Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

1 files changed, 196 insertions, 117 deletions

diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 18c68de..6766744 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -4,7 +4,7 @@
 #                      !!!!! IMPORTANT NOTES !!!!!
 #
 # This Makefile will be loaded into 'high-level.mk', which is called by the
-# `./project configure' script. It is not included into the project
+# './project configure' script. It is not included into the project
 # afterwards.
 #
 # This Makefile contains instructions to build all the Python-related
@@ -12,8 +12,8 @@
 #
 # ------------------------------------------------------------------------
 #
-# Copyright (C) 2019-2021 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -35,7 +35,7 @@
 # Python enviroment
 # -----------------
 #
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
 # have found several other Python-related environment variables on some
 # systems which might interfere. To be safe, we are removing all their
 # values.
@@ -62,19 +62,20 @@ python-major-version = $(shell echo $(python-version) | awk 'BEGIN{FS="."} \
 # While this Makefile is for Python programs, in some cases, we need
 # certain programs (like Python itself), or libraries for the modules.
 $(ibidir)/libffi-$(libffi-version):
-        # Prepare the source.
-	tarball=libffi-$(libffi-version).tar.gz
+
+#	Prepare the source.
+	tarball=libffi-$(libffi-version).tar.lz
 	$(call import-source, $(libffi-url), $(libffi-checksum))
 
-        # Build libffi.
+#	Build libffi.
 	$(call gbuild, libffi-$(libffi-version), , \
                        CFLAGS="-DNO_JAVA_RAW_API=1")
 
-        # On some Fedora systems, libffi installs in `lib64', not
-        # `lib'. This will cause problems when building setuptools
-        # later. To fix this problem, we'll first check if this has indeed
-        # happened (it exists under `lib64', but not under `lib'). If so,
-        # we'll put a copy of the installed libffi libraries in `lib'.
+#	On some Fedora systems, libffi installs in 'lib64', not 'lib'. This
+#	will cause problems when building setuptools later. To fix this
+#	problem, we'll first check if this has indeed happened (it exists
+#	under 'lib64', but not under 'lib'). If so, we'll put a copy of the
+#	installed libffi libraries in 'lib'.
 	if [ -f $(idir)/lib64/libffi.a ] && ! [ -f $(idir)/lib/libffi.a ]; then
 	  cp $(idir)/lib64/libffi* $(ildir)/
 	fi
@@ -82,17 +83,17 @@ $(ibidir)/libffi-$(libffi-version):
 
 $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 
-        # Download the source.
-	tarball=python-$(python-version).tar.gz
+#	Download the source.
+	tarball=python-$(python-version).tar.lz
 	$(call import-source, $(python-url), $(python-checksum))
 
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+#	On Mac systems, the build complains about 'clang' specific
+#	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
-	$(call gbuild, Python-$(python-version),, \
+	$(call gbuild, python-$(python-version),, \
 	       --without-ensurepip \
 	       --with-system-ffi \
 	       --enable-shared, -j$(numthreads))
@@ -110,10 +111,10 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 # Non-PiP Python module installation
 # ----------------------------------
 #
-# To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used). Note that the
+# To build Python packages with direct access to a 'setup.py' (if no direct
+# access to 'setup.py' is needed, pip can be used). Note that the
 # software's packaged source code is the first prerequisite that is in the
-# `tdir' directory.
+# 'tdir' directory.
 #
 # Arguments of this function are the numbers
 #   1) Unpack command
@@ -122,8 +123,8 @@ $(ibidir)/python-$(python-version): $(ibidir)/libffi-$(libffi-version)
 #   4) Official software name (for paper).
 #
 # Hooks:
-#   pyhook_before: optional steps before running `python setup.py build'
-#   pyhook_after: optional steps after running `python setup.py install'
+#   pyhook_before: optional steps before running 'python setup.py build'
+#   pyhook_after: optional steps after running 'python setup.py install'
 pybuild = cd $(ddir); rm -rf $(2); \
 	if ! $(1) $(tdir)/$$tarball; then \
 	  echo; echo "Tar error"; exit 1; \
@@ -153,13 +154,13 @@ pybuild = cd $(ddir); rm -rf $(2); \
 $(ipydir)/asn1crypto-$(asn1crypto-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=asn1crypto-$(asn1crypto-version).tar.gz
 	$(call import-source, $(asn1crypto-url), $(asn1crypto-checksum))
-	$(call pybuild, tar xf, asn1crypto-$(asn1crypto-version), , \
+	$(call pybuild, tar -xf, asn1crypto-$(asn1crypto-version), , \
 	                Asn1crypto $(asn1crypto-version))
 
 $(ipydir)/asteval-$(asteval-version): $(ipydir)/numpy-$(numpy-version)
 	tarball=asteval-$(asteval-version).tar.gz
 	$(call import-source, $(asteval-url), $(asteval-checksum))
-	$(call pybuild, tar xf, asteval-$(asteval-version), , \
+	$(call pybuild, tar -xf, asteval-$(asteval-version), , \
 	                ASTEVAL $(asteval-version))
 
 $(ipydir)/astroquery-$(astroquery-version): \
@@ -168,7 +169,7 @@ $(ipydir)/astroquery-$(astroquery-version): \
                      $(ipydir)/requests-$(requests-version)
 	tarball=astroquery-$(astroquery-version).tar.gz
 	$(call import-source, $(astroquery-url), $(astroquery-checksum))
-	$(call pybuild, tar xf, astroquery-$(astroquery-version), , \
+	$(call pybuild, tar -xf, astroquery-$(astroquery-version), , \
 	                Astroquery $(astroquery-version))
 
 $(ipydir)/astropy-$(astropy-version): \
@@ -177,87 +178,84 @@ $(ipydir)/astropy-$(astropy-version): \
                   $(ipydir)/scipy-$(scipy-version) \
                   $(ipydir)/numpy-$(numpy-version) \
                   $(ipydir)/pyyaml-$(pyyaml-version) \
+                  $(ipydir)/jinja2-$(jinja2-version) \
+                  $(ipydir)/pyerfa-$(pyerfa-version) \
                   $(ipydir)/html5lib-$(html5lib-version) \
-                  $(ipydir)/beautifulsoup4-$(beautifulsoup4-version)
-
-        # Download the source.
-	tarball=astropy-$(astropy-version).tar.gz
+                  $(ipydir)/beautifulsoup4-$(beautifulsoup4-version) \
+                  $(ipydir)/extension-helpers-$(extension-helpers-version)
+	tarball=astropy-$(astropy-version).tar.lz
 	$(call import-source, $(astropy-url), $(astropy-checksum))
-
-        # Currently, when the Expat library is already built in a project
-        # (for example as a dependency of another program), Astropy's
-        # internal building of Expat will conflict with the project's. So
-        # we have added Expat as a dependency of Astropy (so it is always
-        # built before it, and we tell Astropy to use the project's
-        # libexpat.
-	pyhook_before () {
-	  echo ""                   >> setup.cfg
-	  echo "[build]"            >> setup.cfg
-	  echo "use_system_expat=1" >> setup.cfg
-	}
-	$(call pybuild, tar xf, astropy-$(astropy-version))
+	$(call pybuild, tar -xf, astropy-$(astropy-version))
 	cp $(dtexdir)/astropy.tex $(ictdir)/
 	echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
 $(ipydir)/beautifulsoup4-$(beautifulsoup4-version): \
                          $(ipydir)/soupsieve-$(soupsieve-version)
-	tarball=beautifulsoup4-$(beautifulsoup4-version).tar.gz
+	tarball=beautifulsoup4-$(beautifulsoup4-version).tar.lz
 	$(call import-source, $(beautifulsoup4-url), $(beautifulsoup4-checksum))
-	$(call pybuild, tar xf, beautifulsoup4-$(beautifulsoup4-version), , \
+	$(call pybuild, tar -xf, beautifulsoup4-$(beautifulsoup4-version), , \
 	                BeautifulSoup $(beautifulsoup4-version))
 
+$(ipydir)/beniget-$(beniget-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=beniget-$(beniget-version).tar.lz
+	$(call import-source, $(beniget-url), $(beniget-checksum))
+	$(call pybuild, tar -xf, beniget-$(beniget-version), , \
+	                Beniget $(beniget-version))
+
 $(ipydir)/certifi-$(certifi-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=certifi-$(certifi-version).tar.gz
 	$(call import-source, $(certifi-url), $(certifi-checksum))
-	$(call pybuild, tar xf, certifi-$(certifi-version), , \
+	$(call pybuild, tar -xf, certifi-$(certifi-version), , \
 	                Certifi $(certifi-version))
 
 $(ipydir)/cffi-$(cffi-version): \
                $(ibidir)/libffi-$(libffi-version) \
                $(ipydir)/pycparser-$(pycparser-version)
-	tarball=cffi-$(cffi-version).tar.gz
+	tarball=cffi-$(cffi-version).tar.lz
 	$(call import-source, $(cffi-url), $(cffi-checksum))
-	$(call pybuild, tar xf, cffi-$(cffi-version), ,cffi $(cffi-version))
+	$(call pybuild, tar -xf, cffi-$(cffi-version), ,cffi $(cffi-version))
 
 $(ipydir)/chardet-$(chardet-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=chardet-$(chardet-version).tar.gz
 	$(call import-source, $(chardet-url), $(chardet-checksum))
-	$(call pybuild, tar xf, chardet-$(chardet-version), , \
+	$(call pybuild, tar -xf, chardet-$(chardet-version), , \
 	                Chardet $(chardet-version))
 
 $(ipydir)/corner-$(corner-version): $(ipydir)/matplotlib-$(matplotlib-version)
 	tarball=corner-$(corner-version).tar.gz
 	$(call import-source, $(corner-url), $(corner-checksum))
-	$(call pybuild, tar xf, corner-$(corner-version), , \
+	$(call pybuild, tar -xf, corner-$(corner-version), , \
 	                Corner $(corner-version))
 	cp $(dtexdir)/corner.tex $(ictdir)/
 	echo "Corner $(corner-version) \citep{corner}" > $@
 
 $(ipydir)/cryptography-$(cryptography-version): \
                        $(ipydir)/cffi-$(cffi-version) \
-                       $(ipydir)/asn1crypto-$(asn1crypto-version)
-	tarball=cryptography-$(cryptography-version).tar.gz
+                       $(ipydir)/asn1crypto-$(asn1crypto-version) \
+                       $(ipydir)/setuptools-rust-$(setuptools-rust-version)
+	tarball=cryptography-$(cryptography-version).tar.lz
 	$(call import-source, $(cryptography-url), $(cryptography-checksum))
-	$(call pybuild, tar xf, cryptography-$(cryptography-version), , \
+	$(call pybuild, tar -xf, cryptography-$(cryptography-version), , \
 	                Cryptography $(cryptography-version))
 
 $(ipydir)/cycler-$(cycler-version): $(ipydir)/six-$(six-version)
-	tarball=cycler-$(cycler-version).tar.gz
+	tarball=cycler-$(cycler-version).tar.lz
 	$(call import-source, $(cycler-url), $(cycler-checksum))
-	$(call pybuild, tar xf, cycler-$(cycler-version), , \
+	$(call pybuild, tar -xf, cycler-$(cycler-version), , \
 	                Cycler $(cycler-version))
 
 $(ipydir)/cython-$(cython-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=cython-$(cython-version).tar.gz
+	tarball=Cython-$(cython-version).tar.lz
 	$(call import-source, $(cython-url), $(cython-checksum))
-	$(call pybuild, tar xf, Cython-$(cython-version))
+	$(call pybuild, tar -xf, Cython-$(cython-version))
 	cp $(dtexdir)/cython.tex $(ictdir)/
 	echo "Cython $(cython-version) \citep{cython2011}" > $@
 
 $(ipydir)/esutil-$(esutil-version): $(ipydir)/numpy-$(numpy-version)
-	tarball=esutil-$(esutil-version).tar.gz
+	export CFLAGS="-std=c++14 $$CFLAGS"
+	tarball=esutil-$(esutil-version).tar.lz
 	$(call import-source, $(esutil-url), $(esutil-checksum))
-	$(call pybuild, tar xf, esutil-$(esutil-version), , \
+	$(call pybuild, tar -xf, esutil-$(esutil-version), , \
 	                esutil $(esutil-version))
 
 $(ipydir)/eigency-$(eigency-version): \
@@ -266,7 +264,7 @@ $(ipydir)/eigency-$(eigency-version): \
                   $(ipydir)/cython-$(cython-version)
 	tarball=eigency-$(eigency-version).tar.gz
 	$(call import-source, $(eigency-url), $(eigency-checksum))
-	$(call pybuild, tar xf, eigency-$(eigency-version), , \
+	$(call pybuild, tar -xf, eigency-$(eigency-version), , \
 	                eigency $(eigency-version))
 
 $(ipydir)/emcee-$(emcee-version): \
@@ -274,28 +272,35 @@ $(ipydir)/emcee-$(emcee-version): \
                 $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=emcee-$(emcee-version).tar.gz
 	$(call import-source, $(emcee-url), $(emcee-checksum))
-	$(call pybuild, tar xf, emcee-$(emcee-version), , \
+	$(call pybuild, tar -xf, emcee-$(emcee-version), , \
 	                emcee $(emcee-version))
 
 $(ipydir)/entrypoints-$(entrypoints-version): \
                       $(ipydir)/setuptools-$(setuptools-version)
 	tarball=entrypoints-$(entrypoints-version).tar.gz
 	$(call import-source, $(entrypoints-url), $(entrypoints-checksum))
-	$(call pybuild, tar xf, entrypoints-$(entrypoints-version), , \
+	$(call pybuild, tar -xf, entrypoints-$(entrypoints-version), , \
 	                EntryPoints $(entrypoints-version))
 
+$(ipydir)/extension-helpers-$(extension-helpers-version): \
+                    $(ipydir)/setuptools-$(setuptools-version)
+	tarball=extension-helpers-$(extension-helpers-version).tar.lz
+	$(call import-source, $(extension-helpers-url), $(extension-helpers-checksum))
+	$(call pybuild, tar -xf, extension-helpers-$(extension-helpers-version), , \
+	                Extension-Helpers $(extension-helpers-version))
+
 $(ipydir)/flake8-$(flake8-version): \
                  $(ipydir)/pyflakes-$(pyflakes-version) \
                  $(ipydir)/pycodestyle-$(pycodestyle-version)
 	tarball=flake8-$(flake8-version).tar.gz
 	$(call import-source, $(flake8-url), $(flake8-checksum))
-	$(call pybuild, tar xf, flake8-$(flake8-version), , \
+	$(call pybuild, tar -xf, flake8-$(flake8-version), , \
 	                Flake8 $(flake8-version))
 
 $(ipydir)/future-$(future-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=future-$(future-version).tar.gz
 	$(call import-source, $(future-url), $(future-checksum))
-	$(call pybuild, tar xf, future-$(future-version), , \
+	$(call pybuild, tar -xf, future-$(future-version), , \
 	                Future $(future-version))
 
 $(ipydir)/galsim-$(galsim-version): \
@@ -304,12 +309,18 @@ $(ipydir)/galsim-$(galsim-version): \
                  $(ipydir)/eigency-$(eigency-version) \
                  $(ipydir)/pybind11-$(pybind11-version) \
                  $(ipydir)/lsstdesccoord-$(lsstdesccoord-version)
-	tarball=galsim-$(galsim-version).tar.gz
+	tarball=galsim-$(galsim-version).tar.lz
 	$(call import-source, $(galsim-url), $(galsim-checksum))
-	$(call pybuild, tar xf, GalSim-$(galsim-version))
+	$(call pybuild, tar -xf, galsim-$(galsim-version))
 	cp $(dtexdir)/galsim.tex $(ictdir)/
 	echo "Galsim $(galsim-version) \citep{galsim}" > $@
 
+$(ipydir)/gast-$(gast-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=gast-$(gast-version).tar.lz
+	$(call import-source, $(gast-url), $(gast-checksum))
+	$(call pybuild, tar -xf, gast-$(gast-version), , \
+	                Gast $(gast-version))
+
 $(ipydir)/h5py-$(h5py-version): \
                $(ipydir)/six-$(six-version) \
                $(ibidir)/hdf5-$(hdf5-version) \
@@ -321,15 +332,15 @@ $(ipydir)/h5py-$(h5py-version): \
 	export HDF5_DIR=$(ildir)
 	tarball=h5py-$(h5py-version).tar.gz
 	$(call import-source, $(h5py-url), $(h5py-checksum))
-	$(call pybuild, tar xf, h5py-$(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
+# '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'
+# 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
+# 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 $@
@@ -339,34 +350,40 @@ $(ipydir)/html5lib-$(html5lib-version): \
                    $(ipydir)/webencodings-$(webencodings-version)
 	tarball=html5lib-$(html5lib-version).tar.gz
 	$(call import-source, $(html5lib-url), $(html5lib-checksum))
-	$(call pybuild, tar xf, html5lib-$(html5lib-version), , \
+	$(call pybuild, tar -xf, html5lib-$(html5lib-version), , \
 	                HTML5lib $(html5lib-version))
 
 $(ipydir)/idna-$(idna-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=idna-$(idna-version).tar.gz
 	$(call import-source, $(idna-url), $(idna-checksum))
-	$(call pybuild, tar xf, idna-$(idna-version), , \
+	$(call pybuild, tar -xf, idna-$(idna-version), , \
 	       idna $(idna-version))
 
 $(ipydir)/jeepney-$(jeepney-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=jeepney-$(jeepney-version).tar.gz
 	$(call import-source, $(jeepney-url), $(jeepney-checksum))
-	$(call pybuild, tar xf, jeepney-$(jeepney-version), , \
+	$(call pybuild, tar -xf, jeepney-$(jeepney-version), , \
 	                Jeepney $(jeepney-version))
 
+$(ipydir)/jinja2-$(jinja2-version): $(ipydir)/markupsafe-$(markupsafe-version)
+	tarball=jinja2-$(jinja2-version).tar.lz
+	$(call import-source, $(jinja2-url), $(jinja2-checksum))
+	$(call pybuild, tar -xf, jinja2-$(jinja2-version), , \
+	                Jinja2 $(jinja2-version))
+
 $(ipydir)/keyring-$(keyring-version): \
                   $(ipydir)/entrypoints-$(entrypoints-version) \
                   $(ipydir)/secretstorage-$(secretstorage-version) \
                   $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=keyring-$(keyring-version).tar.gz
 	$(call import-source, $(keyring-url), $(keyring-checksum))
-	$(call pybuild, tar xf, keyring-$(keyring-version), , \
+	$(call pybuild, tar -xf, keyring-$(keyring-version), , \
 	                Keyring $(keyring-version))
 
 $(ipydir)/kiwisolver-$(kiwisolver-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=kiwisolver-$(kiwisolver-version).tar.gz
+	tarball=kiwisolver-$(kiwisolver-version).tar.lz
 	$(call import-source, $(kiwisolver-url), $(kiwisolver-checksum))
-	$(call pybuild, tar xf, kiwisolver-$(kiwisolver-version), , \
+	$(call pybuild, tar -xf, kiwisolver-$(kiwisolver-version), , \
 	                Kiwisolver $(kiwisolver-version))
 
 $(ipydir)/lmfit-$(lmfit-version): \
@@ -379,20 +396,28 @@ $(ipydir)/lmfit-$(lmfit-version): \
                 $(ipydir)/uncertainties-$(uncertainties-version)
 	tarball=lmfit-$(lmfit-version).tar.gz
 	$(call import-source, $(lmfit-url), $(lmfit-checksum))
-	$(call pybuild, tar xf, lmfit-$(lmfit-version), , \
+	$(call pybuild, tar -xf, lmfit-$(lmfit-version), , \
 	                LMFIT $(lmfit-version))
 
 $(ipydir)/lsstdesccoord-$(lsstdesccoord-version): \
-                        $(ipydir)/setuptools-$(setuptools-version)
+                        $(ipydir)/cython-$(cython-version)
 	tarball=lsstdesccoord-$(lsstdesccoord-version).tar.gz
 	$(call import-source, $(lsstdesccoord-url), $(lsstdesccoord-checksum))
-	$(call pybuild, tar xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
+	$(call pybuild, tar -xf, LSSTDESC.Coord-$(lsstdesccoord-version), , \
 	                LSSTDESC.Coord $(lsstdesccoord-version))
 
+$(ipydir)/markupsafe-$(markupsafe-version): \
+                     $(ipydir)/setuptools-$(setuptools-version)
+	tarball=markupsafe-$(markupsafe-version).tar.lz
+	$(call import-source, $(markupsafe-url), $(markupsafe-checksum))
+	$(call pybuild, tar -xf, markupsafe-$(markupsafe-version), , \
+	                MarkupSafe $(markupsafe-version))
+
 $(ipydir)/matplotlib-$(matplotlib-version): \
                      $(itidir)/texlive \
                      $(ipydir)/numpy-$(numpy-version) \
                      $(ipydir)/cycler-$(cycler-version) \
+                     $(ipydir)/pillow-$(pillow-version) \
                      $(ibidir)/freetype-$(freetype-version) \
                      $(ipydir)/pyparsing-$(pyparsing-version) \
                      $(ipydir)/kiwisolver-$(kiwisolver-version) \
@@ -400,33 +425,33 @@ $(ipydir)/matplotlib-$(matplotlib-version): \
                      $(ibidir)/imagemagick-$(imagemagick-version) \
                      $(ipydir)/python-dateutil-$(python-dateutil-version)
 
-        # Download the source.
-	tarball=matplotlib-$(matplotlib-version).tar.gz
+#	Prepare the source.
+	tarball=matplotlib-$(matplotlib-version).tar.lz
 	$(call import-source, $(matplotlib-url), $(matplotlib-checksum))
 
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+#	On Mac systems, the build complains about 'clang' specific
+#	features, so we can't use our own GCC build here.
 	if [ x$(on_mac_os) = xyes ]; then
 	  export CC=clang
 	  export CXX=clang++
 	fi
-	$(call pybuild, tar xf, matplotlib-$(matplotlib-version))
+	$(call pybuild, tar -xf, matplotlib-$(matplotlib-version))
 	cp $(dtexdir)/matplotlib.tex $(ictdir)/
 	echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
 $(ipydir)/mpi4py-$(mpi4py-version): \
                  $(ibidir)/openmpi-$(openmpi-version) \
                  $(ipydir)/setuptools-$(setuptools-version)
-	tarball=mpi4py-$(mpi4py-version).tar.gz
+	tarball=mpi4py-$(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))
 	cp $(dtexdir)/mpi4py.tex $(ictdir)/
 	echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
 $(ipydir)/mpmath-$(mpmath-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=mpmath-$(mpmath-version).tar.gz
 	$(call import-source, $(mpmath-url), $(mpmath-checksum))
-	$(call pybuild, tar xf, mpmath-$(mpmath-version), , \
+	$(call pybuild, tar -xf, mpmath-$(mpmath-version), , \
 	                mpmath $(mpmath-version))
 
 $(ipydir)/numpy-$(numpy-version): \
@@ -434,7 +459,7 @@ $(ipydir)/numpy-$(numpy-version): \
                 $(ipydir)/cython-$(cython-version) \
                 $(ibidir)/openblas-$(openblas-version) \
                 $(ipydir)/setuptools-$(setuptools-version)
-	tarball=numpy-$(numpy-version).zip
+	tarball=numpy-$(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"
@@ -443,28 +468,48 @@ $(ipydir)/numpy-$(numpy-version): \
 	fi
 	export CFLAGS="--std=c99 $$CFLAGS"
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
-	$(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
+	$(call pybuild, tar -xf, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version))
 	cp $(dtexdir)/numpy.tex $(ictdir)/
 	echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
+$(ipydir)/packaging-$(packaging-version): \
+                    $(ipydir)/pyparsing-$(pyparsing-version)
+	tarball=packaging-$(packaging-version).tar.lz
+	$(call import-source, $(packaging-url), $(packaging-checksum))
+	$(call pybuild, tar -xf, packaging-$(packaging-version), , \
+	                Packaging $(packaging-version))
+
 $(ipydir)/pexpect-$(pexpect-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pexpect-$(pexpect-version).tar.gz
 	$(call import-source, $(pexpect-url), $(pexpect-checksum))
-	$(call pybuild, tar xf, pexpect-$(pexpect-version), , \
+	$(call pybuild, tar -xf, pexpect-$(pexpect-version), , \
 	                Pexpect $(pexpect-version))
 
+$(ipydir)/pillow-$(pillow-version): $(ibidir)/libjpeg-$(libjpeg-version) \
+                 $(ipydir)/setuptools-$(setuptools-version)
+	tarball=Pillow-$(pillow-version).tar.lz
+	$(call import-source, $(pillow-url), $(pillow-checksum))
+	$(call pybuild, tar -xf, Pillow-$(pillow-version), , \
+	                Pillow $(pillow-version))
+
 $(ipydir)/pip-$(pip-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pip-$(pip-version).tar.gz
 	$(call import-source, $(pip-url), $(pip-checksum))
-	$(call pybuild, tar xf, pip-$(pip-version), , \
+	$(call pybuild, tar -xf, pip-$(pip-version), , \
 	                PiP $(pip-version))
 
+$(ipydir)/ply-$(ply-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=ply-$(ply-version).tar.lz
+	$(call import-source, $(ply-url), $(ply-checksum))
+	$(call pybuild, tar -xf, ply-$(ply-version), , \
+	                ply $(ply-version))
+
 $(ipydir)/pycodestyle-$(pycodestyle-version): \
                       $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pycodestyle-$(pycodestyle-version).tar.gz
 	$(call import-source, $(pycodestyle-url), $(pycodestyle-checksum))
-	$(call pybuild, tar xf, pycodestyle-$(pycodestyle-version), , \
+	$(call pybuild, tar -xf, pycodestyle-$(pycodestyle-version), , \
 	                pycodestyle $(pycodestyle-version))
 
 $(ipydir)/pybind11-$(pybind11-version): \
@@ -476,31 +521,40 @@ $(ipydir)/pybind11-$(pybind11-version): \
 	pyhook_after() {
 	  cp -r include/pybind11 $(iidir)/python$(python-major-version)m/
 	}
-	$(call pybuild, tar xf, pybind11-$(pybind11-version), , \
+	$(call pybuild, tar -xf, pybind11-$(pybind11-version), , \
 	                pybind11 $(pybind11-version))
 
 $(ipydir)/pycparser-$(pycparser-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pycparser-$(pycparser-version).tar.gz
 	$(call import-source, $(pycparser-url), $(pycparser-checksum))
-	$(call pybuild, tar xf, pycparser-$(pycparser-version), , \
+	$(call pybuild, tar -xf, pycparser-$(pycparser-version), , \
 	                pycparser $(pycparser-version))
 
+$(ipydir)/pyerfa-$(pyerfa-version): \
+                 $(ipydir)/numpy-$(numpy-version) \
+                 $(ipydir)/packaging-$(packaging-version)
+	tarball=pyerfa-$(pyerfa-version).tar.lz
+	$(call import-source, $(pyerfa-url), $(pyerfa-checksum))
+	$(call pybuild, tar -xf, pyerfa-$(pyerfa-version), , \
+	                PyERFA $(pyerfa-version))
+
 $(ipydir)/pyflakes-$(pyflakes-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pyflakes-$(pyflakes-version).tar.gz
 	$(call import-source, $(pyflakes-url), $(pyflakes-checksum))
-	$(call pybuild, tar xf, pyflakes-$(pyflakes-version), , \
+	$(call pybuild, tar -xf, pyflakes-$(pyflakes-version), , \
 	                pyflakes $(pyflakes-version))
 
-$(ipydir)/pyparsing-$(pyparsing-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=pyparsing-$(pyparsing-version).tar.gz
+$(ipydir)/pyparsing-$(pyparsing-version): \
+                    $(ipydir)/setuptools-$(setuptools-version)
+	tarball=pyparsing-$(pyparsing-version).tar.lz
 	$(call import-source, $(pyparsing-url), $(pyparsing-checksum))
-	$(call pybuild, tar xf, pyparsing-$(pyparsing-version), , \
+	$(call pybuild, tar -xf, pyparsing-$(pyparsing-version), , \
 	                PyParsing $(pyparsing-version))
 
 $(ipydir)/pypkgconfig-$(pypkgconfig-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=pkgconfig-$(pypkgconfig-version).tar.gz
 	$(call import-source, $(pypkgconfig-url), $(pypkgconfig-checksum))
-	$(call pybuild, tar xf, pkgconfig-$(pypkgconfig-version), ,
+	$(call pybuild, tar -xf, pkgconfig-$(pypkgconfig-version), ,
 	                pkgconfig $(pypkgconfig-version))
 
 $(ipydir)/python-dateutil-$(python-dateutil-version): \
@@ -508,15 +562,26 @@ $(ipydir)/python-dateutil-$(python-dateutil-version): \
                           $(ipydir)/setuptools_scm-$(setuptools_scm-version)
 	tarball=python-dateutil-$(python-dateutil-version).tar.gz
 	$(call import-source, $(python-dateutil-url), $(python-dateutil-checksum))
-	$(call pybuild, tar xf, python-dateutil-$(python-dateutil-version), , \
+	$(call pybuild, tar -xf, python-dateutil-$(python-dateutil-version), , \
 	                python-dateutil $(python-dateutil-version))
 
+$(ipydir)/pythran-$(pythran-version): \
+                  $(ipydir)/ply-$(ply-version) \
+                  $(ipydir)/gast-$(gast-version) \
+                  $(ibidir)/boost-$(boost-version) \
+                  $(ipydir)/beniget-$(beniget-version) \
+                  $(ipydir)/setuptools_scm-$(setuptools_scm-version)
+	tarball=pythran-$(pythran-version).tar.lz
+	$(call import-source, $(pythran-url), $(pythran-checksum))
+	$(call pybuild, tar -xf, pythran-$(pythran-version), , \
+	                pythran $(pythran-version))
+
 $(ipydir)/pyyaml-$(pyyaml-version): \
                  $(ibidir)/yaml-$(yaml-version) \
                  $(ipydir)/cython-$(cython-version)
 	tarball=pyyaml-$(pyyaml-version).tar.gz
 	$(call import-source, $(pyyaml-url), $(pyyaml-checksum))
-	$(call pybuild, tar xf, PyYAML-$(pyyaml-version), , \
+	$(call pybuild, tar -xf, PyYAML-$(pyyaml-version), , \
 	                PyYAML $(pyyaml-version))
 
 $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
@@ -526,13 +591,14 @@ $(ipydir)/requests-$(requests-version): $(ipydir)/idna-$(idna-version) \
                     $(ipydir)/urllib3-$(urllib3-version)
 	tarball=requests-$(requests-version).tar.gz
 	$(call import-source, $(requests-url), $(requests-checksum))
-	$(call pybuild, tar xf, requests-$(requests-version), , \
+	$(call pybuild, tar -xf, requests-$(requests-version), , \
 	                Requests $(requests-version))
 
 $(ipydir)/scipy-$(scipy-version): \
                   $(ipydir)/numpy-$(numpy-version) \
+                  $(ipydir)/pythran-$(pythran-version) \
                   $(ipydir)/pybind11-$(pybind11-version)
-	tarball=scipy-$(scipy-version).tar.gz
+	tarball=scipy-$(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"
@@ -540,7 +606,7 @@ $(ipydir)/scipy-$(scipy-version): \
 	  export LDFLAGS="$(LDFLAGS) -shared"
 	fi
 	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"
-	$(call pybuild, tar xf, scipy-$(scipy-version),$$conf)
+	$(call pybuild, tar -xf, scipy-$(scipy-version),$$conf)
 	cp $(dtexdir)/scipy.tex $(ictdir)/
 	echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
 
@@ -549,68 +615,81 @@ $(ipydir)/secretstorage-$(secretstorage-version): \
                         $(ipydir)/cryptography-$(cryptography-version)
 	tarball=secretstorage-$(secretstorage-version).tar.gz
 	$(call import-source, $(secretstorage-url), $(secretstorage-checksum))
-	$(call pybuild, tar xf, SecretStorage-$(secretstorage-version), , \
+	$(call pybuild, tar -xf, SecretStorage-$(secretstorage-version), , \
 	                SecretStorage $(secretstorage-version))
 
 $(ipydir)/setuptools-$(setuptools-version): \
                      $(ibidir)/unzip-$(unzip-version) \
                      $(ibidir)/python-$(python-version)
-	tarball=setuptools-$(setuptools-version).zip
+	tarball=setuptools-$(setuptools-version).tar.lz
 	$(call import-source, $(setuptools-url), $(setuptools-checksum))
-	$(call pybuild, unzip, setuptools-$(setuptools-version), , \
+	$(call pybuild, tar -xf, setuptools-$(setuptools-version), , \
 	                Setuptools $(setuptools-version))
 
 $(ipydir)/setuptools_scm-$(setuptools_scm-version): \
                          $(ipydir)/setuptools-$(setuptools-version)
 	tarball=setuptools_scm-$(setuptools_scm-version).tar.gz
 	$(call import-source, $(setuptools_scm-url), $(setuptools_scm-checksum))
-	$(call pybuild, tar xf, setuptools_scm-$(setuptools_scm-version), , \
+	$(call pybuild, tar -xf, setuptools_scm-$(setuptools_scm-version), , \
 	                Setuptools-scm $(setuptools_scm-version))
 
+$(ipydir)/setuptools-rust-$(setuptools-rust-version): \
+                          $(ipydir)/setuptools-$(setuptools-version)
+	tarball=setuptools-rust-$(setuptools-rust-version).tar.lz
+	$(call import-source, $(setuptools-rust-url), $(setuptools-rust-checksum))
+	$(call pybuild, tar -xf, setuptools-rust-$(setuptools-rust-version), , \
+	                Setuptools-scm $(setuptools-rust-version))
+
 $(ipydir)/sip_tpv-$(sip_tpv-version): \
                   $(ipydir)/sympy-$(sympy-version) \
                   $(ipydir)/astropy-$(astropy-version)
 	tarball=sip_tpv-$(sip_tpv-version).tar.gz
 	$(call import-source, $(sip_tpv-url), $(sip_tpv-checksum))
-	$(call pybuild, tar xf, sip_tpv-$(sip_tpv-version), ,)
+	$(call pybuild, tar -xf, sip_tpv-$(sip_tpv-version), ,)
 	cp $(dtexdir)/sip_tpv.tex $(ictdir)/
 	echo "sip_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@
 
 
 $(ipydir)/six-$(six-version): $(ipydir)/setuptools-$(setuptools-version)
-	tarball=six-$(six-version).tar.gz
+	tarball=six-$(six-version).tar.lz
 	$(call import-source, $(six-url), $(six-checksum))
-	$(call pybuild, tar xf, six-$(six-version), , \
+	$(call pybuild, tar -xf, six-$(six-version), , \
 	                Six $(six-version))
 
 $(ipydir)/soupsieve-$(soupsieve-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=soupsieve-$(soupsieve-version).tar.gz
 	$(call import-source, $(soupsieve-url), $(soupsieve-checksum))
-	$(call pybuild, tar xf, soupsieve-$(soupsieve-version), , \
+	$(call pybuild, tar -xf, soupsieve-$(soupsieve-version), , \
 	                SoupSieve $(soupsieve-version))
 
 $(ipydir)/sympy-$(sympy-version): $(ipydir)/mpmath-$(mpmath-version)
 	tarball=sympy-$(sympy-version).tar.gz
 	$(call import-source, $(sympy-url), $(sympy-checksum))
-	$(call pybuild, tar xf, sympy-$(sympy-version), ,)
+	$(call pybuild, tar -xf, sympy-$(sympy-version), ,)
 	cp $(dtexdir)/sympy.tex $(ictdir)/
 	echo "SymPy $(sympy-version) \citep{sympy}" > $@
 
 $(ipydir)/uncertainties-$(uncertainties-version): $(ipydir)/numpy-$(numpy-version)
-	tarball=uncertainties-$(uncertainties-version).tar.gz
+	tarball=uncertainties-$(uncertainties-version).tar.lz
 	$(call import-source, $(uncertainties-url), $(uncertainties-checksum))
-	$(call pybuild, tar xf, uncertainties-$(uncertainties-version), , \
+	$(call pybuild, tar -xf, uncertainties-$(uncertainties-version), , \
 	                uncertainties $(uncertainties-version))
 
 $(ipydir)/urllib3-$(urllib3-version): $(ipydir)/setuptools-$(setuptools-version)
 	tarball=urllib3-$(urllib3-version).tar.gz
 	$(call import-source, $(urllib3-url), $(urllib3-checksum))
-	$(call pybuild, tar xf, urllib3-$(urllib3-version), , \
+	$(call pybuild, tar -xf, urllib3-$(urllib3-version), , \
 	                Urllib3 $(urllib3-version))
 
 $(ipydir)/webencodings-$(webencodings-version): \
                        $(ipydir)/setuptools-$(setuptools-version)
 	tarball=webencodings-$(webencodings-version).tar.gz
 	$(call import-source, $(webencodings-url), $(webencodings-checksum))
-	$(call pybuild, tar xf, webencodings-$(webencodings-version), , \
+	$(call pybuild, tar -xf, webencodings-$(webencodings-version), , \
 	                Webencodings $(webencodings-version))
+
+$(ipydir)/wheel-$(wheel-version): $(ipydir)/setuptools-$(setuptools-version)
+	tarball=wheel-$(wheel-version).tar.lz
+	$(call import-source, $(wheel-url), $(wheel-checksum))
+	$(call pybuild, tar -xf, wheel-$(wheel-version), , \
+	                Wheel $(wheel-version))