lmfit and its dependencies added, Python tarballs as prerequisite

Python's `lmfit' module and all its major dependencies (`asteval',
`corner', `emcee' and `uncertainties') have been included in the template.

While doing this I noticed that if the tarballs are the last prerequisite
of each software building rule, then when building in parallel, the
template will immediately start building packages as soon as the first one
is downloaded. Not like the current way that it will attempt to download
several, then start building. For now, this has been implemented in the
Python build rules for all the modules and we'll later do the same for the
other programs and libraries. This also motivated a simplification of the
`pybuild' function: it now internally looks into the prerequisites and
selects the tarball from the prerequisite that is in the tarballs
directory.

This isn't a problem for the build, but I just don't understand why Python
can't recognize the version of `emcee', Python reads the version of `emcee'
as `0.0.0'! But it doesn't cause any crash in the build, so for now its
fine.

1 files changed, 226 insertions, 184 deletions

diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 14e7b75..9b107f0 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -63,16 +63,19 @@ python-major-version = $(shell echo $(python-version) | awk 'BEGIN{FS="."} \
 # another format, we'll do the modification before the download so the
 # downloaded file has our desired format.
 pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \
+                        asteval-$(asteval-version).tar.gz \
                         astroquery-$(astroquery-version).tar.gz \
                         astropy-$(astropy-version).tar.gz \
                         beautifulsoup4-$(beautifulsoup4-version).tar.gz \
                         certifi-$(certifi-version).tar.gz \
                         cffi-$(cffi-version).tar.gz \
                         chardet-$(chardet-version).tar.gz \
+                        corner-$(corner-version).tar.gz \
                         cryptography-$(cryptography-version).tar.gz \
                         cycler-$(cycler-version).tar.gz \
                         cython-$(cython-version).tar.gz \
                         eigency-$(eigency-version).tar.gz \
+                        emcee-$(emcee-version).tar.gz \
                         esutil-$(esutil-version).tar.gz \
                         entrypoints-$(entrypoints-version).tar.gz \
                         flake8-$(flake8-version).tar.gz \
@@ -85,6 +88,7 @@ pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \
                         kiwisolver-$(kiwisolver-version).tar.gz \
                         keyring-$(keyring-version).tar.gz \
                         libffi-$(libffi-version).tar.gz \
+                        lmfit-$(lmfit-version).tar.gz \
                         lsstdesccoord-$(lsstdesccoord-version).tar.gz \
                         matplotlib-$(matplotlib-version).tar.gz \
                         mpi4py-$(mpi4py-version).tar.gz \
@@ -109,6 +113,7 @@ pytarballs = $(foreach t, asn1crypto-$(asn1crypto-version).tar.gz \
                         six-$(six-version).tar.gz \
                         soupsieve-$(soupsieve-version).tar.gz \
                         sympy-$(sympy-version).tar.gz \
+                        uncertainties-$(uncertainties-version).tar.gz \
                         urllib3-$(urllib3-version).tar.gz \
                         webencodings-$(webencodings-version).tar.gz \
                         virtualenv-$(virtualenv-version).tar.gz \
@@ -178,15 +183,18 @@ $(pytarballs): $(tdir)/%:
 	  hash=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5
 	  h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
 	elif [ $$n = asn            ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4; c=$(asn1crypto-checksum)
+	elif [ $$n = asteval        ]; then h=50/3f/29b7935c6dc09ee96dc347edc66c57e8ef68d595dd35b763a36a117acc8c; c=$(asteval-checksum)
 	elif [ $$n = astroquery     ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396; c=$(astroquery-checksum)
 	elif [ $$n = astropy        ]; then h=b9/10/523355eb8cb9839552c8f0fbc9425a1c87c8ff2e55f4df85469a5a4164d3; c=$(astropy-checksum)
 	elif [ $$n = beautifulsoup  ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748; c=$(beautifulsoup4-checksum)
 	elif [ $$n = certifi        ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed; c=$(certifi-checksum)
 	elif [ $$n = cffi           ]; then h=64/7c/27367b38e6cc3e1f49f193deb761fe75cda9f95da37b67b422e62281fcac; c=$(cffi-checksum)
 	elif [ $$n = chardet        ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d; c=$(chardet-checksum)
+	elif [ $$n = corner         ]; then h=65/af/a7ba022f2d5787f51db91b5550cbe8e8c40a6eebd8f15119e743a09a9c19; c=$(corner-checksum)
 	elif [ $$n = cryptography   ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449; c=$(cryptography-checksum)
 	elif [ $$n = cycler         ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488; c=$(cycler-checksum)
 	elif [ $$n = eigency        ]; then h=fb/6e/bc4359fbfb0bb0b588ec328251b0d0836bdd7c0a4c568959ea06df023e18; c=$(eigency-checksum)
+	elif [ $$n = emcee          ]; then h=f0/c0/cd433f2aedeef9b1e5ed7d236c82564f7518fe7fe2238fa141ea9ce08e73; c=$(emcee-checksum)
 	elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c; c=$(entrypoints-checksum)
 	elif [ $$n = esutil         ]; then h=5b/91/77e38282fd3d47b55e351544ab179eb209b309a8d2d40f8cdb6241beda00; c=$(esutil-checksum)
 	elif [ $$n = flake          ]; then h=8d/a7/99222c9200af533c1ecb1120d99adbd1c033b57296ac5cb39d121db007a8; c=$(flake8-checksum)
@@ -197,6 +205,7 @@ $(pytarballs): $(tdir)/%:
 	elif [ $$n = jeepney        ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263; c=$(jeepney-checksum)
 	elif [ $$n = keyring        ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2; c=$(keyring-checksum)
 	elif [ $$n = kiwisolver     ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864; c=$(kiwisolver-checksum)
+	elif [ $$n = lmfit          ]; then h=59/6e/117794cf85b7345361877e49245870490ae438f1981dea3c6af1316b30e7; c=$(lmfit-checksum)
 	elif [ $$n = matplotlib     ]; then h=12/d1/7b12cd79c791348cb0c78ce6e7d16bd72992f13c9f1e8e43d2725a6d8adf; c=$(matplotlib-checksum)
 	elif [ $$n = mpi            ]; then h=04/f5/a615603ce4ab7f40b65dba63759455e3da610d9a155d4d4cece1d8fd6706; c=$(mpi4py-checksum)
 	elif [ $$n = mpmath         ]; then h=ca/63/3384ebb3b51af9610086b23ea976e6d27d6d97bf140a76a365bd77a3eb32; c=$(mpmath-checksum)
@@ -212,12 +221,13 @@ $(pytarballs): $(tdir)/%:
 	elif [ $$n = requests       ]; then h=52/2c/514e4ac25da2b08ca5a464c50463682126385c4272c18193876e91f4bc38; c=$(requests-checksum)
 	elif [ $$n = scipy          ]; then h=ee/5b/5afcd1c46f97b3c2ac3489dbc95d6ca28eacf8e3634e51f495da68d97f0f; c=$(scipy-checksum)
 	elif [ $$n = secretstorage  ]; then h=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5; c=$(secretstorage-checksum)
-	elif [ $$n = setuptools     ]; then h=c2/f7/c7b501b783e5a74cf1768bc174ee4fb0a8a6ee5af6afa92274ff964703e0; c=$(setuptools-checksum)
-	elif [ $$n = setuptools_scm ]; then h=54/85/514ba3ca2a022bddd68819f187ae826986051d130ec5b972076e4f58a9f3; c=$(setuptools_scm-checksum)
+	elif [ $$n = setuptools     ]; then h=11/0a/7f13ef5cd932a107cd4c0f3ebc9d831d9b78e1a0e8c98a098ca17b1d7d97; c=$(setuptools-checksum)
+	elif [ $$n = setuptools_scm ]; then h=83/44/53cad68ce686585d12222e6769682c4bdb9686808d2739671f9175e2938b; c=$(setuptools_scm-checksum)
 	elif [ $$n = six            ]; then h=dd/bf/4138e7bfb757de47d1f4b6994648ec67a51efe58fa907c1e11e350cddfca; c=$(six-checksum)
 	elif [ $$n = sip_tpv        ]; then h=27/93/a973aab2a3bf0c12cb385611819710921e13b090304c6bd015026cf9c502; c=$(sip_tpv-checksum)
 	elif [ $$n = soupsieve      ]; then h=0c/52/e9088bb9b96e2d39fc3b33fcda5b4fde9d71473536ac660a1ca9a0958a2f; c=$(soupsieve-checksum)
 	elif [ $$n = sympy          ]; then h=54/2e/6adb11fe599d4cfb7e8833753350ac51aa2c0603c226b36f9051cc9d2425; c=$(sympy-checksum)
+	elif [ $$n = uncertainties  ]; then h=2a/c2/babbe5b16141859dd799ed31c03987100a7b6d0ca7c0ed4429c96ce60fdf; c=$(uncertainties-checksum)
 	elif [ $$n = urllib         ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1; c=$(urllib3-checksum)
 	elif [ $$n = virtualenv     ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688; c=$(virtualenv-checksum)
 	elif [ $$n = webencodings   ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47; c=$(webencodings-checksum)
@@ -285,15 +295,16 @@ $(ibidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz
 	   fi \
 	&& echo "Libffi $(libffi-version)" > $@
 
-$(ibidir)/python: $(tdir)/python-$(python-version).tar.gz \
-                  $(ibidir)/libffi
+$(ibidir)/python: $(ibidir)/libffi \
+                  $(tdir)/python-$(python-version).tar.gz
         # 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, $(filter $(tdir)/%,$^), \
+	       Python-$(python-version),, \
 	       --without-ensurepip \
 	       --with-system-ffi \
 	       --enable-shared) \
@@ -315,27 +326,28 @@ $(ibidir)/python: $(tdir)/python-$(python-version).tar.gz \
 # access to `setup.py' is needed, pip can be used).
 # Arguments of this function are the numbers
 #   1) Unpack command
-#   2) Package name
-#   3) Unpacked directory name after unpacking the tarball
-#   4) site.cfg file (optional)
-#   5) Official software name.(for paper).
-#   6) Manual step after installation.
-pybuild = cd $(ddir); rm -rf $(3); \
-	 if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi; \
-	 cd $(3); \
-	 if [ "x$(strip $(4))" != x ]; then \
+#   2) Unpacked directory name after unpacking the tarball
+#   3) site.cfg file (optional).
+#   4) Official software name (for paper).
+#   5) Manual step after installation.
+pybuild = cd $(ddir); rm -rf $(2); \
+	 if ! $(1) $(filter $(tdir)/%,$^); then \
+	   echo; echo "Tar error"; exit 1; \
+	 fi; \
+	 cd $(2); \
+	 if [ "x$(strip $(3))" != x ]; then \
 	   sed -e 's|@LIBDIR[@]|'"$(ildir)"'|' \
 	       -e 's|@INCDIR[@]|'"$(idir)/include"'|' \
-	       $(4) > site.cfg; \
+	       $(3) > site.cfg; \
 	 fi; \
-	 if [ x"$(6)" = x ]; then after="echo no after"; \
-	 else after="$(6)"; fi \
+	 if [ x"$(5)" = x ]; then after="echo no after"; \
+	 else after="$(5)"; fi \
 	 && python setup.py build \
 	 && python setup.py install \
 	 && $$after \
 	 && cd .. \
-	 && rm -rf $(3) \
-	 && echo "$(5)" > $@
+	 && rm -rf $(2) \
+	 && echo "$(4)" > $@
 
 
 
@@ -345,114 +357,131 @@ pybuild = cd $(ddir); rm -rf $(3); \
 # ---------------
 #
 # All the necessary Python modules go here.
-$(ipydir)/asn1crypto: $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \
-                      $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, asn1crypto-$(asn1crypto-version), , \
+$(ipydir)/asn1crypto: $(ipydir)/setuptools \
+                      $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \
+	$(call pybuild, tar xf, asn1crypto-$(asn1crypto-version), , \
 	                Asn1crypto $(asn1crypto-version))
 
-$(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz \
-                      $(ipydir)/beautifulsoup4 \
-                      $(ipydir)/html5lib \
-                      $(ipydir)/requests \
+$(ipydir)/asteval: $(ipydir)/numpy \
+                   $(tdir)/asteval-$(asteval-version).tar.gz
+	$(call pybuild, tar xf, asteval-$(asteval-version), , \
+	                ASTEVAL $(asteval-version))
+
+$(ipydir)/astroquery: $(ipydir)/numpy \
                       $(ipydir)/astropy \
                       $(ipydir)/keyring \
-                      $(ipydir)/numpy
-	$(call pybuild, tar xf, $<, astroquery-$(astroquery-version), ,\
+                      $(ipydir)/html5lib \
+                      $(ipydir)/requests \
+                      $(ipydir)/beautifulsoup4 \
+                      $(tdir)/astroquery-$(astroquery-version).tar.gz
+	$(call pybuild, tar xf, astroquery-$(astroquery-version), ,\
 	                Astroquery $(astroquery-version))
 
-$(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
-                   $(ipydir)/h5py \
+$(ipydir)/astropy: $(ipydir)/h5py \
+                   $(ipydir)/scipy \
                    $(ipydir)/numpy \
-                   $(ipydir)/scipy
-	$(call pybuild, tar xf, $<, astropy-$(astropy-version)) \
+                   $(tdir)/astropy-$(astropy-version).tar.gz
+	$(call pybuild, tar xf, astropy-$(astropy-version)) \
 	&& cp $(dtexdir)/astropy.tex $(ictdir)/ \
 	&& echo "Astropy $(astropy-version) \citep{astropy2013,astropy2018}" > $@
 
-$(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
-                          $(ipydir)/soupsieve
-	$(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version), ,\
+$(ipydir)/beautifulsoup4: $(ipydir)/soupsieve \
+                          $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz
+	$(call pybuild, tar xf, beautifulsoup4-$(beautifulsoup4-version), ,\
 	                BeautifulSoup $(beautifulsoup4-version))
 
-$(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \
-                   $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, certifi-$(certifi-version), ,\
+$(ipydir)/certifi: $(ipydir)/setuptools \
+                   $(tdir)/certifi-$(certifi-version).tar.gz
+	$(call pybuild, tar xf, certifi-$(certifi-version), ,\
 	                Certifi $(certifi-version))
 
-$(ipydir)/cffi: $(tdir)/cffi-$(cffi-version).tar.gz \
+$(ipydir)/cffi: $(ibidir)/libffi \
                 $(ipydir)/pycparser \
-                $(ibidir)/libffi
-	$(call pybuild, tar xf, $<, cffi-$(cffi-version), ,\
+                $(tdir)/cffi-$(cffi-version).tar.gz
+	$(call pybuild, tar xf, cffi-$(cffi-version), ,\
 	                cffi $(cffi-version))
 
-$(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \
-                   $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, chardet-$(chardet-version), ,\
+$(ipydir)/chardet: $(ipydir)/setuptools \
+                   $(tdir)/chardet-$(chardet-version).tar.gz
+	$(call pybuild, tar xf, chardet-$(chardet-version), ,\
 	                Chardet $(chardet-version))
 
-$(ipydir)/cryptography: $(tdir)/cryptography-$(cryptography-version).tar.gz \
+$(ipydir)/corner: $(ipydir)/matplotlib \
+                  $(tdir)/corner-$(corner-version).tar.gz
+	$(call pybuild, tar xf, corner-$(corner-version), ,\
+	                Corner $(corner-version)) \
+	&& cp $(dtexdir)/corner.tex $(ictdir)/ \
+	&& echo "Corner $(corner-version) \citep{corner}" > $@
+
+$(ipydir)/cryptography: $(ipydir)/cffi \
                         $(ipydir)/asn1crypto \
-                        $(ipydir)/cffi
-	$(call pybuild, tar xf, $<, cryptography-$(cryptography-version), ,\
+                        $(tdir)/cryptography-$(cryptography-version).tar.gz
+	$(call pybuild, tar xf, cryptography-$(cryptography-version), ,\
 	                Cryptography $(cryptography-version))
 
-$(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \
-                  $(ipydir)/six
-	$(call pybuild, tar xf, $<, cycler-$(cycler-version), ,\
+$(ipydir)/cycler: $(ipydir)/six \
+                  $(tdir)/cycler-$(cycler-version).tar.gz
+	$(call pybuild, tar xf, cycler-$(cycler-version), ,\
 	                Cycler $(cycler-version))
 
-$(ipydir)/cython: $(tdir)/cython-$(cython-version).tar.gz \
-                  $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, Cython-$(cython-version)) \
+$(ipydir)/cython: $(ipydir)/setuptools \
+                  $(tdir)/cython-$(cython-version).tar.gz
+	$(call pybuild, tar xf, Cython-$(cython-version)) \
 	&& cp $(dtexdir)/cython.tex $(ictdir)/ \
 	&& echo "Cython $(cython-version) \citep{cython2011}" > $@
 
-$(ipydir)/esutil: $(tdir)/esutil-$(esutil-version).tar.gz \
-                  $(ipydir)/numpy
-	$(call pybuild, tar xf, $<, esutil-$(esutil-version), ,\
+$(ipydir)/esutil: $(ipydir)/numpy \
+                  $(tdir)/esutil-$(esutil-version).tar.gz
+	$(call pybuild, tar xf, esutil-$(esutil-version), ,\
 	                esutil $(esutil-version))
 
-$(ipydir)/eigency: $(tdir)/eigency-$(eigency-version).tar.gz \
-                   $(ibidir)/eigen
-	$(call pybuild, tar xf, $<, eigency-$(eigency-version), ,\
+$(ipydir)/eigency: $(ibidir)/eigen \
+                   $(tdir)/eigency-$(eigency-version).tar.gz
+	$(call pybuild, tar xf, eigency-$(eigency-version), ,\
 	                eigency $(eigency-version))
 
-$(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
-                       $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version), ,\
+$(ipydir)/emcee: $(ipydir)/numpy \
+                 $(ipydir)/setuptools_scm \
+                 $(tdir)/emcee-$(emcee-version).tar.gz
+	$(call pybuild, tar xf, emcee-$(emcee-version), ,\
+	                emcee $(emcee-version))
+
+$(ipydir)/entrypoints: $(ipydir)/setuptools \
+                       $(tdir)/entrypoints-$(entrypoints-version).tar.gz
+	$(call pybuild, tar xf, entrypoints-$(entrypoints-version), ,\
 	                EntryPoints $(entrypoints-version))
 
-$(ipydir)/flake8: $(tdir)/flake8-$(flake8-version).tar.gz \
+$(ipydir)/flake8: $(ipydir)/pyflakes \
                   $(ipydir)/pycodestyle \
-                  $(ipydir)/pyflakes
-	$(call pybuild, tar xf, $<, flake8-$(flake8-version), ,\
+                  $(tdir)/flake8-$(flake8-version).tar.gz
+	$(call pybuild, tar xf, flake8-$(flake8-version), ,\
 	                Flake8 $(flake8-version))
 
-$(ipydir)/future: $(tdir)/future-$(future-version).tar.gz \
-                  $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, future-$(future-version), ,\
+$(ipydir)/future: $(ipydir)/setuptools \
+                  $(tdir)/future-$(future-version).tar.gz
+	$(call pybuild, tar xf, future-$(future-version), ,\
 	                Future $(future-version))
 
-$(ipydir)/galsim: $(tdir)/galsim-$(galsim-version).tar.gz \
-                  $(ipydir)/lsstdesccoord \
-                  $(ipydir)/pybind11 \
+$(ipydir)/galsim: $(ipydir)/future \
                   $(ipydir)/astropy \
                   $(ipydir)/eigency \
-                  $(ipydir)/future
-	$(call pybuild, tar xf, $<, GalSim-$(galsim-version), ,) \
+                  $(ipydir)/pybind11 \
+                  $(ipydir)/lsstdesccoord \
+                  $(tdir)/galsim-$(galsim-version).tar.gz
+	$(call pybuild, tar xf, GalSim-$(galsim-version), ,) \
 	&& cp $(dtexdir)/galsim.tex $(ictdir)/ \
 	&& echo "Galsim $(galsim-version) \citep{galsim}" > $@
 
-$(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
-                $(ipydir)/pypkgconfig \
-                $(ipydir)/setuptools \
+$(ipydir)/h5py: $(ipydir)/six \
+                $(ibidir)/hdf5 \
+                $(ipydir)/numpy \
                 $(ipydir)/cython \
                 $(ipydir)/mpi4py \
-                $(ipydir)/numpy \
-                $(ibidir)/hdf5 \
-                $(ipydir)/six
+                $(ipydir)/pypkgconfig \
+                $(tdir)/h5py-$(h5py-version).tar.gz
 	export HDF5_MPI=ON; \
 	export HDF5_DIR=$(ildir); \
-	$(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
@@ -465,201 +494,214 @@ $(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
 $(ipydir)/healpy: $(ibidir)/healpix
 	touch $@
 
-$(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz  \
+$(ipydir)/html5lib: $(ipydir)/six \
                     $(ipydir)/webencodings \
-                    $(ipydir)/six
-	$(call pybuild, tar xf, $<, html5lib-$(html5lib-version), ,\
+                    $(tdir)/html5lib-$(html5lib-version).tar.gz
+	$(call pybuild, tar xf, html5lib-$(html5lib-version), ,\
 	                HTML5lib $(html5lib-version))
 
-$(ipydir)/idna: $(tdir)/idna-$(idna-version).tar.gz \
-                $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, idna-$(idna-version), ,\
+$(ipydir)/idna: $(ipydir)/setuptools \
+                $(tdir)/idna-$(idna-version).tar.gz
+	$(call pybuild, tar xf, idna-$(idna-version), ,\
 	       idna $(idna-version))
 
-$(ipydir)/jeepney: $(tdir)/jeepney-$(jeepney-version).tar.gz \
-                   $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, jeepney-$(jeepney-version), ,\
+$(ipydir)/jeepney: $(ipydir)/setuptools \
+                   $(tdir)/jeepney-$(jeepney-version).tar.gz \
+	$(call pybuild, tar xf, jeepney-$(jeepney-version), ,\
 	                Jeepney $(jeepney-version))
 
-$(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz \
-                   $(ipydir)/setuptools_scm \
+$(ipydir)/keyring: $(ipydir)/entrypoints \
                    $(ipydir)/secretstorage \
-                   $(ipydir)/entrypoints
-	$(call pybuild, tar xf, $<, keyring-$(keyring-version), ,\
+                   $(ipydir)/setuptools_scm \
+                   $(tdir)/keyring-$(keyring-version).tar.gz
+	$(call pybuild, tar xf, keyring-$(keyring-version), ,\
 	                Keyring $(keyring-version))
 
-$(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz \
-                      $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version), ,\
+$(ipydir)/kiwisolver: $(ipydir)/setuptools \
+                      $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz
+	$(call pybuild, tar xf, kiwisolver-$(kiwisolver-version), ,\
 	                Kiwisolver $(kiwisolver-version))
 
-$(ipydir)/lsstdesccoord: $(tdir)/lsstdesccoord-$(lsstdesccoord-version).tar.gz \
-                      $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, LSSTDESC.Coord-$(lsstdesccoord-version), ,\
+$(ipydir)/lmfit: $(ipydir)/six \
+                 $(ipydir)/scipy \
+                 $(ipydir)/emcee \
+                 $(ipydir)/corner \
+                 $(ipydir)/asteval \
+                 $(ipydir)/matplotlib \
+                 $(ipydir)/uncertainties \
+                 $(tdir)/lmfit-$(lmfit-version).tar.gz
+	$(call pybuild, tar xf, lmfit-$(lmfit-version), ,\
+	                LMFIT $(lmfit-version))
+
+$(ipydir)/lsstdesccoord: $(ipydir)/setuptools \
+                         $(tdir)/lsstdesccoord-$(lsstdesccoord-version).tar.gz
+	$(call pybuild, tar xf, LSSTDESC.Coord-$(lsstdesccoord-version), ,\
 	                LSSTDESC.Coord $(lsstdesccoord-version))
 
-$(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz \
-                      $(ipydir)/python-dateutil \
+$(ipydir)/matplotlib: $(ipydir)/numpy \
+                      $(ipydir)/cycler \
+                      $(itidir)/texlive \
+                      $(ibidir)/freetype \
+                      $(ipydir)/pyparsing \
+                      $(ipydir)/kiwisolver \
                       $(ibidir)/ghostscript \
                       $(ibidir)/imagemagick \
-                      $(ipydir)/kiwisolver \
-                      $(ipydir)/pyparsing \
-                      $(ibidir)/freetype \
-                      $(itidir)/texlive \
-                      $(ipydir)/cycler \
-                      $(ipydir)/numpy
-	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) \
+                      $(ipydir)/python-dateutil \
+                      $(tdir)/matplotlib-$(matplotlib-version).tar.gz
+	$(call pybuild, tar xf, matplotlib-$(matplotlib-version)) \
 	&& cp $(dtexdir)/matplotlib.tex $(ictdir)/ \
 	&& echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
 
-$(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz    \
+$(ipydir)/mpi4py: $(ibidir)/openmpi \
                   $(ipydir)/setuptools \
-                  $(ibidir)/openmpi
-	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version)) \
+                  $(tdir)/mpi4py-$(mpi4py-version).tar.gz
+	$(call pybuild, tar xf, mpi4py-$(mpi4py-version)) \
 	&& cp $(dtexdir)/mpi4py.tex $(ictdir)/ \
 	&& echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
 
-$(ipydir)/mpmath: $(tdir)/mpmath-$(mpmath-version).tar.gz \
-                     $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, mpmath-$(mpmath-version), ,\
+$(ipydir)/mpmath: $(ipydir)/setuptools \
+                  $(tdir)/mpmath-$(mpmath-version).tar.gz
+	$(call pybuild, tar xf, mpmath-$(mpmath-version), ,\
 	                mpmath $(mpmath-version))
 
-$(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
-                 $(ipydir)/setuptools \
+$(ipydir)/numpy: $(ibidir)/unzip \
                  $(ibidir)/openblas \
-                 $(ibidir)/unzip
+                 $(ipydir)/setuptools \
+                 $(tdir)/numpy-$(numpy-version).zip
 	if [ x$(on_mac_os) = xyes ]; then \
 	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \
 	else \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
 	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
-	$(call pybuild, unzip, $<, numpy-$(numpy-version),$$conf, \
+	$(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version)) \
 	&& cp $(dtexdir)/numpy.tex $(ictdir)/ \
 	&& echo "Numpy $(numpy-version) \citep{numpy2011}" > $@
 
-$(ibidir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
-                $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pip-$(pip-version), ,\
+$(ibidir)/pip3: $(ipydir)/setuptools \
+                $(tdir)/pip-$(pip-version).tar.gz
+	$(call pybuild, tar xf, pip-$(pip-version), ,\
 	                PiP $(pip-version))
 
-$(ipydir)/pycodestyle: $(tdir)/pycodestyle-$(pycodestyle-version).tar.gz \
-                       $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pycodestyle-$(pycodestyle-version), ,\
+$(ipydir)/pycodestyle: $(ipydir)/setuptools \
+                       $(tdir)/pycodestyle-$(pycodestyle-version).tar.gz
+	$(call pybuild, tar xf, pycodestyle-$(pycodestyle-version), ,\
 	                pycodestyle $(pycodestyle-version))
 
-$(ipydir)/pybind11: $(tdir)/pybind11-$(pybind11-version).tar.gz \
-                    $(ipydir)/setuptools \
+$(ipydir)/pybind11: $(ibidir)/eigen \
                     $(ibidir)/boost \
-                    $(ibidir)/eigen
-	$(call pybuild, tar xf, $<, pybind11-$(pybind11-version), ,\
+                    $(ipydir)/setuptools \
+                    $(tdir)/pybind11-$(pybind11-version).tar.gz
+	$(call pybuild, tar xf, pybind11-$(pybind11-version), ,\
 	                pybind11 $(pybind11-version),
 	                cp -r include/pybind11 $(iidir)/python$(python-major-version)m/)
 
-$(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \
-                     $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pycparser-$(pycparser-version), ,\
+$(ipydir)/pycparser: $(ipydir)/setuptools \
+                     $(tdir)/pycparser-$(pycparser-version).tar.gz
+	$(call pybuild, tar xf, pycparser-$(pycparser-version), ,\
 	                pycparser $(pycparser-version))
 
-$(ipydir)/pyflakes: $(tdir)/pyflakes-$(pyflakes-version).tar.gz \
-                    $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pyflakes-$(pyflakes-version), ,\
+$(ipydir)/pyflakes: $(ipydir)/setuptools \
+                    $(tdir)/pyflakes-$(pyflakes-version).tar.gz
+	$(call pybuild, tar xf, pyflakes-$(pyflakes-version), ,\
 	                pyflakes $(pyflakes-version))
 
-$(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \
-                     $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version), ,\
+$(ipydir)/pyparsing: $(ipydir)/setuptools \
+                     $(tdir)/pyparsing-$(pyparsing-version).tar.gz
+	$(call pybuild, tar xf, pyparsing-$(pyparsing-version), ,\
 	                PyParsing $(pyparsing-version))
 
-$(ipydir)/pypkgconfig: $(tdir)/pkgconfig-$(pypkgconfig-version).tar.gz \
-                       $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, pkgconfig-$(pypkgconfig-version), ,
+$(ipydir)/pypkgconfig: $(ipydir)/setuptools \
+                       $(tdir)/pkgconfig-$(pypkgconfig-version).tar.gz
+	$(call pybuild, tar xf, pkgconfig-$(pypkgconfig-version), ,
 	                pkgconfig $(pypkgconfig-version))
 
-$(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz  \
+$(ipydir)/python-dateutil: $(ipydir)/six \
                            $(ipydir)/setuptools_scm \
-                           $(ipydir)/six
-	$(call pybuild, tar xf, $<, python-dateutil-$(python-dateutil-version), ,\
+                           $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz
+	$(call pybuild, tar xf, python-dateutil-$(python-dateutil-version), ,\
 	                python-dateutil $(python-dateutil-version))
 
-$(ipydir)/pyyaml: $(tdir)/pyyaml-$(pyyaml-version).tar.gz \
-                  $(ibidir)/yaml \
+$(ipydir)/pyyaml: $(ibidir)/yaml \
                   $(ipydir)/cython \
-                  $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, PyYAML-$(pyyaml-version), ,\
+                  $(tdir)/pyyaml-$(pyyaml-version).tar.gz
+	$(call pybuild, tar xf, PyYAML-$(pyyaml-version), ,\
 	                PyYAML $(pyyaml-version))
 
-$(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz \
+$(ipydir)/requests: $(ipydir)/idna \
+                    $(ipydir)/numpy \
                     $(ipydir)/certifi \
                     $(ipydir)/chardet \
                     $(ipydir)/urllib3 \
-                    $(ipydir)/numpy \
-                    $(ipydir)/idna
-	$(call pybuild, tar xf, $<, requests-$(requests-version), ,\
+                    $(tdir)/requests-$(requests-version).tar.gz
+	$(call pybuild, tar xf, requests-$(requests-version), ,\
 	                Requests $(requests-version))
 
-$(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
-                 $(ipydir)/numpy
+$(ipydir)/scipy: $(ipydir)/numpy \
+                 $(tdir)/scipy-$(scipy-version).tar.gz
 	if [ x$(on_mac_os) = xyes ]; then \
 	  export LDFLAGS="$(LDFLAGS) -undefined dynamic_lookup -bundle"; \
 	else \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
 	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
-	$(call pybuild, tar xf, $<, scipy-$(scipy-version),$$conf) \
+	$(call pybuild, tar xf, scipy-$(scipy-version),$$conf) \
 	&& cp $(dtexdir)/scipy.tex $(ictdir)/ \
 	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
 
-$(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
+$(ipydir)/secretstorage: $(ipydir)/jeepney \
                          $(ipydir)/cryptography \
-                         $(ipydir)/jeepney
-	$(call pybuild, tar xf, $<, SecretStorage-$(secretstorage-version), ,\
+                         $(tdir)/secretstorage-$(secretstorage-version).tar.gz
+	$(call pybuild, tar xf, SecretStorage-$(secretstorage-version), ,\
 	                SecretStorage $(secretstorage-version))
 
-$(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
+$(ipydir)/setuptools: $(ibidir)/unzip \
                       $(ibidir)/python \
-                      $(ibidir)/unzip
-	$(call pybuild, unzip, $<, setuptools-$(setuptools-version), ,\
+                      $(tdir)/setuptools-$(setuptools-version).zip
+	$(call pybuild, unzip, setuptools-$(setuptools-version), ,\
 	                Setuptools $(setuptools-version))
 
-$(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.gz \
-                          $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version), ,\
+$(ipydir)/setuptools_scm: $(ipydir)/setuptools \
+                          $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.gz
+	$(call pybuild, tar xf, setuptools_scm-$(setuptools_scm-version), ,\
 	                Setuptools-scm $(setuptools_scm-version))
 
-$(ipydir)/sip_tpv: $(tdir)/sip_tpv-$(sip_tpv-version).tar.gz \
-                  $(ipydir)/astropy \
-                  $(ipydir)/numpy \
-                  $(ipydir)/sympy
-	$(call pybuild, tar xf, $<, sip_tpv-$(sip_tpv-version), ,) \
+$(ipydir)/sip_tpv: $(ipydir)/sympy \
+                   $(ipydir)/astropy \
+                   $(tdir)/sip_tpv-$(sip_tpv-version).tar.gz
+	$(call pybuild, tar xf, sip_tpv-$(sip_tpv-version), ,) \
 	&& cp $(dtexdir)/sip_tpv.tex $(ictdir)/ \
 	&& echo "sip\_tpv $(sip_tpv-version) \citep{sip-tpv}" > $@
 
 
-$(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \
-               $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, six-$(six-version), ,\
+$(ipydir)/six: $(ipydir)/setuptools \
+               $(tdir)/six-$(six-version).tar.gz
+	$(call pybuild, tar xf, six-$(six-version), ,\
 	                Six $(six-version))
 
-$(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \
-                     $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version), ,\
+$(ipydir)/soupsieve: $(ipydir)/setuptools \
+                     $(tdir)/soupsieve-$(soupsieve-version).tar.gz
+	$(call pybuild, tar xf, soupsieve-$(soupsieve-version), ,\
 	                SoupSieve $(soupsieve-version))
 
-$(ipydir)/sympy: $(tdir)/sympy-$(sympy-version).tar.gz \
-                     $(ipydir)/setuptools \
-                     $(ipydir)/mpmath
-	$(call pybuild, tar xf, $<, sympy-$(sympy-version), ,) \
+$(ipydir)/sympy: $(ipydir)/mpmath \
+                 $(tdir)/sympy-$(sympy-version).tar.gz
+	$(call pybuild, tar xf, sympy-$(sympy-version), ,) \
 	&& cp $(dtexdir)/sympy.tex $(ictdir)/ \
 	&& echo "SymPy $(sympy-version) \citep{sympy}" > $@
 
-$(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \
-                   $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, urllib3-$(urllib3-version), ,\
+$(ipydir)/uncertainties: $(ipydir)/numpy \
+                         $(tdir)/uncertainties-$(uncertainties-version).tar.gz
+	$(call pybuild, tar xf, uncertainties-$(uncertainties-version), ,\
+	                uncertainties $(uncertainties-version))
+
+$(ipydir)/urllib3: $(ipydir)/setuptools \
+                   $(tdir)/urllib3-$(urllib3-version).tar.gz
+	$(call pybuild, tar xf, urllib3-$(urllib3-version), ,\
 	                Urllib3 $(urllib3-version))
 
-$(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \
-                        $(ipydir)/setuptools
-	$(call pybuild, tar xf, $<, webencodings-$(webencodings-version), ,\
+$(ipydir)/webencodings: $(ipydir)/setuptools \
+                        $(tdir)/webencodings-$(webencodings-version).tar.gz
+	$(call pybuild, tar xf, webencodings-$(webencodings-version), ,\
 	                Webencodings $(webencodings-version))