers-data-checksum = b8bb1aacf67fdab241e95952919a8691db09488493d0e4ea6eb7a65822c6e4bfb7fc55d4ee2f6a0e9e563fb671d16b06474d38f0ad4d3b0f41d6dc341dc7ec7a
 astroquery-checksum = 43846791d8469a26cf6bb8819db58b830cfe50a34bc0091c2e843dd7dc78b1317530855d432a3a567a9f6a6f4d2682382a32edc91ea01716246b99b3625ec521
 beautifulsoup4-checksum = bf8fd3e54da63a506f294f0e5f1201fd46bf2edcc2db23e99eda995313b8a8d24db3cd2d1903853c539a9320bfb9eb4b29e311772bfddc0d125f0b4aec71e384
@@ -180,7 +189,9 @@ beniget-checksum = 32a19d77323a0a21544ce7fbbb71cc5f4c66949dba280d81deb36f3836454
 certifi-checksum = 6a6bf1ff98caefcdbf78a8c83e11e155368bacdd806f0ae0c6afa8f513667df6598e594b3584de61acdca3d6049f4a776937f2aa8672b602bd6db7b737f6074e
 cffi-checksum = 50e2b8215ddedfa8f1d569680cc0023cf061c2c52b7b86b6b26ced56e5107b362aaf6dc10a77b9dbbbfca2e5611f7cfb42c59501f9ab7da29fb3ad3ccf418cb4
 chardet-checksum = 61a03b23447a2bfe52ceed4dd1b9afdb5784da1933a623776883ee9f297e341f633e27f0ce0230bd5fdc5fdb5382105ab42736a74a417ddeb9f83af57455dba5
+colorama-checksum = 0cc6b4d622a2a7bae2903bd8773182674bb8d9a654f9105231418b28f585aab30e0ed8c35aa0494ee1a81c024381bf90654febeb3b16eb78b5e1fdc421d9773c
 contourpy-checksum = dab72dc7b9c64b1c06674ac4c7ba4d1058bfa5922763087dbe9d30237fe38045201e3801423541cc65ef0cd6c92eb5f4ffb4b6ff8da21d79f2f23a36ddc4bcf3
+cosmodesi-mpytools-checksum = 0d25d990d405c7ab829ce27e274a158defa33d7c3fcabf6f15098903e0a51f6029271e167047427a529b01fd23ccdcffb060af53d6254f184fd2d0de365100af
 corner-checksum = ebd625ab1e4591b4c21d25ec706c35d37f560b727e1e0d6a79948c4a112ee6f21d3ca30162901a27715074e1345f3bdee1a0345c63e5fec24113e495fb094127
 cppy-checksum = 562b41f22d2819fa7be65ad7d05b18afa9646999277df8a5e6399c69d66320ed0119a5d2653de5711ccaf65360d55fadd85611bf2f7c42348e2f74fbf4eed45e
 cryptography-checksum = 051b5007512521638981a8e975c7bbcb688b1a1c384babc81ba105c7bc2a7e776a8bf46af5939627528b2b57d99aaacf215a041018c47f6d3ae6d7a0e8eafccf
@@ -190,62 +201,87 @@ eigency-checksum = 1e7cdfc43071da5edba30a0d32cd655442b516f15c166b049a195d151dec8
 emcee-checksum = dd60aace8879525fd3fe42b747d82170b24b2ed21f538f9186ba96b9d04c084812e3303f5d2e04119dabd2f9d3286d510b4d4a5324c71dd24b1c7e5f0a9a0ac6
 entrypoints-checksum = aa1274362d3a4b00266103319ca51aa266605b4999c89a9d0673eb61bfae9e646cb0ec6b86c95544493f6fe048385a2c7641d64adca8f45815546fb1e663c858
 esutil-checksum = 7f1f22b0a05855819e3bd9bc2eee14942c2f536fb99f4af03575eb41d3d3fd1d2e6091ad076bfab4d51a8f30e213b607af35ed00d063fb2895b58f7a57cde5ae
+exceptiongroup-checksum = 4ee3a8196deb7a3ef437a7d0e837313b89226ebadfd9fd294371f32b1bb35c8070236b30967b33fcfe0291728f4b9dc4b662c7eb2ac916253a2314dcf292d188
 extension-helpers-checksum = 3a8d971e33542931754baf1626141b6407c11e98d58088f9898aaffcb2dcd9592adc094b236a7fdd74837b6aa4d38e7191763d7a414fb34d6e923985c7db3534
 features-checksum = 91b88e02ebcccfaac9a9cf4b8f00e177880e119287514c781fd591c06231428f4f7aa479bb9ba74f59b2544f12ec08061486f75bf91aac8480d23bdc91e2c511
 flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c846cf98ecadee35fc2dedd588116c8cd982529972dd2411ab139621912b69132a1e
 flit-core-checksum = 59912228fbab70435a438c978c2cfdf7c1fd4e14f45ea223c9b1cb58a56b86ef932b42e1fcc69cadf3fd5c8ca52d407a99428aa874d58029fcaeb2b6acc6bbd5
+flit-scm-checksum = 5f5e9ee88b62bab18bafa842d91181d46addd8dc874e64e0dae7d9a99ac2c92ce00bf92ba9be1aedb0464272a682b9dc58ee7322118710259b3a88861112f57a
 fonttools-checksum = 3bec5dbc51d93d439a9cfffdb45e1de4d1b79d6bd91c5510eaf4b21fed077648deb6c4858c95222f93bfe5da1f9c82cc57e8b3df67f214ee29425037f1261e22
 future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030
 galsim-checksum = 65393c4bcf52a3e723604a956aac5f58f490e41c7d5ddbd5d61660658738e2496aa30f632d4d83b765aaf1e46ac691fcd02fc827380e07c8f921c160a9f6a6fd
 gast-checksum = 8311f48788daf060bee54ad8986eae054c2a426adcf97f1503cde37c4da2827cd0f664188e51f5c2f932a0a4ded78166a8466465595a640106060c8b6c7072a5
 gpep517-checksum = e937f18c9593c76c15f8b2e77143aa11a0a822b1ff686860d5539f4418b02ca7764d71dbef817e8fe8453f9bf3c45fc2f97af1244cc30068701347f584ace91f
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diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index 3566d3c..f976930 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -52,7 +52,6 @@
 #patchelf-url = https://github.com/NixOS/patchelf/releases/download/$(patchelf-version)
 #perl-url = $(shell echo https://www.cpan.org/src/$$(echo $(perl-version) | sed -e's/\./ /g' | awk '{printf("%d.0", $$1)}'))
 #pkgconfig-url = http://pkg-config.freedesktop.org/releases
-#podlators-url = https://www.eyrie.org/~eagle/software/podlators/
 #readline-url = http://ftp.gnu.org/gnu/readline
 #sed-url = http://ftp.gnu.org/gnu/sed
 #tar-url = http://ftp.gnu.org/gnu/tar
@@ -94,6 +93,9 @@
 #expat-url = https://github.com/libexpat/libexpat/releases
 #fftw-url = https://fftw.org
 #flex-url = https://github.com/westes/flex/files/981163
+#framel: 2025-05-23 from https://software.igwn.org/lscsoft/source/framel-8.47.3.tar.xz;
+#  see also https://git.ligo.org/virgo/virgoapp/Fr
+#framel-url = https://software.igwn.org/lscsoft/source
 #freetype-url = https://download.savannah.gnu.org/releases/freetype
 #gdb-url = http://ftp.gnu.org/gnu/gdb
 #ghostscript-url = https://www.ghostscript.com/releases/gsdnld.html
@@ -140,9 +142,12 @@
 #scamp-url = http://akhlaghi.org/maneage-software
 #scons-url = https://sourceforge.net/projects/scons/files/scons/$(scons-version)/scons-$(scons-version).tar.gz/download
 #sextractor-url = http://akhlaghi.org/maneage-software
+#sqlite-url - https://sqlite.org
 #swarp-url = https://www.astromatic.net/download/swarp
 #swig-url = https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version)
+#tcltk-defaults - 2025-05-24 - repacked from Debian/testing https://packages.debian.org/source/testing/tcltk-defaults
 #tides-url = http://akhlaghi.org/maneage-software
+#tzdb-url = https://www.iana.org/time-zones
 #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.40
 #valgrind-url = https://sourceware.org/pub/valgrind
 #vim-url = ftp://ftp.vim.org/pub/vim/unix
@@ -195,8 +200,10 @@
 # But be sure to send us a link to the tarball so we upload it to Maneage's
 # backup servers.
 #astropy-url = https://files.pythonhosted.org/packages/45/12/a1c582b3f9df5e2680eae0ed82c8057ae06d6130a1f7a5c0770fa899737e
+#astropy-healpix-url = https://files.pythonhosted.org/packages/5c/8a/dfd71e4db13706383ca2cea0b2831eb10da2c286d4494f183f80fc03cbc2
 #astropy-iers-data-url = https://files.pythonhosted.org/packages/a1/4d/b9511aba29d4330437497166a7049ab9bac53e344c54e44a35390724ca37
 #contourpy-url = https://files.pythonhosted.org/packages/25/c2/fc7193cc5383637ff390a712e88e4ded0452c9fbcf84abe3de5ea3df1866
+#cosmodesi-mpytools = https://github.com/cosmodesi/mpytools/archive
 #cppy-url = https://files.pythonhosted.org/packages/45/ed/b35645a1b285bce356f30cc0fe77a042375c385660ccd61e0cdc4c1f7c44
 #cycler-url = https://files.pythonhosted.org/packages/a9/95/a3dbbb5028f35eafb79008e7522a75244477d2838f38cbb722248dabc2a8
 #cython-url = https://files.pythonhosted.org/packages/5a/25/886e197c97a4b8e254173002cdc141441e878ff29aaa7d9ba560cd6e4866
@@ -205,7 +212,9 @@
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 #fonttools-url = https://files.pythonhosted.org/packages/1c/8c/9ffa2a555af0e5e5d0e2ed7fdd8c9bef474ed676995bb4c57c9cd0014248
 #gpep517-url = https://files.pythonhosted.org/packages/1c/53/e6ad6aa7036d62ac009986e1e5180465353344afd958ddc8ac15e3b632bc
+#healpy-url = https://files.pythonhosted.org/packages/a4/db/4d1e7fcd429151edb1e2c6d10365f86de217097e276c0b44dbc197028d21
 #kiwisolver-url = https://files.pythonhosted.org/packages/82/59/7c91426a8ac292e1cdd53a63b6d9439abd573c875c3f92c146767dd33faf
+#ligo-skymap-url = https://files.pythonhosted.org/packages/f5/f5/fa82a88c104a9d1fcf863e05a56b213b512db05bc72b5c4f1c7c7d3bc118
 #matplotlib-url = https://files.pythonhosted.org/packages/68/dd/fa2e1a45fce2d09f4aea3cee169760e672c8262325aa5796c49d543dc7e6
 #meson-url = https://files.pythonhosted.org/packages/02/98/bbcaf6caaaa0510a68834f119ac793a8abade6ff827fc2791eeb6f8b4a66
 #meson-python-url = https://files.pythonhosted.org/packages/67/66/91d242ea8dd1729addd36069318ba2cd03874872764f316c3bb51b633ed2
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
+
 
 
 
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 4e85807..92fa8f0 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -105,12 +105,13 @@ endif
 export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
 
 # This is the "basic" tools where we are relying on the host operating
-# system, but are slowly populating our basic software envirnoment. To run
-# (system or template) programs, 'LD_LIBRARY_PATH' is necessary, so here,
-# we'll first tell the programs to look into any possible pre-defined
-# 'LD_LIBRARY_PATH', then we'll add our own newly installed libraries.  We
-# will also make sure that there is no "current directory" in it (by
-# removing a starting or trailing ':' and any occurance of '::'.
+# system, but are slowly populating our basic software envirnoment. So
+# here, we are also appending the host's 'LD_LIBRARY_PATH' to Maneage's
+# installed library path. It is just important to keep Maneage's library
+# directories first so when something has been built, the newly built
+# software use (link-with) Maneage's libraries, not the host's. We will
+# also make sure that there is no "current directory" in it (by removing a
+# starting or trailing ':' and any occurance of '::').
 #
 # But first: in case LD_LIBRARY_PATH is empty, give it the default value of
 # $(sys_library_sh_path) (which was the location of the libraries needed by
@@ -120,7 +121,7 @@ export CPPFLAGS := -I$(idir)/include $(CPPFLAGS) $(noccwarnings)
 ifeq ($(strip $(LD_LIBRARY_PATH)),)
 export LD_LIBRARY_PATH=$(sys_library_sh_path)
 endif
-export LD_LIBRARY_PATH := $(shell echo $(LD_LIBRARY_PATH):$(ildir) \
+export LD_LIBRARY_PATH := $(shell echo $(ildir):$(LD_LIBRARY_PATH) \
                                   | sed -e's/::/:/g' -e's/^://' -e's/:$$//')
 
 # RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
@@ -253,6 +254,23 @@ $(ibidir)/low-level-links: $(ibidir)/grep-$(grep-version) \
 #	systems)
 	$(call makelink,ldd)
 
+#	zic: On some systems like Debian GNU/Linux, 'zic' may be in
+#	'/usr/sbin' and is available to users. But it is not normally in
+#	the 'PATH' of a non-root user. This is because the executables
+#	there are normally system-level commands, and most are executable
+#	only by the root user.
+	$(call makelink,zic)
+	if [ "x$$(command -v zic)" = x ]; then
+	   zicfullpath=$$(PATH=$${PATH}:/usr/sbin command -v zic)
+	   if [ "x$${zicfullpath}" = x ]; then
+	      printf "Warning: 'zic' not found. You may need it for"
+	      printf " higher-level packages such as 'tzdb'. Install"
+	      printf " 'zic' if needed.\n"
+	   else
+	      ln -sf $$(realpath $${zicfullpath}) $(ibdir)/zic
+	   fi
+	fi
+
 #	We want this to be empty (so it doesn't interefere with the other
 #	files in 'ibidir'.
 	touch $@
@@ -376,8 +394,8 @@ $(ibidir)/tar-$(tar-version): \
 # Patchelf is necessary for some software on GNU/Linux systems, its job is
 # to manually insert RPATH into the dynamically-linked executable. Since
 # all the other software depend on Pathelf, to avoid manually repeating as
-# a prerequisite (and forgetting in others causing bugs), we'll put it as a
-# dependancy of 'tar'.
+# a prerequisite (and forgetting in others causing bugs), it is installed
+# in this phase (right after 'tar').
 $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
 	tarball=patchelf-$(patchelf-version).tar.lz
 	$(call import-source, $(patchelf-url), $(patchelf-checksum))
@@ -388,7 +406,47 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
 	  echo "PatchELF $(patchelf-version)" > $@
 	fi
 
+$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version)
 
+#	Download the tarball.
+	tarball=pkg-config-$(pkgconfig-version).tar.lz
+	$(call import-source, $(pkgconfig-url), $(pkgconfig-checksum))
+
+#	An existing 'libiconv' can cause a conflict with 'pkg-config' (this
+#	is why 'libiconv' depends on 'pkg-config'). On a clean build,
+#	'pkg-config' is built first. But when we don't have a clean build
+#	(and 'libiconv' exists) there will be a problem. So before
+#	re-building 'pkg-config', we'll remove any installation of
+#	'libiconv'.
+	rm -f $(ildir)/libiconv* $(idir)/include/iconv.h
+
+#	Some Mac OS systems may have a version of the GNU C Compiler (GCC)
+#	installed that doesn't support some necessary features of building
+#	Glib (as part of pkg-config), so we will disable pkg-config's
+#	internal Glib for Mac systems, and to be further safe, we'll make
+#	sure it will use LLVM's Clang.
+#
+#	On macOS systems, to ensure that Clang can build pkg-config, take
+#	the following steps:
+#	1. Install the latest Glib via Homebrew:
+#	    brew install glib
+#	2. Set these environment variables before configuring Maneage:
+#	    export GLIB_CFLAGS=$(pkg-config --cflags glib-2.0)
+#	    export GLIB_LIBS=$(pkg-config --libs glib-2.0)
+#   	3. Ensure PKG_CONFIG_PATH includes Homebrew's pkgconfig:
+#	    export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH
+	if [ x$(on_mac_os) = xyes ]; then
+	  extra_pkgconf=""
+	  export compiler="CC=clang"
+	else
+	  export compiler=""
+	  extra_pkgconf="--with-internal-glib"
+	fi
+	export CFLAGS="-std=$(std_c_old) $$CFLAGS"
+	$(call gbuild, pkg-config-$(pkgconfig-version), static, \
+		$$compiler $$extra_pkgconf \
+		--with-pc-path=$(ildir)/pkgconfig, V=1)
+	echo "pkg-config $(pkgconfig-version)" > $@
 
 
 
@@ -408,7 +466,10 @@ $(ibidir)/patchelf-$(patchelf-version): $(ibidir)/tar-$(tar-version)
 # function (for tilde expansion). The first can be disabled with
 # '--disable-load', but unfortunately I don't know any way to fix the
 # second. So, we'll have to build it dynamically for now.
-$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
+$(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version) \
+                                      $(ibidir)/pkg-config-$(pkgconfig-version)
+
+#	Prepare the input.
 	tarball=ncurses-$(ncurses-version).tar.lz
 	$(call import-source, $(ncurses-url), $(ncurses-checksum))
 
@@ -424,12 +485,18 @@ $(ibidir)/ncurses-$(ncurses-version): $(ibidir)/patchelf-$(patchelf-version)
 	rm -f $(ibdir)/bash* $(ibdir)/awk* $(ibdir)/gawk*
 
 #	Standard build process.
-	export CFLAGS="-std=gnu17 $$CFLAGS"
+	export CFLAGS="-std=$(std_c_old) $$CFLAGS"
 	$(call gbuild, ncurses-$(ncurses-version), static, \
-	               --with-shared --enable-rpath --without-normal \
-	               --without-debug --with-cxx-binding \
-	               --with-cxx-shared --enable-widec --enable-pc-files \
-	               --with-pkg-config=$(ildir)/pkgconfig, -j$(numthreads))
+	               --with-shared \
+	               --enable-rpath \
+	               --enable-widec \
+	               --without-debug \
+	               --without-normal \
+	               --enable-pc-files \
+	               --with-cxx-shared \
+	               --with-cxx-binding \
+	               --with-pkg-config=$(ildir)/pkgconfig, \
+	               -j$(numthreads))
 
 #	Unfortunately there are many problems with 'ncurses' using "normal"
 #	(or 8-bit) characters. The standard way that will work is to build
@@ -567,7 +634,7 @@ $(ibidir)/bash-$(bash-version): \
 	export CFLAGS="$$CFLAGS \
 	               -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \
 	               -DSTANDARD_UTILS_PATH='\"$(ibdir)\"'  \
-	               -DSYS_BASHRC='\"$(BASH_ENV)\"' "
+	               -DSYS_BASHRC='\"$(BASH_ENV)\"'"
 	$(call gbuild, bash-$(bash-version),, $$stopt \
 	               --with-installed-readline=$(ildir) \
 	               --with-curses=yes, \
@@ -584,9 +651,6 @@ $(ibidir)/bash-$(bash-version): \
 #	shell. By convention, 'sh' is just a symbolic link to the preferred
 #	shell executable. So we'll define '$(ibdir)/sh' as a symbolic link
 #	to the Bash that we just built and installed.
-#
-#	Just to be sure that the installation step above went well, before
-#	making the link, we'll see if the file actually exists there.
 	ln -fs $(ibdir)/bash $(ibdir)/sh
 	echo "GNU Bash $(bash-version)" > $@
 
@@ -599,6 +663,7 @@ $(ibidir)/bash-$(bash-version): \
 
 
 
+
 # Level 4: Most other programs
 # ----------------------------
 
@@ -612,15 +677,21 @@ perl-conflddlflags =
 else
 perl-conflddlflags = -Dlddlflags="-shared $$LDFLAGS"
 endif
-$(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
+$(ibidir)/perl-$(perl-version): $(ibidir)/tar-$(tar-version)
+
+#	Import tarball.
 	tarball=perl-$(perl-version).tar.lz
 	$(call import-source, $(perl-url), $(perl-checksum))
+
+#	Extract the version strings.
 	major_version=$$(echo $(perl-version) \
 	                     | sed -e's/\./ /g' \
 	                     | awk '{printf("%d", $$1)}')
 	base_version=$$(echo $(perl-version) \
 	                     | sed -e's/\./ /g' \
 	                     | awk '{printf("%d.%d", $$1, $$2)}')
+
+#	Unpack, build and install.
 	cd $(ddir)
 	rm -rf perl-$(perl-version)
 	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
@@ -631,15 +702,15 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	            -Duseshrplib \
 	            -Dprefix=$(idir) \
 	            -Dvendorprefix=$(idir) \
-	            -Dprivlib=$(idir)/share/perl$$major_version/core_perl \
-	            -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/core_perl \
-	            -Dsitelib=$(idir)/share/perl$$major_version/site_perl \
-	            -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/site_perl \
-	            -Dvendorlib=$(idir)/share/perl$$major_version/vendor_perl \
-	            -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/vendor_perl \
-	            -Dscriptdir=$(idir)/bin/core_perl \
-	            -Dsitescript=$(idir)/bin/site_perl \
-	            -Dvendorscript=$(idir)/bin/vendor_perl \
+	            -Dprivlib=$(idir)/share/perl$$major_version/perl-core \
+	            -Darchlib=$(idir)/lib/perl$$major_version/$$base_version/perl-core \
+	            -Dsitelib=$(idir)/share/perl$$major_version/perl-site \
+	            -Dsitearch=$(idir)/lib/perl$$major_version/$$base_version/perl-site \
+	            -Dvendorlib=$(idir)/share/perl$$major_version/perl-vendor \
+	            -Dvendorarch=$(idir)/lib/perl$$major_version/$$base_version/perl-vendor \
+	            -Dscriptdir=$(idir)/bin/perl-core \
+	            -Dsitescript=$(idir)/bin/perl-site \
+	            -Dvendorscript=$(idir)/bin/perl-vendor \
 	            -Dinc_version_list=none \
 	            -Dman1ext=1perl \
 	            -Dman3ext=3perl \
@@ -650,7 +721,14 @@ $(ibidir)/perl-$(perl-version): $(ibidir)/patchelf-$(patchelf-version)
 	make install
 	cd ..
 	rm -rf perl-$(perl-version)
-	cd $$topdir
+
+#	Symbolic links to necessary Perl programs (that Perl installs in
+#	the 'perl-core' directory.
+	ln -sf $(ibdir)/perl-core/xsubpp $(ibdir)/xsubpp
+	ln -sf $(ibdir)/perl-core/pod2man $(ibdir)/pod2man
+	ln -sf $(ibdir)/perl-core/pod2text $(ibdir)/pod2text
+
+#	Final target.
 	echo "Perl $(perl-version)" > $@
 
 
@@ -719,29 +797,6 @@ $(ibidir)/coreutils-$(coreutils-version): \
 	rm -rf coreutils-$(coreutils-version)
 	echo "GNU Coreutils $(coreutils-version)" > $@
 
-# Podlators
-#
-# POD is short for "Plain Old Documentation", that is the format used in
-# Perl's documentation. Podlators provies two executables pod2man and
-# pod2text convert this into the roff format (used in man pages) or pod2 It
-# is used by some software like OpenSSL to create their man pages.
-$(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version)
-	tarball=podlators-$(podlators-version).tar.lz
-	$(call import-source, $(podlators-url), $(podlators-checksum))
-	cd $(ddir)
-	rm -rf podlators-$(podlators-version)
-	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
-	cd podlators-$(podlators-version)
-	$(shsrcdir)/prep-source.sh $(ibdir)
-	perl Makefile.PL
-	make
-	make install
-	ln -sf $(ibdir)/site_perl/pod2man $(ibdir)/pod2man
-	ln -sf $(ibdir)/site_perl/pod2text $(ibdir)/pod2text
-	cd ..
-	rm -rf podlators-$(podlators-version)
-	echo "podlators $(podlators-version)" > $@
-
 # OpenSSL
 #
 # Until we find a nice and generic way to create an updated CA file in the
@@ -749,8 +804,9 @@ $(ibidir)/podlators-$(podlators-version): $(ibidir)/perl-$(perl-version)
 # along with the other tarballs.
 $(idir)/etc:; mkdir $@
 $(idir)/etc/ssl: | $(idir)/etc; mkdir $@
-$(ibidir)/openssl-$(openssl-version): $(ibidir)/podlators-$(podlators-version) \
-                  | $(idir)/etc/ssl
+$(ibidir)/openssl-$(openssl-version): $(ibidir)/perl-$(perl-version) \
+                                      $(ibidir)/patchelf-$(patchelf-version) \
+                                      | $(idir)/etc/ssl
 
 #	First download the certificates and copy them into the
 #	installation directory.
@@ -906,7 +962,7 @@ $(ibidir)/diffutils-$(diffutils-version): \
 	echo "GNU Diffutils $(diffutils-version)" > $@
 
 $(ibidir)/file-$(file-version): $(ibidir)/coreutils-$(coreutils-version)
-	export CFLAGS="-std=c99 $$CFLAGS"
+	export CFLAGS="-std=$(std_c_old) $$CFLAGS"
 	tarball=file-$(file-version).tar.lz
 	$(call import-source, $(file-url), $(file-checksum))
 	$(call gbuild, file-$(file-version), static, \
@@ -958,6 +1014,8 @@ $(ibidir)/help2man-$(help2man-version): \
 	$(call gbuild, help2man-$(help2man-version), static, ,V=1)
 	echo "Help2man $(Help2man-version)" > $@
 
+# Even though libiconv does not use pkg-config, pkg-config conflicts with
+# it, see the comments in pkg-config for more.
 $(ibidir)/libiconv-$(libiconv-version): \
                    $(ibidir)/pkg-config-$(pkgconfig-version)
 	tarball=libiconv-$(libiconv-version).tar.lz
@@ -973,12 +1031,14 @@ $(ibidir)/libunistring-$(libunistring-version): \
 	               -j$(numthreads))
 	echo "GNU libunistring $(libunistring-version)" > $@
 
-$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/patchelf-$(patchelf-version)
+$(ibidir)/libxml2-$(libxml2-version): $(ibidir)/tar-$(tar-version)
 #	The libxml2 tarball also contains Python bindings which are built
 #	and installed to a system directory by default. If you don't need
 #	the Python bindings, the easiest solution is to compile without
 #	Python support: './configure --without-python'. If you really need
-#	the Python bindings, use '--with-python-install-dir=DIR' instead.
+#	its Python bindings:
+#	  1. Add the Python dependency.
+#	  2. Add the '--with-python-install-dir=DIR' configure option.
 	tarball=libxml2-$(libxml2-version).tar.lz
 	$(call import-source, $(libxml2-url), $(libxml2-checksum))
 	$(call gbuild, libxml2-$(libxml2-version), static, \
@@ -1017,7 +1077,7 @@ $(ibidir)/gmp-$(gmp-version): \
               $(ibidir)/coreutils-$(coreutils-version)
 	tarball=gmp-$(gmp-version).tar.lz
 	$(call import-source, $(gmp-url), $(gmp-checksum))
-	export CFLAGS="-std=gnu17 $$CFLAGS"
+	export CFLAGS="-std=$(std_c_old) $$CFLAGS"
 	$(call gbuild, gmp-$(gmp-version), static, \
 	               --enable-cxx --enable-fat, \
 	               -j$(numthreads))
@@ -1085,33 +1145,6 @@ $(ibidir)/mpfr-$(mpfr-version): $(ibidir)/gmp-$(gmp-version)
 	$(call gbuild, mpfr-$(mpfr-version), static)
 	echo "GNU Multiple Precision Floating-Point Reliably $(mpfr-version)" > $@
 
-$(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/patchelf-$(patchelf-version)
-
-#	Download the tarball.
-	tarball=pkg-config-$(pkgconfig-version).tar.lz
-	$(call import-source, $(pkgconfig-url), $(pkgconfig-checksum))
-
-#	An existing 'libiconv' can cause a conflict with 'pkg-config', this
-#	is why 'libiconv' depends on 'pkg-config'. On a clean build,
-#	'pkg-config' is built first. But when we don't have a clean build
-#	(and 'libiconv' exists) there will be a problem. So before
-#	re-building 'pkg-config', we'll remove any installation of
-#	'libiconv'.
-	rm -f $(ildir)/libiconv* $(idir)/include/iconv.h
-
-#	Some Mac OS systems may have a version of the GNU C Compiler (GCC)
-#	installed that doesn't support some necessary features of building
-#	Glib (as part of pkg-config). So to be safe, for Mac systems, we'll
-#	make sure it will use LLVM's Clang.
-	if [ x$(on_mac_os) = xyes ]; then export compiler="CC=clang"
-	else                              export compiler=""
-	fi
-	export CFLAGS="-std=gnu17 $$CFLAGS"
-	$(call gbuild, pkg-config-$(pkgconfig-version), static, \
-	               $$compiler --with-internal-glib \
-	               --with-pc-path=$(ildir)/pkgconfig, V=1)
-	echo "pkg-config $(pkgconfig-version)" > $@
-
 $(ibidir)/sed-$(sed-version): $(ibidir)/coreutils-$(coreutils-version)
 	tarball=sed-$(sed-version).tar.lz
 	$(call import-source, $(sed-url), $(sed-checksum))
@@ -1219,6 +1252,7 @@ $(ibidir)/binutils-$(binutils-version): \
 	  $(call makelink,ld)
 	  $(call makelink,nm)
 	  $(call makelink,ps)
+	  $(call makelink,lipo)
 	  $(call makelink,strip)
 	  $(call makelink,ranlib)
 	  echo "" > $@
@@ -1442,6 +1476,14 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 	      -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \
 	      -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
 
+#	  Bug in GCC 15.2.0 using glibc 2.43 (see [1]) as fixed in [2].
+#	  [1] https://patchwork.ozlabs.org/project/gcc/patch/e1679277-d7c9-49aa-8365-a8dca082d9bd@web.de
+#	  [2] https://github.com/johnny-mnemonic/toolchain-autobuilds/commit/9585fdfc
+	  sed -e's|char \*q = strchr (p + 1,|const char \*q = strchr (p + 1,|' \
+	      libgomp/affinity-fmt.c > affinity-fmt-tmp.c
+	  mv affinity-fmt-tmp.c libgomp/affinity-fmt.c
+
+
 #	  Set the build directory for the processing.
 	  mkdir build
 	  cd build
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)" > $@
 
 
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index c499996..6153f0a 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -83,7 +83,11 @@ $(ibidir)/libffi-$(libffi-version):
 	fi
 	echo "Libffi $(libffi-version)" > $@
 
-$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
+# 2025-05-26 '--with-system-ffi' seems to be obsolete
+# TODO: For a recommended list of dependencies, see
+#  https://github.com/pyenv/pyenv/wiki#suggested-build-environment
+$(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version) \
+                                    $(ibidir)/sqlite-$(sqlite-version)
 
 #	Download the source.
 	tarball=python-$(python-version).tar.lz
@@ -346,12 +350,27 @@ $(ipydir)/astropy-$(astropy-version): \
 	rm -fv $(idir)/bin/fits{diff,check,header,info,2bitmap}
 	rm -fv $(idir)/bin/{samp_hub,showtable,volint,wcslint}
 
+#	Uncomment the 'export' command below only when building from a git
+#	tarball, e.g. for testing if a bug still occurs:
+#	export SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ASTROPY=7.2.0.87
+
 #	Do the basic build.
 	$(call pybuild, tar -xf, astropy-$(astropy-version),,, \
 	                GPEP517)
 	cp -pv $(dtexdir)/astropy.tex $(ictdir)/
 	echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
+$(ipydir)/astropy-healpix-$(astropy-healpix-version): \
+                       $(ipydir)/extension-helpers-$(extension-helpers-version) \
+                       $(ipydir)/numpy-$(numpy-version)
+	tarball=astropy-healpix-$(astropy-healpix-version).tar.lz
+	$(call import-source, $(astropy-healpix-url), \
+	         $(astropy-healpix-checksum))
+	$(call pybuild, tar -xf, \
+	                astropy-healpix-$(astropy-healpix-version),,, \
+	                GPEP517)
+	echo "Astropy-healpix $(astropy-healpix-version)" > $@
+
 $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \
                             $(ipydir)/setuptools-$(setuptools-version)
 	tarball=astropy-iers-data-$(astropy-iers-data-version).tar.lz
@@ -360,7 +379,7 @@ $(ipydir)/astropy-iers-data-$(astropy-iers-data-version): \
 	$(call pybuild, tar -xf, \
 	                astropy-iers-data-$(astropy-iers-data-version),,, \
 	                GPEP517)
-	echo "Astropy-Iers-Data $(astropy-iers-data-version)" > $@
+	echo "Astropy-IERS-data $(astropy-iers-data-version)" > $@
 
 $(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \
                          $(ipydir)/soupsieve-$(soupsieve-version)
@@ -400,6 +419,13 @@ $(ipydir)/chardet-$(chardet-version): \
 	$(call pybuild, tar -xf, chardet-$(chardet-version), , \
 	                Chardet $(chardet-version))
 
+$(ipydir)/colorama-$(colorama-version): \
+                  $(ipydir)/hatchling-$(hatchling-version)
+	tarball=colorama-$(colorama-version).tar.lz
+	$(call import-source, $(colorama-url), $(colorama-checksum))
+	$(call pybuild, tar -xf, \
+	            colorama-$(colorama-version),,, GPEP517)
+
 $(ipydir)/contourpy-$(contourpy-version): \
                      $(ipydir)/pybind11-$(pybind11-version) \
                      $(ipydir)/meson-python-$(meson-python-version)
@@ -417,6 +443,15 @@ $(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version)
 	cp $(dtexdir)/corner.tex $(ictdir)/
 	echo "Corner $(corner-version) \citep{corner}" > $@
 
+$(ipydir)/cosmodesi-mpytools-$(cosmodesi-mpytools-version): \
+                    $(ipydir)/numpy-$(numpy-version) \
+                    $(ipydir)/scipy-$(scipy-version)
+	tarball=cosmodesi-mpytools-$(cosmodesi-mpytools-version).tar.lz
+	$(call import-source, $(cosmodesi-mpytools-url), $(cosmodesi-mpytools-checksum))
+	$(call pybuild, tar -xf, cosmodesi-mpytools-$(cosmodesi-mpytools-version), , \
+	                Cosmodesi-mpytools $(cosmodesi-mpytools-version), GPEP517)
+	echo "Cosmodesi-mpytools $(cosmodesi-mpytools-version)" > $@
+
 $(ipydir)/cppy-$(cppy-version): \
                $(ipydir)/setuptools-scm-$(setuptools-scm-version)
 	tarball=cppy-$(cppy-version).tar.lz
@@ -482,6 +517,15 @@ $(ipydir)/entrypoints-$(entrypoints-version): \
 	$(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \
 	                EntryPoints $(entrypoints-version))
 
+$(ipydir)/exceptiongroup-$(exceptiongroup-version): \
+	   $(ipydir)/setuptools-$(setuptools-version) \
+           $(ipydir)/flit-scm-$(flit-scm-version)
+	tarball=exceptiongroup-$(exceptiongroup-version).tar.lz
+	$(call import-source, $(exceptiongroup-url), $(exceptiongroup-checksum))
+	$(call pybuild, tar -xf, exceptiongroup-$(exceptiongroup-version), , \
+	                Exceptiongroup $(exceptiongroup-version), GPEP517)
+
+
 $(ipydir)/extension-helpers-$(extension-helpers-version): \
                     $(ipydir)/setuptools-scm-$(setuptools-scm-version)
 	tarball=extension-helpers-$(extension-helpers-version).tar.lz
@@ -507,6 +551,16 @@ $(ipydir)/flit-core-$(flit-core-version): \
 	$(call pybuild, tar -xf, flit-core-$(flit-core-version), , \
 	                Flit-core $(flit-core-version), GPEP517)
 
+
+$(ipydir)/flit-scm-$(flit-scm-version): \
+                     $(ipydir)/flit-core-$(flit-core-version) \
+                     $(ipydir)/setuptools-scm-$(setuptools-scm-version)
+	tarball=flit-scm-$(flit-scm-version).tar.lz
+	$(call import-source, $(flit-scm-url), $(flit-scm-checksum))
+	$(call pybuild, tar -xf, flit-scm-$(flit-scm-version), , \
+	                flit-scm $(flit-scm-version), GPEP517)
+
+
 # Although cython is not an obligatory prerequisite of fonttools, we force
 # it as a prerequisite for reproducibility; otherwise build parallelism may
 # lead to some builds with and some builds without cython, depending on how
@@ -558,6 +612,23 @@ $(ipydir)/gpep517-$(gpep517-version): \
 	                BOOT_GPEP517)
 	echo "gpep517 $(gpep517-version)" > $@
 
+$(ipydir)/hatchling-$(hatchling-version): \
+                  $(ipydir)/packaging-$(packaging-version) \
+                  $(ipydir)/pathspec-$(pathspec-version) \
+                  $(ipydir)/pluggy-$(pluggy-version) \
+                  $(ipydir)/trove-classifiers-$(trove-classifiers-version)
+	tarball=hatchling-$(hatchling-version).tar.lz
+	$(call import-source, $(hatchling-url), $(hatchling-checksum))
+	$(call pybuild, tar -xf, \
+	            hatchling-$(hatchling-version),,, GPEP517)
+
+$(ipydir)/hatch-vcs-$(hatch-vcs-version): \
+	   $(ipydir)/hatchling-$(hatchling-version)
+	tarball=hatch-vcs-$(hatch-vcs-version).tar.lz
+	$(call import-source, $(hatch-vcs-url), $(hatch-vcs-checksum))
+	$(call pybuild, tar -xf, hatch-vcs-$(hatch-vcs-version), , \
+	                Hatch-vcs $(hatch-vcs-version), GPEP517)
+
 $(ipydir)/h5py-$(h5py-version): \
                $(ipydir)/six-$(six-version) \
                $(ibidir)/hdf5-$(hdf5-version) \
@@ -572,15 +643,38 @@ $(ipydir)/h5py-$(h5py-version): \
 	$(call pybuild, tar -xf, h5py-$(h5py-version), , \
 	                h5py $(h5py-version))
 
-# 'healpy' is actually installed as part of the HEALPix package. It will be
-# installed with its C/C++ libraries if any other Python library is
-# requested with HEALPix. So actually calling for 'healpix' (when 'healpix'
-# is requested) is not necessary. But some users might not know about this
-# and just ask for 'healpy'. To avoid confusion in such cases, we'll just
-# set 'healpy' to be dependent on 'healpix' and not download any tarball
-# for it, or write anything in the final target.
-$(ipydir)/healpy-$(healpy-version): $(ibidir)/healpix-$(healpix-version)
-	touch $@
+# As of 2025-05-20, there are at least three python healpix packages at
+# pypi.org, with versions:
+#
+# https://pypi.org/project/healpy  1.18.1
+# https://pypi.org/project/healpix 2024.2
+# https://pypi.org/project/astropy-healpix 1.1.2
+#
+# Maneage provides both 'healpy' and 'astropy-healpix', independently. We
+# ignore pypix 'healpix', whose name risks confusion with the C/C++/fortran
+# version of healpix.
+#
+# For simplicity and error tracing, you should best install either healpy
+# or astropy-healpix, not both. For example, astropy_healpix/healpy.py has
+# an interface to provide 'healpy' type function names. However, it may be
+# possible to use both if your python imports avoid namespace clashes.  See
+# the documentation and source code of the respective packages to study how
+# they relate to one another.
+#
+# The 'healpy' package requires the C/C++ 'healpix' package to be built
+# in order to use the shared 'libsharp' library.
+$(ipydir)/healpy-$(healpy-version): \
+                       $(ibidir)/healpix-$(healpix-version) \
+                       $(ipydir)/matplotlib-$(matplotlib-version) \
+                       $(ipydir)/scipy-$(scipy-version)
+	tarball=healpy-$(healpy-version).tar.lz
+	$(call import-source, $(healpy-url), \
+	         $(healpy-checksum))
+	$(call pybuild, tar -xf, \
+	                healpy-$(healpy-version),,, \
+	                GPEP517)
+	echo "Healpy $(healpy-version)" > $@
+
 
 $(ipydir)/html5lib-$(html5lib-version): \
                    $(ipydir)/six-$(six-version) \
@@ -612,6 +706,13 @@ $(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version)
 	$(call pybuild, tar -xf, jinja2-$(jinja2-version), , \
 	                Jinja2 $(jinja2-version))
 
+$(ipydir)/joblib-$(joblib-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=joblib-$(joblib-version).tar.lz
+	$(call import-source, $(joblib-url), $(joblib-checksum))
+	$(call pybuild, tar -xf, \
+	            joblib-$(joblib-version),,, GPEP517)
+
 $(ipydir)/keyring-$(keyring-version): \
                   $(ipydir)/entrypoints-$(entrypoints-version) \
                   $(ipydir)/secretstorage-$(secretstorage-version) \
@@ -631,6 +732,48 @@ $(ipydir)/kiwisolver-$(kiwisolver-version): \
 	cp -pv $(dtexdir)/kiwisolver.tex $(ictdir)/
 	echo "Kiwisolver $(kiwisolver-version) \citep{cassowary2001}" > $@
 
+# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining
+# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these
+# to igwn-ligolw and igwn-segments, respectively [1].
+# [1] https://github.com/ahnitz/ligo-segments/issues/1
+$(ipydir)/igwn-segments-$(igwn-segments-version): \
+                         $(ipydir)/setuptools-$(setuptools-version)
+	tarball=igwn-segments-$(igwn-segments-version).tar.lz
+	$(call import-source, $(igwn-segments-url), $(igwn-segments-checksum))
+	$(call pybuild, tar -xf, \
+	            igwn-segments-$(igwn-segments-version),, \
+	            Igwn-segments $(igwn-segments-version), GPEP517)
+
+
+$(ipydir)/iniconfig-$(iniconfig-version): \
+	   $(ipydir)/hatch-vcs-$(hatch-vcs-version)
+	tarball=iniconfig-$(iniconfig-version).tar.lz
+	$(call import-source, $(iniconfig-url), $(iniconfig-checksum))
+	$(call pybuild, tar -xf, iniconfig-$(iniconfig-version), , \
+	                Iniconfig $(iniconfig-version), GPEP517)
+
+# Upstream this is called ligo.skymap with a full stop '.'; we replace it
+# by a hyphen '-' to reduce the chance of regex errors.
+#
+# 2025-05-19 Warning: this might have some undetected dependencies.
+$(ipydir)/ligo-skymap-$(ligo-skymap-version): \
+                       $(ibidir)/gsl-$(gsl-version) \
+                       $(ipydir)/tqdm-$(tqdm-version) \
+                       $(ibidir)/sqlite-$(sqlite3-version) \
+                       $(ipydir)/astropy-$(astropy-version) \
+                       $(ipydir)/lalsuite-$(lalsuite-version) \
+                       $(ipydir)/igwn-ligolw-$(igwn-ligolw-version) \
+                       $(ipydir)/igwn-segments-$(igwn-segments-version) \
+                       $(ipydir)/astropy-healpix-$(astropy-healpix-version)
+	tarball=ligo-skymap-$(ligo-skymap-version).tar.lz
+	$(call import-source, $(ligo-skymap-url), \
+	         $(ligo-skymap-checksum))
+	$(call pybuild, tar -xf, \
+	                ligo-skymap-$(ligo-skymap-version),,, \
+	                GPEP517)
+	echo "ligo-skymap $(ligo-skymap-version)" > $@
+
+
 $(ipydir)/lmfit-$(lmfit-version): \
                 $(ipydir)/six-$(six-version) \
                 $(ipydir)/scipy-$(scipy-version) \
@@ -644,6 +787,14 @@ $(ipydir)/lmfit-$(lmfit-version): \
 	$(call pybuild, tar -xf, lmfit-$(lmfit-version), , \
 	                LMFIT $(lmfit-version))
 
+$(ipydir)/lscsoft-glue-$(lscsoft-glue-version): \
+                    $(ipydir)/gpep517-$(gpep517-version) \
+                    $(ipydir)/python-installer-$(python-installer-version)
+	tarball=lscsoft-glue-$(lscsoft-glue-version).tar.lz
+	$(call import-source, $(lscsoft-glue-url), $(lscsoft-glue-checksum))
+	$(call pybuild, tar -xf, \
+	            lscsoft-glue-$(lscsoft-glue-version),,, GPEP517)
+
 $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
                         $(ipydir)/cffi-$(cffi-version) \
                         $(ipydir)/numpy-$(numpy-version) \
@@ -661,11 +812,19 @@ $(ipydir)/markupsafe-$(markupsafe-version): \
 	$(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \
 	                MarkupSafe $(markupsafe-version))
 
+# As of 2026-04-19: Matplotlib needs internet to download and build its
+# custom versions of 'freetype' and 'qhull'. The proposed option to 'python
+# -m pip instsall' in [1] for using system libraries was tested, but did
+# not work in this setup (our 'pybuild' uses 'python -m gpep517
+# install-from-source', not 'pip').
+#
+# [1] https://matplotlib.org/stable/install/dependencies.html
 $(ipydir)/matplotlib-$(matplotlib-version): \
                      $(itidir)/texlive \
                      $(ipydir)/numpy-$(numpy-version) \
                      $(ipydir)/cycler-$(cycler-version) \
                      $(ipydir)/pillow-$(pillow-version) \
+                     $(ibidir)/freetype-$(freetype-version) \
                      $(ipydir)/fonttools-$(fonttools-version) \
                      $(ipydir)/contourpy-$(contourpy-version) \
                      $(ipydir)/kiwisolver-$(kiwisolver-version) \
@@ -706,12 +865,11 @@ $(ipydir)/meson-python-$(meson-python-version): \
 	echo "Meson-Python $(meson-python-version)" > $@
 
 $(ipydir)/mpi4py-$(mpi4py-version): \
-                 $(ipydir)/gpep517-$(gpep517-version) \
                  $(ibidir)/openmpi-$(openmpi-version) \
-                 $(ipydir)/python-installer-$(python-installer-version)
+                 $(ipydir)/cython-$(cython-version)
 	tarball=mpi4py-$(mpi4py-version).tar.lz
 	$(call import-source, $(mpi4py-url), $(mpi4py-checksum))
-	$(call pybuild, tar -xf, mpi4py-$(mpi4py-version))
+	$(call pybuild, tar -xf, mpi4py-$(mpi4py-version),,, GPEP517)
 	cp $(dtexdir)/mpi4py.tex $(ictdir)/
 	echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
@@ -723,8 +881,17 @@ $(ipydir)/mpmath-$(mpmath-version): \
 	$(call pybuild, tar -xf, mpmath-$(mpmath-version), , \
 	                mpmath $(mpmath-version))
 
-# Until 2025-02-22: we had 'export CFLAGS="--std=c99 $$CFLAGS"' before
-# calling pybuild; but that doesn't seem to be necessary.
+$(ipydir)/networkx-$(networkx-version): \
+                       $(ipydir)/setuptools-$(setuptools-version)
+	tarball=networkx-$(networkx-version).tar.lz
+	$(call import-source, $(networkx-url), $(networkx-checksum))
+	$(call pybuild, tar -xf, \
+	                networkx-$(networkx-version),,, \
+	                GPEP517)
+	echo "networkx $(networkx-version)" > $@
+
+# Numpy's MacOS builds using Xcode prior to 26.3 needed the following flags
+# added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'.
 $(ipydir)/numpy-$(numpy-version): \
                 $(ipydir)/cython-$(cython-version) \
                 $(ibidir)/openblas-$(openblas-version) \
@@ -732,9 +899,6 @@ $(ipydir)/numpy-$(numpy-version): \
                 $(ipydir)/meson-python-$(meson-python-version)
 	tarball=numpy-$(numpy-version).tar.lz
 	$(call import-source, $(numpy-url), $(numpy-checksum))
-	if [ x$(on_mac_os) = xyes ]; then
-	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
-	fi
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
 	$(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version), GPEP517)
@@ -748,6 +912,23 @@ $(ipydir)/packaging-$(packaging-version): \
 	$(call pybuild, tar -xf, packaging-$(packaging-version), , \
 	                Packaging $(packaging-version), GPEP517)
 
+$(ipydir)/pandas-$(pandas-version): \
+                  $(ipydir)/numpy-$(numpy-version) \
+                  $(ipydir)/versioneer-$(versioneer-version) \
+                  $(ipydir)/pytz-$(pytz-version)
+	tarball=pandas-$(pandas-version).tar.lz
+	$(call import-source, $(pandas-url), $(pandas-checksum))
+	$(call pybuild, tar -xf, pandas-$(pandas-version), , \
+	                Pandas $(pandas-version), GPEP517)
+	echo "pandas $(pandas-version)" > $@
+
+$(ipydir)/pathspec-$(pathspec-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=pathspec-$(pathspec-version).tar.lz
+	$(call import-source, $(pathspec-url), $(pathspec-checksum))
+	$(call pybuild, tar -xf, \
+	            pathspec-$(pathspec-version),,, GPEP517)
+
 $(ipydir)/pexpect-$(pexpect-version): \
                   $(ipydir)/gpep517-$(gpep517-version) \
                   $(ipydir)/python-installer-$(python-installer-version)
@@ -773,6 +954,13 @@ $(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \
 # 	$(call pybuild, tar -xf, pip-$(pip-version), , \
 # 	                PiP $(pip-version))
 
+$(ipydir)/pluggy-$(pluggy-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=pluggy-$(pluggy-version).tar.lz
+	$(call import-source, $(pluggy-url), $(pluggy-checksum))
+	$(call pybuild, tar -xf, \
+	            pluggy-$(pluggy-version),,, GPEP517)
+
 $(ipydir)/ply-$(ply-version): \
               $(ipydir)/gpep517-$(gpep517-version) \
               $(ipydir)/python-installer-$(python-installer-version)
@@ -828,6 +1016,13 @@ $(ipydir)/pyflakes-$(pyflakes-version): \
 	$(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \
 	                pyflakes $(pyflakes-version))
 
+$(ipydir)/pygments-$(pygments-version): \
+	   $(ipydir)/hatchling-$(hatchling-version)
+	tarball=pygments-$(pygments-version).tar.lz
+	$(call import-source, $(pygments-url), $(pygments-checksum))
+	$(call pybuild, tar -xf, pygments-$(pygments-version), , \
+	                Pygments $(pygments-version), GPEP517)
+
 $(ipydir)/pyparsing-$(pyparsing-version): \
                     $(ipydir)/gpep517-$(gpep517-version) \
                     $(ipydir)/flit-core-$(flit-core-version) \
@@ -854,8 +1049,26 @@ $(ipydir)/pyproject-metadata-$(pyproject-metadata-version): \
 	$(call pybuild, tar -xf, \
 	            pyproject-metadata-$(pyproject-metadata-version),,, GPEP517)
 
+
+$(ipydir)/pytest-$(pytest-version): \
+                       $(ipydir)/setuptools-scm-$(setuptools-scm-version) \
+                       $(ipydir)/colorama-$(colorama-version) \
+                       $(ipydir)/exceptiongroup-$(exceptiongroup-version) \
+                       $(ipydir)/iniconfig-$(iniconfig-version) \
+                       $(ipydir)/packaging-$(packaging-version) \
+                       $(ipydir)/pluggy-$(pluggy-version) \
+                       $(ipydir)/pygments-$(pygments-version)
+	tarball=pytest-$(pytest-version).tar.lz
+	$(call import-source, $(pytest-url), $(pytest-checksum))
+	$(call pybuild, tar -xf, \
+	                pytest-$(pytest-version),,, \
+	                GPEP517)
+	echo "pytest $(pytest-version)" > $@
+
+
 $(ipydir)/python-dateutil-$(python-dateutil-version): \
-                          $(ipydir)/setuptools-scm-$(setuptools-scm-version)
+                          $(ipydir)/setuptools-scm-$(setuptools-scm-version) \
+                          $(ipydir)/six-$(six-version)
 	tarball=python-dateutil-$(python-dateutil-version).tar.lz
 	$(call import-source, $(python-dateutil-url), $(python-dateutil-checksum))
 	$(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \
@@ -885,6 +1098,37 @@ $(ipydir)/python-installer-$(python-installer-version): \
 	                BOOT_INSTALLER)
 	echo "Python-installer $(python-installer-version)" > $@
 
+# 2025-05-21: As of Feb 2025, it appears the lscsoft group is not maintaining
+# python-ligo-lw and ligo-segments; the LIGO Computing Group forked these
+# to igwn-ligolw and igwn-segments, respectively [1].
+# [1] https://github.com/ahnitz/ligo-segments/issues/1
+$(ipydir)/igwn-ligolw-$(igwn-ligolw-version): \
+                  $(ipydir)/setuptools-scm-$(setuptools-scm-version)
+	tarball=igwn-ligolw-$(igwn-ligolw-version).tar.lz
+	$(call import-source, $(igwn-ligolw-url), \
+	         $(igwn-ligolw-checksum))
+	$(call pybuild, tar -xf, \
+	                igwn-ligolw-$(igwn-ligolw-version),,, \
+	                GPEP517)
+	echo "igwn-ligolw $(igwn-ligolw-version)" > $@
+
+$(ipydir)/pyfftw-$(pyfftw-version): $(ipydir)/numpy-$(numpy-version) \
+	$(ibidir)/fftw-$(fftw-version)
+	tarball=pyfftw-$(pyfftw-version).tar.lz
+	$(call import-source, $(pyfftw-url), $(pyfftw-checksum))
+	$(call pybuild, tar -xf, pyfftw-$(pyfftw-version), , \
+	                Pyfftw $(pyfftw-version), GPEP517)
+
+
+# Called 'fitsio' in pypi.org: https://pypi.org/project/fitsio
+$(ipydir)/python3-fitsio-$(python3-fitsio-version): \
+                  $(ibidir)/patch-$(patch-version) \
+                  $(ipydir)/numpy-$(numpy-version)
+	tarball=python3-fitsio-$(python3-fitsio-version).tar.lz
+	$(call import-source, $(python3-fitsio-url), $(python3-fitsio-checksum))
+	$(call pybuild, tar -xf, python3-fitsio-$(python3-fitsio-version), , \
+	                Python3 Fitsio $(python3-fitsio-version), GPEP517)
+
 $(ipydir)/pythran-$(pythran-version): \
                   $(ipydir)/ply-$(ply-version) \
                   $(ipydir)/gast-$(gast-version) \
@@ -904,6 +1148,13 @@ $(ipydir)/pyyaml-$(pyyaml-version): \
 	$(call pybuild, tar -xf, pyyaml-$(pyyaml-version), , \
 	                PyYAML $(pyyaml-version), GPEP517)
 
+$(ipydir)/pytz-$(pytz-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=pytz-$(pytz-version).tar.lz
+	$(call import-source, $(pytz-url), $(pytz-checksum))
+	$(call pybuild, tar -xf, pytz-$(pytz-version), , \
+	                Pytz $(pytz-version), GPEP517)
+
 $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
                    $(ipydir)/numpy-$(numpy-version) \
                    $(ipydir)/certifi-$(certifi-version) \
@@ -914,41 +1165,39 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
 	$(call pybuild, tar -xf, requests-$(requests-version), , \
 	                Requests $(requests-version))
 
-# 'pythran' is disabled in the build of Scipy because of complications it
-# caused on some systems. We explicitly disable it using a preprocessor
-# directive. 'Pythran' can in principle speed up compilation of scientific
-# software [1][2].
+# Scipy building notes:
+#
+# 1. 'pythran' is disabled in the build of Scipy because of complications
+#    it caused on some systems. 'Pythran' can in principle speed up
+#    compilation of scientific software [1][2]. We explicitly disable it by
+#    modifying the source. Technically it should also be possible to pass
+#    the following option to the gpep517 build recipes with correct
+#    escaping of single and double quotes, but this has not tried as of
+#    2025-02-25.
+#        --config-json='{"setup-args":"-Duse-pythran=false"}'
+#
+# 2. Scipy's MacOS builds using Xcode prior to 26.3 needed the following
+#    flags added to 'LDFLAGS': '-undefined dynamic_lookup -bundle'.
+#
 # [1] https://pythran.readthedocs.io/en/latest
-# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html
+# [2] https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran
 $(ipydir)/scipy-$(scipy-version): \
                   $(ipydir)/numpy-$(numpy-version) \
                   $(ipydir)/pybind11-$(pybind11-version)
+
+#	Import the tarball.
 	tarball=scipy-$(scipy-version).tar.lz
 	$(call import-source, $(scipy-url), $(scipy-checksum))
-	if [ x$(on_mac_os) = xyes ]; then
-	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"
-	else
-#	  Same question as for 'numpy': why '-shared'? This obstructs
-#	  the meson build.
-#	  export LDFLAGS="$(LDFLAGS) -shared"
-	  :
-	fi
-	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
 
-#	Disable pythran: see
-#	https://docs.scipy.org/doc/scipy-1.15.2/dev/roadmap-detailed.html#use-of-pythran
-#	export SCIPY_USE_PYTHRAN=0 # deprecated(?)
-#	Option 1: Hack the source:
+#	Disable pythran (see above).
 	pyhook_before() {
 	   mv -iv meson.options meson.options.orig; \
 	   sed -e 's/\(use-pythran.*value: *\)true/\1false/' \
 	        meson.options.orig > meson.options
 	}
 
-#	Option 2: pass the string
-#	   --config-json='{"setup-args": "-Duse-pythran=false"}'
-#	to gpep517 with correct escaping of single and double quotes.
-#	Not tried as of 2025-02-25.
+#	Build Scipy.
+	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
 	$(call pybuild, tar -xf, scipy-$(scipy-version),$$conf,, GPEP517)
 	cp $(dtexdir)/scipy.tex $(ictdir)/
 	echo "Scipy $(scipy-version) \citep{scipy2020}" > $@
@@ -1003,6 +1252,26 @@ $(ipydir)/sip_tpv-$(sip_tpv-version): \
 	cp $(dtexdir)/sip_tpv.tex $(ictdir)/
 	echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@
 
+$(ipydir)/scikit-base-$(scikit-base-version): \
+                     $(ipydir)/gpep517-$(gpep517-version) \
+                     $(ipydir)/python-installer-$(python-installer-version)
+	tarball=scikit-base-$(scikit-base-version).tar.lz
+	$(call import-source, $(scikit-base-url), $(scikit-base-checksum))
+	$(call pybuild, tar -xf, scikit-base-$(scikit-base-version), , \
+	                Scikit-base $(scikit-base-version), GPEP517)
+	echo "scikit-base $(scikit-base-version)" > $@
+
+$(ipydir)/scikit-learn-$(scikit-learn-version): \
+                  $(ipydir)/joblib-$(joblib-version) \
+                  $(ipydir)/threadpoolctl-$(threadpoolctl-version) \
+                  $(ipydir)/numpy-$(numpy-version) \
+                  $(ipydir)/scipy-$(scipy-version)
+	tarball=scikit-learn-$(scikit-learn-version).tar.lz
+	$(call import-source, $(scikit-learn-url), $(scikit-learn-checksum))
+	$(call pybuild, tar -xf, scikit-learn-$(scikit-learn-version), , \
+	                Scikit-learn $(scikit-learn-version), GPEP517)
+	echo "scikit-learn $(scikit-learn-version)" > $@
+
 $(ipydir)/six-$(six-version): \
                      $(ipydir)/setuptools-$(setuptools-version)
 	tarball=six-$(six-version).tar.lz
@@ -1026,6 +1295,29 @@ $(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version)
 	cp $(dtexdir)/sympy.tex $(ictdir)/
 	echo "SymPy $(sympy-version) \citep{sympy}" > $@
 
+$(ipydir)/threadpoolctl-$(threadpoolctl-version): \
+                     $(ipydir)/flit-core-$(flit-core-version)
+	tarball=threadpoolctl-$(threadpoolctl-version).tar.lz
+	$(call import-source, $(threadpoolctl-url), $(threadpoolctl-checksum))
+	$(call pybuild, tar -xf, threadpoolctl-$(threadpoolctl-version), , \
+	                threadpoolctl $(threadpoolctl-version), GPEP517)
+	echo "threadpoolctl $(threadpoolctl-version)" > $@
+
+$(ipydir)/tqdm-$(tqdm-version): \
+                    $(ipydir)/setuptools-scm-$(setuptools-scm-version)
+	tarball=tqdm-$(tqdm-version).tar.lz
+	$(call import-source, $(tqdm-url), $(tqdm-checksum))
+	$(call pybuild, tar -xf, \
+	            tqdm-$(tqdm-version),, \
+	            Tqdm $(tqdm-version), GPEP517)
+
+$(ipydir)/trove-classifiers-$(trove-classifiers-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=trove-classifiers-$(trove-classifiers-version).tar.lz
+	$(call import-source, $(trove-classifiers-url), $(trove-classifiers-checksum))
+	$(call pybuild, tar -xf, \
+	            trove-classifiers-$(trove-classifiers-version),,, GPEP517)
+
 $(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version)
 	tarball=uncertainties-$(uncertainties-version).tar.lz
 	$(call import-source, $(uncertainties-url), $(uncertainties-checksum))
@@ -1040,6 +1332,13 @@ $(ipydir)/urllib3-$(urllib3-version): \
 	$(call pybuild, tar -xf, urllib3-$(urllib3-version), , \
 	                Urllib3 $(urllib3-version))
 
+$(ipydir)/versioneer-$(versioneer-version): \
+                  $(ipydir)/setuptools-$(setuptools-version)
+	tarball=versioneer-$(versioneer-version).tar.lz
+	$(call import-source, $(versioneer-url), $(versioneer-checksum))
+	$(call pybuild, tar -xf, versioneer-$(versioneer-version), , \
+	                Versioneer $(versioneer-version), GPEP517)
+
 $(ipydir)/webencodings-$(webencodings-version): \
                        $(ipydir)/setuptools-$(setuptools-version) \
                        $(ipydir)/setuptools-scm-$(setuptools-scm-version)
diff --git a/reproduce/software/make/xorg.mk b/reproduce/software/make/xorg.mk
index db42d70..33847f3 100644
--- a/reproduce/software/make/xorg.mk
+++ b/reproduce/software/make/xorg.mk
@@ -120,6 +120,7 @@ $(ibidir)/fontconfig-$(fontconfig-version): \
                      $(ibidir)/libxml2-$(libxml2-version) \
                      $(ibidir)/freetype-$(freetype-version) \
                      $(ibidir)/util-linux-$(util-linux-version)
+
 #	Import the source.
 	tarball=fontconfig-$(fontconfig-version).tar.lz
 	$(call import-source, $(fontconfig-url), $(fontconfig-checksum))
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index 1785977..8760db6 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -195,13 +195,14 @@ done
 #
 # Make sure that the build directory is given and that it exists.
 if [ x$build_dir = x ]; then
-    printf "$scriptname: '--build-dir' not provided, this is the location "
-    printf "that all built analysis files will be kept on the host OS\n"
+    printf "$scriptname: '--build-dir' not provided, this is the "
+    printf "location that all built analysis files will be kept on "
+    printf "the host OS\n"
     exit 1;
 else
     if ! [ -d $build_dir ]; then
-        printf "$scriptname: '$build_dir' (value to '--build-dir') doesn't "
-        printf "exist\n"
+        printf "$scriptname: '$build_dir' (value to '--build-dir') "
+        printf "doesn't exist\n"
         exit 1;
     fi
 fi
@@ -364,7 +365,7 @@ From: $base_sif
      else \\
         printf "$scriptname: '\$maneage_apptainer_stat' (value "; \\
         printf "to 'maneage_apptainer_stat' environment variable) "; \\
-        printf "is not recognized: should be either 'shell' or 'run'"; \\
+        printf "is not recognized: should be either 'shell' or 'run'\n"; \\
         exit 1; \\
      fi; \\
   else \\
@@ -399,7 +400,7 @@ fi
 if ! [ x"$build_only" = x ]; then
     if [ $quiet = 0 ]; then
         printf "$scriptname: info: Maneaged project has been configured "
-        printf "successfully in the '$sif' image"
+        printf "successfully in the '$sif' image\n"
     fi
     exit 0
 fi
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
diff --git a/reproduce/software/shell/docker-README.md b/reproduce/software/shell/docker-README.md
index 9e09282..dd46f4f 100644
--- a/reproduce/software/shell/docker-README.md
+++ b/reproduce/software/shell/docker-README.md
@@ -35,28 +35,25 @@ software environment) to easily move it from one computer to another.
     systemctl start docker
     ```
 
- 2. Using your favorite text editor, create a `run.sh` in your top Maneage
-    directory (as described in the comments at the start of the `docker.sh`
-    script in this directory). Just activate `--build-only` on the first
-    run so it doesn't go onto doing the analysis and just sets up the
-    software environment. Set the respective directory(s) based on your
-    filesystem (the software directory is optional). The `run.sh` file name
-    is already in `.gitignore` (because it contains local directories), so
-    Git will ignore it and it won't be committed by mistake.
+ 2. At the start of the `docker.sh` script in this directory, you can see
+    the necessary command to run. Just activate `--build-only` on the first
+    run so it doesn't go onto doing the analysis (that can be done at any
+    later time). Set the respective directory(s) based on your filesystem
+    (the software directory is optional). You can put the command in a
+    `run.sh` at the top of the project (it is already in `.gitignore`:
+    because it contains local directories).
 
  3. After the setup is complete, remove the `--build-only` and run the
     command below to confirm that `maneage-base` (the OS of the container)
     and `maneaged` (your project's full Maneage'd environment) images are
     available. If you want different names for these images, add the
-    `--project-name` and `--base-name` options to the `docker.sh` call.
+    `--project-name` and `--base-name` options to the `docker.sh` call. You
+    can see the list of available images with this command:
 
     ```shell
     docker image list
     ```
 
- 4. You are now ready to do your analysis by removing the `--build-only`
-    option.
-
 
 
 
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
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
index 861f3bf..2959255 100755
--- a/reproduce/software/shell/prep-source.sh
+++ b/reproduce/software/shell/prep-source.sh
@@ -47,17 +47,18 @@ fi
 
 
 
-# Find all the files that contain the '/bin/sh' string and correct them to
-# Maneage's own Bash. We are using 'while read' to read the file names line
-# by line. This is necessary to account file names that include the 'SPACE'
-# character (happens in CMake for example!).
+# Find all the files that contain the '/bin/sh' or '/bin/bash' strings and
+# correct them to Maneage's own shell (Dash or Bash). We are using 'while
+# read' to read the file names line by line. This is necessary to account
+# file names that include the 'SPACE' character (happens in CMake for
+# example!).
 #
 # Note that dates are important in the source directory (files depend on
 # each other), so we should read the original date and after making. We are
 # also not using GNU SED's '-i' ('--in-place') option because the host OS
 # may not have GNU SED.
 #
-# Actual situation which prompted the addition of this step: a Maneage'd
+# The situation which prompted the addition of this step: a Maneage'd
 # project (with GNU Bash 5.1.8 and Readline 8.1.1) was being built on a
 # system where '/bin/sh' was GNU Bash 5.2.26 and had Readline 8.2.010. The
 # newer version of Bash needed the newer Readline library function(s) that
@@ -74,7 +75,8 @@ fi
 # hard-coded in the source code of almost all programs (their build
 # scripts); and in special programs like GNU Make, GNU M4 or CMake it is
 # actually hardcoded in the source code (not just build scripts).
-if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash
+bashpath="$bindir"/bash
+if [ -f "$bindir/bash" ]; then shpath="$bashpath"
 else                           shpath="$bindir"/dash
 fi
 
@@ -91,7 +93,7 @@ fi
 # precision up to the seconds. We then use 'sed' to remove the information
 # regarding the timezone, as the format is not accepted by 'touch'.
 # LCTYPE and LANG are also required on macos systems by sed.
-grep -I -r -e'/bin/sh' $(pwd)/* \
+grep -I -r -e'/bin/sh' -e'/bin/bash' $(pwd)/* \
     | sed -e's|:|\t|' \
     | awk 'BEGIN{FS="\t"}{print $1}' \
     | sort \
author	Boud Roukema <boud@cosmo.torun.pl>	2026-01-18 22:50:48 +0600
committer	Mohammad Akhlaghi <mohammad@akhlaghi.org>	2026-05-03 03:00:18 +0200
commit	d99b69fdb52f2fd522f53bba29a42d3ba8af5361 (patch)
tree	c99e3b167a6af946f268a8f597de059b2a2c7dc2 /reproduce
parent	d7264f9cfd6dd17fa2b5a60a8696dfde08ee18de (diff)