New architecture to separate software-building and analysis steps

Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

1 files changed, 506 insertions, 0 deletions

diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
new file mode 100644
index 0000000..5ec99f0
--- /dev/null
+++ b/reproduce/software/make/python.mk
@@ -0,0 +1,506 @@
+# Build the project's Python dependencies.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run by the initial `./configure' script. It is not
+# included into the reproduction pipe after that.
+#
+# ------------------------------------------------------------------------
+#
+# Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2019 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 the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This Makefile is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# A copy of the GNU General Public License is available at
+# <http://www.gnu.org/licenses/>.
+
+
+
+
+
+# Python enviroment
+# -----------------
+#
+# 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.
+export PYTHONPATH             := $(installdir)/lib/python/site-packages
+export PYTHONPATH2            := $(PYTHONPATH)
+export PYTHONPATH3            := $(PYTHONPATH)
+export _LMFILES_              :=
+export LOADEDMODULES          :=
+export MPI_PYTHON_SITEARCH    :=
+export MPI_PYTHON2_SITEARCH   :=
+export MPI_PYTHON3_SITEARCH   :=
+
+
+
+
+
+# Tarballs
+# --------
+#
+# All the necessary tarballs are defined and prepared with this rule.
+#
+# Note that we want the tarballs to follow the convention of NAME-VERSION
+# before the `tar.XX' prefix. For those programs that don't follow this
+# convention, but include the name/version in their tarball names with
+# 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         \
+                        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                 \
+                        cryptography-$(cryptography-version).tar.gz       \
+                        cycler-$(cycler-version).tar.gz                   \
+                        cython-$(cython-version).tar.gz                   \
+                        entrypoints-$(entrypoints-version).tar.gz         \
+                        h5py-$(h5py-version).tar.gz                       \
+                        html5lib-$(html5lib-version).tar.gz               \
+                        idna-$(idna-version).tar.gz                       \
+                        jeepney-$(jeepney-version).tar.gz                 \
+                        kiwisolver-$(kiwisolver-version).tar.gz           \
+                        keyring-$(keyring-version).tar.gz                 \
+                        libffi-$(libffi-version).tar.gz                   \
+                        matplotlib-$(matplotlib-version).tar.gz           \
+                        mpi4py-$(mpi4py-version).tar.gz                   \
+                        numpy-$(numpy-version).zip                        \
+                        pkgconfig-$(pypkgconfig-version).tar.gz           \
+                        pip-$(pip-version).tar.gz                         \
+                        pycparser-$(pycparser-version).tar.gz             \
+                        python-$(python-version).tar.gz                   \
+                        python-dateutil-$(python-dateutil-version).tar.gz \
+                        pyparsing-$(pyparsing-version).tar.gz             \
+                        requests-$(requests-version).tar.gz               \
+                        scipy-$(scipy-version).tar.gz                     \
+                        secretstorage-$(secretstorage-version).tar.gz     \
+                        setuptools-$(setuptools-version).zip              \
+                        setuptools_scm-$(setuptools_scm-version).tar.gz   \
+                        six-$(six-version).tar.gz                         \
+                        soupsieve-$(soupsieve-version).tar.gz             \
+                        urllib3-$(urllib3-version).tar.gz                 \
+                        webencodings-$(webencodings-version).tar.gz       \
+                        virtualenv-$(virtualenv-version).tar.gz           \
+                      , $(tdir)/$(t) )
+pytopurl=https://files.pythonhosted.org/packages
+$(pytarballs): $(tdir)/%:
+	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
+	  cp $(DEPENDENCIES-DIR)/$* $@
+	else
+
+          # Convenience variable
+          # --------------------
+          #
+          # `n' is just for convenience and to avoid having to repeat the
+          # package tarball name in the conditional to find its URL.
+          #
+          # For some packages (for example `python-dateutil', or those with
+          # a number or dash in their name), we need special consideration
+          # because the tokenization above will produce `python' as the
+          # first string.
+	  if [ $* = python-dateutil-$(python-dateutil-version).tar.gz ]; then
+	    n=dateutil
+	  elif [ $* = h5py-$(h5py-version).tar.gz ]; then
+	    n=h5py
+
+          # elif [ $* = strange-tarball5name-version.tar.gz ]; then
+          #  n=strange5-name
+	  else
+            # Remove all numbers, `-' and `.' from the tarball name so we can
+            # search more easily only with the program name.
+	    n=$$(echo $* | sed -e's/[0-9\-]/ /g' -e's/\./ /g'           \
+	              | awk '{print $$1}')
+	  fi
+
+          # Set the top download link of the requested tarball. The ones
+          # that have non-standard filenames (differing from our archived
+          # tarball names) are treated first, then the standard ones.
+	  mergenames=1
+	  if [ $$n = cython         ]; then
+	    mergenames=0
+	    hash=36/da/fcb979fc8cb486a67a013d6aefefbb95a3e19e67e49dff8a35e014046c5e
+	    h=$(pytopurl)/$$hash/Cython-$(cython-version).tar.gz
+	  elif [ $$n = python           ]; then
+	    mergenames=0
+	    h=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz
+	  elif [ $$n = libffi         ]; then
+	    mergenames=0
+	    h=ftp://sourceware.org/pub/libffi/libffi-$(libffi-version).tar.gz
+	  elif [ $$n = secretstorage  ]; then
+	    mergenames=0
+	    hash=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5
+	    h=$(pytopurl)/$$hash/SecretStorage-$(secretstorage-version).tar.gz
+	  elif [ $$n = asn            ]; then h=fc/f1/8db7daa71f414ddabfa056c4ef792e1461ff655c2ae2928a2b675bfed6b4
+	  elif [ $$n = astroquery     ]; then h=61/50/a7a08f9e54d7d9d97e69433cd88231e1ad2901811c9d1ae9ac7ccaef9396
+	  elif [ $$n = astropy        ]; then h=eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
+	  elif [ $$n = beautifulsoup  ]; then h=80/f2/f6aca7f1b209bb9a7ef069d68813b091c8c3620642b568dac4eb0e507748
+	  elif [ $$n = certifi        ]; then h=55/54/3ce77783acba5979ce16674fc98b1920d00b01d337cfaaf5db22543505ed
+	  elif [ $$n = cffi           ]; then h=64/7c/27367b38e6cc3e1f49f193deb761fe75cda9f95da37b67b422e62281fcac
+	  elif [ $$n = chardet        ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d
+	  elif [ $$n = cryptography   ]; then h=07/ca/bc827c5e55918ad223d59d299fff92f3563476c3b00d0a9157d9c0217449
+	  elif [ $$n = cycler         ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488
+	  elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c
+	  elif [ $$n = h5py           ]; then h=43/27/a6e7dcb8ae20a4dbf3725321058923fec262b6f7835179d78ccc8d98deec
+	  elif [ $$n = html           ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f
+	  elif [ $$n = idna           ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7
+	  elif [ $$n = jeepney        ]; then h=16/1d/74adf3b164a8d19a60d0fcf706a751ffa2a1eaa8e5bbb1b6705c92a05263
+	  elif [ $$n = keyring        ]; then h=15/88/c6ce9509438bc02d54cf214923cfba814412f90c31c95028af852b19f9b2
+	  elif [ $$n = kiwisolver     ]; then h=31/60/494fcce70d60a598c32ee00e71542e52e27c978e5f8219fae0d4ac6e2864
+	  elif [ $$n = matplotlib     ]; then h=89/0c/653aec68e9cfb775c4fbae8f71011206e5e7fe4d60fcf01ea1a9d3bc957f
+	  elif [ $$n = mpi            ]; then h=55/a2/c827b196070e161357b49287fa46d69f25641930fd5f854722319d431843
+	  elif [ $$n = numpy          ]; then h=cf/8d/6345b4f32b37945fedc1e027e83970005fc9c699068d2f566b82826515f2
+	  elif [ $$n = pip            ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af
+	  elif [ $$n = pkgconfig      ]; then h=6e/a9/ff67ef67217dfdf2aca847685fe789f82b931a6957a3deac861297585db6
+	  elif [ $$n = pycparser      ]; then h=68/9e/49196946aee219aead1290e00d1e7fdeab8567783e83e1b9ab5585e6206a
+	  elif [ $$n = pyparsing      ]; then h=b9/b8/6b32b3e84014148dcd60dd05795e35c2e7f4b72f918616c61fdce83d27fc
+	  elif [ $$n = dateutil       ]; then h=ad/99/5b2e99737edeb28c71bcbec5b5dda19d0d9ef3ca3e92e3e925e7c0bb364c
+	  elif [ $$n = requests       ]; then h=52/2c/514e4ac25da2b08ca5a464c50463682126385c4272c18193876e91f4bc38
+	  elif [ $$n = scipy          ]; then h=a9/b4/5598a706697d1e2929eaf7fe68898ef4bea76e4950b9efbe1ef396b8813a
+	  elif [ $$n = secretstorage  ]; then h=a6/89/df343dbc2957a317127e7ff2983230dc5336273be34f2e1911519d85aeb5
+	  elif [ $$n = setuptools     ]; then h=c2/f7/c7b501b783e5a74cf1768bc174ee4fb0a8a6ee5af6afa92274ff964703e0
+	  elif [ $$n = setuptools_scm ]; then h=54/85/514ba3ca2a022bddd68819f187ae826986051d130ec5b972076e4f58a9f3
+	  elif [ $$n = six            ]; then h=dd/bf/4138e7bfb757de47d1f4b6994648ec67a51efe58fa907c1e11e350cddfca
+	  elif [ $$n = soupsieve      ]; then h=0c/52/e9088bb9b96e2d39fc3b33fcda5b4fde9d71473536ac660a1ca9a0958a2f
+	  elif [ $$n = urllib         ]; then h=b1/53/37d82ab391393565f2f831b8eedbffd57db5a718216f82f1a8b4d381a1c1
+	  elif [ $$n = virtualenv     ]; then h=51/aa/c395a6e6eaaedfa5a04723b6446a1df783b16cca6fec66e671cede514688
+	  elif [ $$n = webencodings   ]; then h=0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47
+#	  elif [ $$n = strange5-name  ]; then h=XXXXX
+	  else
+	    echo; echo; echo;
+	    echo "'$$n' not recognized as a dependency name to download."
+	    echo; echo; echo;
+	    exit 1
+	  fi
+
+          # Download the requested tarball. Note that some packages may not
+          # follow our naming convention (where the package name is merged
+          # with its version number). In such cases, `w' will be the full
+          # address, not just the top directory address. But since we are
+          # storing all the tarballs in one directory, we want it to have
+          # the same naming convention, so we'll download it to a temporary
+          # name, then rename that.
+	  if [ $$mergenames = 1 ]; then  tarballurl=$(pytopurl)/$$h/"$*"
+	  else                           tarballurl=$$h
+	  fi
+
+          # Download using the script specially defined for this job.
+	  touch $(lockdir)/download
+	  downloader="wget --no-use-server-timestamps -O"
+	  $(downloadwrapper) "$$downloader" $(lockdir)/download \
+	                     $$tarballurl $@
+	fi
+
+
+
+
+
+# Necessary programs and libraries
+# --------------------------------
+#
+# While this Makefile is for Python programs, in some cases, we need
+# certain programs (like Python itself), or libraries for the modules.
+$(ilidir)/libffi: $(tdir)/libffi-$(libffi-version).tar.gz
+	$(call gbuild, $<, libffi-$(libffi-version))        \
+	echo "Libffi $(libffi-version)" > $@
+
+$(ibidir)/python3: $(tdir)/python-$(python-version).tar.gz \
+                   $(ilidir)/libffi
+        # On Mac systems, the build complains about `clang' specific
+        # features, so we can't use our own GCC build here.
+	if [ x$(on_mac_os) = xyes ]; then                   \
+	  export CC=clang;                                  \
+	  export CXX=clang++;                               \
+	fi;                                                 \
+	$(call gbuild, $<, Python-$(python-version),,       \
+	       --without-ensurepip                          \
+	       --with-system-ffi                            \
+	       --enable-shared)                             \
+	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
+	    {printf "%d.%d\n", $$1, $$2}')                  \
+	&& ln -s $(ildir)/python$$v $(ildir)/python         \
+	&& rm -rf $(ipydir)                                 \
+	&& mkdir $(ipydir)                                  \
+	&& echo "Python $(python-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).
+# 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).
+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                       \
+	   sed -e 's|@LIBDIR[@]|'"$(ildir)"'|'                    \
+	       -e 's|@INCDIR[@]|'"$(idir)/include"'|'             \
+	       $(4) > site.cfg;                                   \
+	 fi;                                                      \
+	 python3 setup.py build                                   \
+	 && python3 setup.py install                              \
+	 && cd ..                                                 \
+	 && rm -rf $(3)                                           \
+	 && echo "$(5)" > $@
+
+
+
+
+
+# Python modules
+# ---------------
+#
+# All the necessary Python modules go here.
+$(ipydir)/asn1crypto: $(tdir)/asn1crypto-$(asn1crypto-version).tar.gz \
+                      $(ipydir)/setuptools
+	$(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)/astropy                                \
+                      $(ipydir)/keyring                                \
+                      $(ipydir)/numpy
+	$(call pybuild, tar xf, $<, astroquery-$(astroquery-version), ,\
+	                Astroquery $(astroquery-version))
+
+$(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
+                   $(ipydir)/h5py                            \
+                   $(ipydir)/numpy                           \
+                   $(ipydir)/scipy
+	$(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), ,\
+	                BeautifulSoup $(beautifulsoup4-version))
+
+$(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \
+                   $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, certifi-$(certifi-version), ,\
+	                Certifi $(certifi-version))
+
+$(ipydir)/cffi: $(tdir)/cffi-$(cffi-version).tar.gz \
+                $(ilidir)/libffi                    \
+                $(ipydir)/pycparser
+	$(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), ,\
+	                Chardet $(chardet-version))
+
+$(ipydir)/cryptography: $(tdir)/cryptography-$(cryptography-version).tar.gz \
+                        $(ipydir)/asn1crypto                                \
+                        $(ipydir)/cffi
+	$(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), ,\
+	                Cycler $(cycler-version))
+
+$(ipydir)/cython: $(tdir)/cython-$(cython-version).tar.gz \
+                  $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, Cython-$(cython-version)) \
+	&& cp $(dtexdir)/cython.tex $(ictdir)/                \
+	&& echo "Cython $(cython-version) \citep{cython2011}" > $@
+
+$(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
+                       $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version), ,\
+	                EntryPoints $(entrypoints-version))
+
+$(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
+                $(ilidir)/hdf5                      \
+                $(ipydir)/cython                    \
+                $(ipydir)/pypkgconfig               \
+                $(ipydir)/setuptools
+                #$(ipydir)/mpi4py # AFTER its problem is fixed.
+	#export HDF5_MPI=ON;       # AFTER its problem is fixed.
+	export HDF5_DIR=$(ildir);                          \
+	$(call pybuild, tar xf, $<, h5py-$(h5py-version), ,\
+	                h5py $(h5py-version))
+
+$(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz  \
+                    $(ipydir)/six                                \
+                    $(ipydir)/webencodings
+	$(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), ,\
+	       idna $(idna-version))
+
+$(ipydir)/jeepney: $(tdir)/jeepney-$(jeepney-version).tar.gz \
+                   $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, jeepney-$(jeepney-version), ,\
+	                Jeepney $(jeepney-version))
+
+$(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz    \
+                   $(ipydir)/entrypoints                        \
+                   $(ipydir)/secretstorage                      \
+                   $(ipydir)/setuptools_scm
+	$(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), ,\
+	                Kiwisolver $(kiwisolver-version))
+
+$(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
+                      $(ipydir)/cycler                                  \
+                      $(ilidir)/freetype                                \
+                      $(ipydir)/kiwisolver                              \
+                      $(ipydir)/numpy                                   \
+                      $(ipydir)/pyparsing                               \
+                      $(ipydir)/python-dateutil
+	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version)) \
+	&& cp $(dtexdir)/matplotlib.tex $(ictdir)/                    \
+	&& echo "Matplotlib $(matplotlib-version) \citep{matplotlib2007}" > $@
+
+# Currently mpi4py doesn't build because of some conflict with OpenMPI:
+#
+#  In file included from src/mpi4py.MPI.c:591,
+#                  from src/MPI.c:4:
+#  src/mpi4py.MPI.c: In function '__pyx_f_6mpi4py_3MPI_del_Datatype':
+#  src/mpi4py.MPI.c:15094:36: error: expected expression before '_Static_assert'
+#  __pyx_t_1 = (((__pyx_v_ob[0]) == MPI_UB) != 0);
+#
+# But atleast on my system it fails.
+$(ipydir)/mpi4py: $(tdir)/mpi4py-$(mpi4py-version).tar.gz    \
+                  $(ipydir)/setuptools                       \
+                  $(ilidir)/openmpi
+	$(call pybuild, tar xf, $<, mpi4py-$(mpi4py-version)) \
+	&& cp $(dtexdir)/mpi4py.tex $(ictdir)/                \
+	&& echo "mpi4py $(mpi4py-version) \citep{mpi4py2011}" > $@
+
+$(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
+                 $(ipydir)/setuptools               \
+                 $(ilidir)/openblas                 \
+                 $(ilidir)/fftw                     \
+                 $(ibidir)/unzip
+	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,            \
+	                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), ,\
+	                PiP $(pip-version))
+
+$(ipydir)/pypkgconfig: $(tdir)/pkgconfig-$(pypkgconfig-version).tar.gz \
+                       $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, pkgconfig-$(pypkgconfig-version), ,
+	                pkgconfig $(pypkgconfig-version))
+
+$(ipydir)/pycparser: $(tdir)/pycparser-$(pycparser-version).tar.gz \
+                     $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, pycparser-$(pycparser-version), ,\
+	                pycparser $(pycparser-version))
+
+$(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \
+                     $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version), ,\
+	                PyParsing $(pyparsing-version))
+
+$(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz  \
+                           $(ipydir)/setuptools_scm                                   \
+                           $(ipydir)/six
+	$(call pybuild, tar xf, $<, python-dateutil-$(python-dateutil-version), ,\
+	                python-dateutil $(python-dateutil-version))
+
+$(ipydir)/requests: $(tdir)/requests-$(requests-version).tar.gz   \
+                    $(ipydir)/certifi                             \
+                    $(ipydir)/chardet                             \
+                    $(ipydir)/idna                                \
+                    $(ipydir)/numpy                               \
+                    $(ipydir)/urllib3
+	$(call pybuild, tar xf, $<, requests-$(requests-version), ,\
+	                Requests $(requests-version))
+
+$(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
+                 $(ipydir)/numpy
+	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)           \
+	&& cp $(dtexdir)/scipy.tex $(ictdir)/                                \
+	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@
+
+$(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
+                         $(ipydir)/cryptography                                \
+                         $(ipydir)/jeepney
+	$(call pybuild, tar xf, $<, SecretStorage-$(secretstorage-version), ,\
+	                SecretStorage $(secretstorage-version))
+
+$(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
+                      $(ibidir)/python3                            \
+                      $(ibidir)/unzip
+	$(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), ,\
+	                Setuptools-scm $(setuptools_scm-version))
+
+$(ipydir)/six: $(tdir)/six-$(six-version).tar.gz \
+               $(ipydir)/setuptools
+	$(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), ,\
+	                SoupSieve $(soupsieve-version))
+
+$(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \
+                   $(ipydir)/setuptools
+	$(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), ,\
+	                Webencodings $(webencodings-version))