Imported work on many basic Python modules

With the help of Raul, we were able to build many higher-level Python
packages to enable the installation of packages like Matplotlib and
Astroquery. With this commit, that work is being merged into the master
branch.

7 files changed, 493 insertions, 105 deletions

diff --git a/reproduce/src/bash/git-post-checkout b/reproduce/src/bash/git-post-checkout
index e2a0fd0..153b277 100644
--- a/reproduce/src/bash/git-post-checkout
+++ b/reproduce/src/bash/git-post-checkout
@@ -9,8 +9,13 @@
 # special characters for the installation location of meta-store so our own
 # installation is found by Git.
 
-# File containig the metadata.
+# File containig the metadata and metastore executable.
 MSFILE=".file-metadata"
+MSBIN=@BINDIR@/metastore
+
+# If metastore is not installed, then ignore this script (exit with a
+# status of 0).
+if [ ! -f $MSBIN ]; then exit 0; fi
 
 # Delete all temporary files
 find @TOP_PROJECT_DIR@/ -name "*~" -type f -delete
@@ -32,7 +37,7 @@ fi
 
 # Run metastore.
 exit_on_fail \
-       @BINDIR@/metastore -a -m -e -E -q -O @USER@ -G @GROUP@ -f "$MSFILE"
+       $MSBIN -a -m -e -E -q -O @USER@ -G @GROUP@ -f "$MSFILE"
 
 # Return with a success code (0).
 exit 0
diff --git a/reproduce/src/bash/git-pre-commit b/reproduce/src/bash/git-pre-commit
index ca28757..0fa6c52 100644
--- a/reproduce/src/bash/git-pre-commit
+++ b/reproduce/src/bash/git-pre-commit
@@ -20,8 +20,13 @@
 #     git reset HEAD -- .metadata
 #     git checkout HEAD -- .metadata
 
-# File containig the metadata.
+# File containig the metadata and metastore executable.
 MSFILE=".file-metadata"
+MSBIN=@BINDIR@/metastore
+
+# If metastore is not installed, then ignore this script (exit with a
+# status of 0).
+if [ ! -f $MSBIN ]; then exit 0; fi
 
 # Function to help in reporting a crash.
 exit_on_fail() {
@@ -34,12 +39,12 @@ exit_on_fail() {
 
 # Run metastore.
 exit_on_fail \
-	@BINDIR@/metastore -O @USER@ -G @GROUP@ -s -f "$MSFILE"
+	$MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
 
 # If it's first metastore commit, store again to include $MSFILE in $MSFILE.
 if ! git-ls-tree --name-only HEAD 2>/dev/null | grep -Fqx "$MSFILE"; then
 	exit_on_fail \
-	        @BINDIR@/metastore -O @USER@ -G @GROUP@ -s -f "$MSFILE"
+	        $MSBIN -O @USER@ -G @GROUP@ -s -f "$MSFILE"
 fi
 
 # Check if the metadata file exists.
diff --git a/reproduce/src/make/dependencies-basic.mk b/reproduce/src/make/dependencies-basic.mk
index 4f5362f..cb3a7f2 100644
--- a/reproduce/src/make/dependencies-basic.mk
+++ b/reproduce/src/make/dependencies-basic.mk
@@ -65,8 +65,7 @@ export CPPFLAGS          := -I$(idir)/include $(CPPFLAGS)
 export LD_LIBRARY_PATH   := $(ildir):$(LD_LIBRARY_PATH)
 
 # Define the programs that don't depend on any other.
-top-level-programs = low-level-links ls sed gawk grep diff find \
-                     wget which
+top-level-programs = low-level-links wget gcc
 all: $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 
 
@@ -141,7 +140,7 @@ $(tarballs): $(tdir)/%:
           elif [ $$n = diffutils ]; then w=http://ftpmirror.gnu.org/gnu/diffutils;\
           elif [ $$n = findutils ]; then w=http://akhlaghi.org/src;         \
           elif [ $$n = gawk      ]; then w=http://ftpmirror.gnu.org/gnu/gawk; \
-          elif [ $$n = gcc       ]; then w=http://ftpmirror.gnu.org/gcc/gcc-$(gcc-version); \
+          elif [ $$n = gcc       ]; then w=http://ftp.gnu.org/gnu/gcc/gcc-$(gcc-version); \
           elif [ $$n = gmp       ]; then w=https://gmplib.org/download/gmp; \
           elif [ $$n = grep      ]; then w=http://ftpmirror.gnu.org/gnu/grep; \
           elif [ $$n = gzip      ]; then w=http://ftpmirror.gnu.org/gnu/gzip; \
@@ -210,14 +209,14 @@ makelink = export PATH=$$(echo $(syspath)| tr : '\n' |grep -v ccache  \
 	   if [ x$$a != x ]; then ln -s $$a $(ibdir)/$(1); fi
 $(ibdir) $(ildir):; mkdir $@
 $(ibdir)/low-level-links: | $(ibdir) $(ildir)
+
         # The Assembler
 	$(call makelink,as)
 
-        # The compiler
+        # Compiler (Cmake needs the clang compiler which we aren't building
+        # yet in the pipeline).
 	$(call makelink,clang)
-	$(call makelink,gcc)
-	$(call makelink,g++)
-	$(call makelink,cc)
+	$(call makelink,clang++)
 
         # The linker
 	$(call makelink,ar)
@@ -227,7 +226,9 @@ $(ibdir)/low-level-links: | $(ibdir) $(ildir)
 	$(call makelink,ranlib)
 
         # Mac OS specific
+	$(call makelink,sysctl)
 	$(call makelink,sw_vers)
+	$(call makelink,dsymutil)
 	$(call makelink,install_name_tool)
 
         # On Mac OS, libtool is different compared to GNU Libtool. The
@@ -287,15 +288,34 @@ $(ibdir)/xz: $(tdir)/xz-$(xz-version).tar.gz
 	$(call gbuild, $<, xz-$(xz-version), static)
 
 $(ibdir)/bzip2: $(tdir)/bzip2-$(bzip2-version).tar.gz
-	 tdir=bzip2-$(bzip2-version);                                  \
-	 if [ $(static_build) = yes ]; then                            \
-	   makecommand="make LDFLAGS=-static";                         \
-	 else                                                          \
-	   makecommand="make";                                         \
-	 fi;                                                           \
-	 cd $(ddir) && rm -rf $$tdir && tar xf $< && cd $$tdir &&      \
-	 $$makecommand && make install PREFIX=$(idir) &&               \
-	 cd .. && rm -rf $$tdir
+        # Bzip2 doesn't have a `./configure' script, and its Makefile
+        # doesn't build a shared library. So we can't use the `gbuild'
+        # function here and we need to take some extra steps (inspired
+        # from the "Linux from Scratch" guide for Bzip2):
+        #   1) The `sed' call is for relative installed symbolic links.
+        #   2) The special Makefile-libbz2_so builds the shared library.
+        #
+        # NOTE: the major version number appears in the final symbolic
+        # link.
+	tdir=bzip2-$(bzip2-version);                                  \
+	if [ $(static_build) = yes ]; then                            \
+	  makecommand="make LDFLAGS=-static";                         \
+	  makeshared="echo no-shared";                                \
+	else                                                          \
+	  makecommand="make";                                         \
+	  makeshared="make -f Makefile-libbz2_so";                    \
+	fi;                                                           \
+	cd $(ddir) && rm -rf $$tdir && tar xf $< && cd $$tdir         \
+	&& sed -i 's@\(ln -s -f \)$$(PREFIX)/bin/@\1@' Makefile       \
+	&& $$makeshared                                               \
+	&& cp -a libbz2* $(ildir)/                                    \
+	&& make clean                                                 \
+	&& $$makecommand                                              \
+	&& make install PREFIX=$(idir)                                \
+	&& cd ..                                                      \
+	&& rm -rf $$tdir                                              \
+	&& cd $(ildir)                                                \
+	&& ln -fs libbz2.so.1.0 libbz2.so
 
 # GNU Tar: When built statically, tar gives a segmentation fault on
 # unpacking Bash. So we'll build it dynamically.
@@ -698,6 +718,9 @@ $(ibdir)/ld: $(tdir)/binutils-$(binutils-version).tar.lz
 # We want to build GCC after building all the basic tools that are often
 # used in a configure script to enable GCC's configure script to work as
 # smoothly/robustly as possible.
+#
+# Including Objective C and Objective C++ is necessary for installing
+# `matplotlib'.
 $(ibdir)/gcc: $(tdir)/gcc-$(gcc-version).tar.xz \
               $(ibdir)/ls                       \
               $(ibdir)/sed                      \
@@ -710,38 +733,39 @@ $(ibdir)/gcc: $(tdir)/gcc-$(gcc-version).tar.xz \
               $(ibdir)/bash                     \
               $(ibdir)/which
 
+        # Clean up (possibly existing) gcc installation
+	rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*
+	rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc* \
+		   $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*
+
         # Un-pack all the necessary tools in the top building directory
-	cd $(ddir);                                                     \
-	rm -rf gcc-build gcc-$(gcc-version);                            \
-	tar xf $< &&                                                    \
-	mkdir $(ddir)/gcc-build &&                                      \
-	cd $(ddir)/gcc-build &&                                         \
-	../gcc-$(gcc-version)/configure SHELL=$(ibdir)/bash             \
-	                                --prefix=$(idir)                \
-	                                --with-mpc=$(idir)              \
-	                                --with-mpfr=$(idir)             \
-	                                --with-gmp=$(idir)              \
-	                                --with-isl=$(idir)              \
-	                                --with-build-time-tools=$(idir) \
-	                                --enable-shared                 \
-	                                --disable-multilib              \
-	                                --disable-multiarch             \
-	                                --enable-threads=posix          \
-	                                --enable-libmpx                 \
-	                                --with-local-prefix=$(idir)     \
-	                                --enable-linker-build-id        \
-	                                --with-gnu-as                   \
-	                                --with-gnu-ld                   \
-	                                --enable-lto                    \
-	                                --with-linker-hash-style=gnu    \
-	                                --enable-languages=c,c++,fortran\
-	                                --disable-libada                \
-	                                --disable-nls                   \
-	                                --enable-default-pie            \
-	                                --enable-default-ssp            \
-	                                --enable-cet=auto               \
-	                                --enable-decimal-float &&       \
-	make SHELL=$(ibdir)/bash -j$$(nproc) &&                         \
-	make SHELL=$(ibdir)/bash install &&                             \
-	cd .. &&                                                        \
+	cd $(ddir);                                                        \
+	rm -rf gcc-build gcc-$(gcc-version);                               \
+	tar xf $< &&                                                       \
+	mkdir $(ddir)/gcc-build &&                                         \
+	cd $(ddir)/gcc-build &&                                            \
+	../gcc-$(gcc-version)/configure SHELL=$(ibdir)/bash                \
+	                                --prefix=$(idir)                   \
+	                                --with-mpc=$(idir)                 \
+	                                --with-mpfr=$(idir)                \
+	                                --with-gmp=$(idir)                 \
+	                                --with-isl=$(idir)                 \
+	                                --with-build-time-tools=$(idir)    \
+	                                --enable-shared                    \
+	                                --disable-multilib                 \
+	                                --disable-multiarch                \
+	                                --enable-threads=posix             \
+	                                --with-local-prefix=$(idir)        \
+	                                --enable-linker-build-id           \
+	                                --enable-lto                       \
+	                                --enable-languages=c,c++,fortran,objc,obj-c++ \
+	                                --disable-libada                   \
+	                                --disable-nls                      \
+	                                --enable-default-pie               \
+	                                --enable-default-ssp               \
+	                                --enable-cet=auto                  \
+	                                --enable-decimal-float &&          \
+	make SHELL=$(ibdir)/bash -j$$(nproc) &&                            \
+	make SHELL=$(ibdir)/bash install &&                                \
+	cd .. &&                                                           \
 	rm -rf gcc-build gcc-$(gcc-version)
diff --git a/reproduce/src/make/dependencies-build-rules.mk b/reproduce/src/make/dependencies-build-rules.mk
index 2247518..5216488 100644
--- a/reproduce/src/make/dependencies-build-rules.mk
+++ b/reproduce/src/make/dependencies-build-rules.mk
@@ -102,23 +102,6 @@ gbuild = if [ x$(static_build) = xyes ] && [ "x$(3)" = xstatic ]; then        \
 
 
 
-
-# Python
-# ------
-#
-# To build Python packages with direct access to a `setup.py' (if no direct
-# access to `setup.py' is needed, pip can be used)
-pybuild = cd $(ddir); rm -rf $(2);                                        \
-	 if ! tar xf $(1); then echo; echo "Tar error"; exit 1; fi;           \
-	 cd $(2);                                                             \
-	 python3 setup.py build &&                                            \
-	 python3 setup.py install &&                                          \
-	 cd .. && rm -rf $(2)
-
-
-
-
-
 # CMake
 # -----
 #
diff --git a/reproduce/src/make/dependencies-python.mk b/reproduce/src/make/dependencies-python.mk
new file mode 100644
index 0000000..1e4f611
--- /dev/null
+++ b/reproduce/src/make/dependencies-python.mk
@@ -0,0 +1,365 @@
+# Build the reproduction pipeline Python dependencies.
+#
+# ------------------------------------------------------------------------
+#                      !!!!! IMPORTANT NOTES !!!!!
+#
+# This Makefile will be run by the initial `./configure' script. It is not
+# included into the reproduction pipe after that.
+#
+# ------------------------------------------------------------------------
+#
+# Original author:
+#     Raul Infante-Sainz <infantesainz@gmail.com>
+# Contributing author(s):
+#     Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019, Your Name.
+#
+# 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/>.
+
+
+
+# Top level environment
+include reproduce/config/pipeline/LOCAL.mk
+include reproduce/src/make/dependencies-build-rules.mk
+include reproduce/config/pipeline/dependency-versions.mk
+
+ddir   = $(BDIR)/dependencies
+tdir   = $(BDIR)/dependencies/tarballs
+idir   = $(BDIR)/dependencies/installed
+ibdir  = $(BDIR)/dependencies/installed/bin
+ildir  = $(BDIR)/dependencies/installed/lib
+ilidir = $(BDIR)/dependencies/installed/lib/built
+ipydir = $(BDIR)/dependencies/installed/lib/built/python
+
+# Define the top-level programs to build (installed in `.local/bin').
+top-level-python   = astroquery matplotlib #scipy
+all: $(foreach p, $(top-level-python), $(ipydir)/$(p))
+
+# Other basic environment settings: We are only including the host
+# operating system's PATH environment variable (after our own!) for the
+# compiler and linker. For the library binaries and headers, we are only
+# using our internally built libraries.
+#
+# To investigate:
+#
+#    1) Set SHELL to `$(ibdir)/env - NAME=VALUE $(ibdir)/bash' and set all
+#       the parameters defined bellow as `NAME=VALUE' statements before
+#       calling Bash. This will enable us to completely ignore the user's
+#       native environment.
+#
+#    2) Add `--noprofile --norc' to `.SHELLFLAGS' so doesn't load the
+#       user's environment.
+.ONESHELL:
+.SHELLFLAGS              := --noprofile --norc -ec
+export CCACHE_DISABLE    := 1
+export PATH              := $(ibdir)
+export LD_RUN_PATH       := $(ildir)
+export LD_LIBRARY_PATH   := $(ildir)
+export SHELL             := $(ibdir)/bash
+export CPPFLAGS          := -I$(idir)/include
+export PKG_CONFIG_PATH   := $(ildir)/pkgconfig
+export PKG_CONFIG_LIBDIR := $(ildir)/pkgconfig
+export LDFLAGS           := $(rpath_command) -L$(ildir)
+
+
+
+
+
+# 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.
+tarballs = $(foreach t, astroquery-$(astroquery-version).tar.gz           \
+                        astropy-$(astropy-version).tar.gz                 \
+                        beautifulsoup4-$(beautifulsoup4-version).tar.gz   \
+                        certifi-$(certifi-version).tar.gz                 \
+                        chardet-$(chardet-version).tar.gz                 \
+                        cycler-$(cycler-version).tar.gz                   \
+                        entrypoints-$(entrypoints-version).tar.gz         \
+                        html5lib-$(html5lib-version).tar.gz               \
+                        idna-$(idna-version).tar.gz                       \
+                        kiwisolver-$(kiwisolver-version).tar.gz           \
+                        keyring-$(keyring-version).tar.gz                 \
+                        matplotlib-$(matplotlib-version).tar.gz           \
+                        numpy-$(numpy-version).zip                        \
+                        pip-$(pip-version).tar.gz                         \
+                        python-$(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                     \
+                        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) )
+topurl=https://files.pythonhosted.org/packages
+$(tarballs): $(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 [ $* = 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.
+	  mergenames=1
+	  if [ $$n = python           ]; then
+	    mergenames=0
+	    h=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz
+	  elif [ $$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 = chardet        ]; then h=fc/bb/a5768c230f9ddb03acc9ef3f0d4a3cf93462473795d18e9535498c8f929d
+	  elif [ $$n = cycler         ]; then h=c2/4b/137dea450d6e1e3d474e1d873cd1d4f7d3beed7e0dc973b06e8e10d32488
+	  elif [ $$n = entrypoints    ]; then h=b4/ef/063484f1f9ba3081e920ec9972c96664e2edb9fdc3d8669b0e3b8fc0ad7c
+	  elif [ $$n = html           ]; then h=85/3e/cf449cf1b5004e87510b9368e7a5f1acd8831c2d6691edd3c62a0823f98f
+	  elif [ $$n = idna           ]; then h=ad/13/eb56951b6f7950cadb579ca166e448ba77f9d24efc03edd7e55fa57d04b7
+	  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 = numpy          ]; then h=2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c
+	  elif [ $$n = pip            ]; then h=4c/4d/88bc9413da11702cbbace3ccc51350ae099bb351febae8acc85fec34f9af
+	  elif [ $$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 = 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 [ $$mergenames = 1 ]; then  tarballurl=$(topurl)/$$h/"$*"
+	  else                           tarballurl=$$h
+	  fi
+
+          # If the download fails, Wget will write the error message in the
+          # target file, so Make will think that its done! To avoid this
+          # problem, we'll rename the output.
+	  echo "Downloading $$tarballurl"
+	  if ! wget --no-use-server-timestamps -O$@ $$tarballurl; then
+	     rm -f $@
+	     echo; echo "DOWNLOAD FAILED: $$tarballurl"; echo; exit 1
+	  fi
+	fi
+
+
+
+
+
+# Install without pip
+# --------------------
+#
+# 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
+pybuild = cd $(ddir); rm -rf $(3);                                        \
+	 if ! $(1) $(2); then echo; echo "Tar error"; exit 1; fi;             \
+	 cd $(3);                                                             \
+	 python3 setup.py build &&                                            \
+	 python3 setup.py install &&                                          \
+	 cd .. && rm -rf $(3) &&                                              \
+	 echo "done!" > $@
+
+
+
+
+
+# Python installation
+# -------------------
+#
+$(ibdir)/python3: $(tdir)/python-$(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))        \
+	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
+	    {printf "%d.%d\n", $$1, $$2}')                  \
+	&& ln -s $(ildir)/python$$v $(ildir)/python         \
+	&& rm -rf $(ipydir) && mkdir $(ipydir)
+
+
+
+
+# Python packages
+# ---------------
+#
+$(ipydir)/astroquery: $(tdir)/astroquery-$(astroquery-version).tar.gz  \
+                      $(ipydir)/astropy                                \
+                      $(ipydir)/beautifulsoup4                         \
+                      $(ipydir)/html5lib                               \
+                      $(ipydir)/keyring                                \
+                      $(ipydir)/numpy                                  \
+                      $(ipydir)/requests
+	$(call pybuild, tar xf, $<, astroquery-$(astroquery-version))
+
+$(ipydir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
+                   $(ipydir)/numpy
+	$(call pybuild, tar xf, $<, astropy-$(astropy-version))
+
+$(ipydir)/beautifulsoup4: $(tdir)/beautifulsoup4-$(beautifulsoup4-version).tar.gz \
+                          $(ipydir)/soupsieve
+	$(call pybuild, tar xf, $<, beautifulsoup4-$(beautifulsoup4-version))
+
+$(ipydir)/certifi: $(tdir)/certifi-$(certifi-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, certifi-$(certifi-version))
+
+$(ipydir)/chardet: $(tdir)/chardet-$(chardet-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, chardet-$(chardet-version))
+
+$(ipydir)/cycler: $(tdir)/cycler-$(cycler-version).tar.gz \
+                   $(ipydir)/six
+	$(call pybuild, tar xf, $<, cycler-$(cycler-version))
+
+$(ipydir)/entrypoints: $(tdir)/entrypoints-$(entrypoints-version).tar.gz \
+                       $(ibdir)/python3
+	$(call pybuild, tar xf, $<, entrypoints-$(entrypoints-version))
+
+$(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz  \
+                    $(ipydir)/six                                \
+                    $(ipydir)/webencodings
+	$(call pybuild, tar xf, $<, html5lib-$(html5lib-version))
+
+$(ipydir)/idna: $(tdir)/idna-$(idna-version).tar.gz \
+                $(ibdir)/python3
+	$(call pybuild, tar xf, $<, idna-$(idna-version))
+
+$(ipydir)/keyring: $(tdir)/keyring-$(keyring-version).tar.gz    \
+                   $(ipydir)/entrypoints                        \
+                   $(ipydir)/setuptools_scm
+	$(call pybuild, tar xf, $<, keyring-$(keyring-version))
+
+$(ipydir)/kiwisolver: $(tdir)/kiwisolver-$(kiwisolver-version).tar.gz    \
+                   $(ipydir)/setuptools
+	$(call pybuild, tar xf, $<, kiwisolver-$(kiwisolver-version))
+
+
+$(ipydir)/matplotlib: $(tdir)/matplotlib-$(matplotlib-version).tar.gz   \
+                      $(ipydir)/cycler                                  \
+                      $(ilidir)/freetype                                \
+                      $(ipydir)/numpy                                   \
+                      $(ipydir)/pyparsing                               \
+                      $(ipydir)/python-dateutil                         \
+                      $(ipydir)/kiwisolver
+	$(call pybuild, tar xf, $<, matplotlib-$(matplotlib-version))
+
+$(ipydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
+                 $(ibdir)/python3
+	export BLAS=None; \
+	export ATLAS=None; \
+	export LAPACK=None; \
+	$(call pybuild, unzip, $<, numpy-$(numpy-version))
+
+$(ibdir)/pip3: $(tdir)/pip-$(pip-version).tar.gz \
+               $(ibdir)/python3
+	$(call pybuild, tar xf, $<, pip-$(pip-version))
+
+$(ipydir)/pyparsing: $(tdir)/pyparsing-$(pyparsing-version).tar.gz \
+                     $(ibdir)/python3
+	$(call pybuild, tar xf, $<, pyparsing-$(pyparsing-version))
+
+$(ipydir)/python-dateutil: $(tdir)/python-dateutil-$(python-dateutil-version).tar.gz  \
+                           $(ipydir)/six
+	$(call pybuild, tar xf, $<, python-dateutil-$(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))
+
+$(ipydir)/scipy: $(tdir)/scipy-$(scipy-version).tar.gz \
+                 $(ipydir)/numpy
+	$(call pybuild, tar xf, $<, scipy-$(scipy-version))
+
+$(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
+                      $(ibdir)/python3
+	$(call pybuild, unzip, $<, setuptools-$(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)/six: $(tdir)/six-$(six-version).tar.gz \
+               $(ibdir)/python3
+	$(call pybuild, tar xf, $<, six-$(six-version))
+
+$(ipydir)/soupsieve: $(tdir)/soupsieve-$(soupsieve-version).tar.gz \
+                     $(ibdir)/python3
+	$(call pybuild, tar xf, $<, soupsieve-$(soupsieve-version))
+
+$(ipydir)/urllib3: $(tdir)/urllib3-$(urllib3-version).tar.gz \
+                   $(ibdir)/python3
+	$(call pybuild, tar xf, $<, urllib3-$(urllib3-version))
+
+$(ipydir)/webencodings: $(tdir)/webencodings-$(webencodings-version).tar.gz \
+                        $(ibdir)/python3
+	$(call pybuild, tar xf, $<, webencodings-$(webencodings-version))
+
diff --git a/reproduce/src/make/dependencies.mk b/reproduce/src/make/dependencies.mk
index 92febb1..deb9f39 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -43,11 +43,11 @@ ildir  = $(BDIR)/dependencies/installed/lib
 ilidir = $(BDIR)/dependencies/installed/lib/built
 
 # Define the top-level programs to build (installed in `.local/bin').
-top-level-python   = astropy
-top-level-programs = astnoisechisel metastore flock unzip zip
+top-level-programs  = astnoisechisel flock metastore unzip zip
+top-level-libraries = freetype
 all: $(ddir)/texlive-versions.tex                       \
-     $(foreach p, $(top-level-python),   $(ilidir)/$(p)) \
-     $(foreach p, $(top-level-programs), $(ibdir)/$(p))
+     $(foreach p, $(top-level-programs), $(ibdir)/$(p)) \
+     $(foreach p, $(top-level-libraries), $(ilidir)/$(p))
 
 # Other basic environment settings: We are only including the host
 # operating system's PATH environment variable (after our own!) for the
@@ -89,11 +89,11 @@ export LDFLAGS           := $(rpath_command) -L$(ildir)
 # 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.
-tarballs = $(foreach t, astropy-$(astropy-version).tar.gz                  \
-                        cfitsio-$(cfitsio-version).tar.gz                  \
+tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
                         cmake-$(cmake-version).tar.gz                      \
                         curl-$(curl-version).tar.gz                        \
                         flock-$(flock-version).tar.xz                      \
+                        freetype-$(freetype-version).tar.gz                \
                         ghostscript-$(ghostscript-version).tar.gz          \
                         git-$(git-version).tar.xz                          \
                         gnuastro-$(gnuastro-version).tar.lz                \
@@ -101,11 +101,10 @@ tarballs = $(foreach t, astropy-$(astropy-version).tar.gz                  \
                         install-tl-unx.tar.gz                              \
                         jpegsrc.$(libjpeg-version).tar.gz                  \
                         libbsd-$(libbsd-version).tar.xz                    \
+                        libpng-$(libpng-version).tar.xz                    \
                         libtool-$(libtool-version).tar.xz                  \
                         libgit2-$(libgit2-version).tar.gz                  \
                         metastore-$(metastore-version).tar.gz              \
-                        numpy-$(numpy-version).zip                         \
-                        python-$(python-version).tar.gz                    \
                         unzip-$(unzip-version).tar.gz                      \
                         tiff-$(libtiff-version).tar.gz                     \
                         wcslib-$(wcslib-version).tar.bz2                   \
@@ -122,8 +121,7 @@ $(tarballs): $(tdir)/%:
 
           # Set the top download link of the requested tarball.
 	  mergenames=1
-	  if   [ $$n = astropy     ]; then w=https://files.pythonhosted.org/packages/eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
-	  elif [ $$n = cfitsio     ]; then
+	  if [ $$n = cfitsio     ]; then
 	    mergenames=0
 	    v=$$(echo $(cfitsio-version) | sed -e's/\.//'             \
 	              | awk '{l=length($$1);                          \
@@ -135,6 +133,7 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = cmake       ]; then w=https://cmake.org/files/v3.12
 	  elif [ $$n = curl        ]; then w=https://curl.haxx.se/download
 	  elif [ $$n = flock       ]; then w=https://github.com/discoteq/flock/releases/download/v$(flock-version)
+	  elif [ $$n = freetype    ]; then w=https://download.savannah.gnu.org/releases/freetype
 	  elif [ $$n = ghostscript ]; then w=https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs926
 	  elif [ $$n = git         ]; then w=http://mirrors.edge.kernel.org/pub/software/scm/git
 	  elif [ $$n = gnuastro    ]; then w=http://ftpmirror.gnu.org/gnu/gnuastro
@@ -142,15 +141,12 @@ $(tarballs): $(tdir)/%:
 	  elif [ $$n = install     ]; then w=http://mirror.ctan.org/systems/texlive/tlnet
 	  elif [ $$n = jpegsrc     ]; then w=http://ijg.org/files
 	  elif [ $$n = libbsd      ]; then w=http://libbsd.freedesktop.org/releases
+	  elif [ $$n = libpng      ]; then w=https://download.sourceforge.net/libpng
 	  elif [ $$n = libtool     ]; then w=http://ftpmirror.gnu.org/gnu/libtool
 	  elif [ $$n = libgit      ]; then
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	  elif [ $$n = metastore   ]; then w=http://akhlaghi.org/src
-	  elif [ $$n = numpy       ]; then w=https://files.pythonhosted.org/packages/2b/26/07472b0de91851b6656cbc86e2f0d5d3a3128e7580f23295ef58b6862d6c
-	  elif [ $$n = python      ]; then
-	    mergenames=0
-	    w=https://www.python.org/ftp/python/$(python-version)/Python-$(python-version).tgz
 	  elif [ $$n = tiff        ]; then w=https://download.osgeo.org/libtiff
 	  elif [ $$n = unzip       ]; then w=ftp://ftp.info-zip.org/pub/infozip/src
 	    mergenames=0; v=$$(echo $(unzip-version) | sed -e's/\.//')
@@ -232,6 +228,12 @@ $(ilidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz
 	$(call gbuild, $<, gsl-$(gsl-version), static) \
 	&& echo "GNU Scientific Library is built" > $@
 
+# Freetype is necessary to install matplotlib
+$(ilidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \
+	                $(ilidir)/libpng
+	$(call gbuild, $<, freetype-$(freetype-version), static) \
+	&& echo "freetype is built" > $@
+
 $(ilidir)/libbsd: $(tdir)/libbsd-$(libbsd-version).tar.xz
 	$(call gbuild, $<, libbsd-$(libbsd-version), static,,V=1) \
 	&& echo "libbsd is built" > $@
@@ -239,6 +241,10 @@ $(ilidir)/libbsd: $(tdir)/libbsd-$(libbsd-version).tar.xz
 $(ilidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
 	$(call gbuild, $<, jpeg-9b, static) && echo "Libjpeg is built" > $@
 
+$(ilidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz
+	$(call gbuild, $<, libpng-$(libpng-version), static) \
+	&& echo "Libpng is built" > $@
+
 $(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
                    $(ilidir)/libjpeg
 	$(call gbuild, $<, tiff-$(libtiff-version), static, \
@@ -314,6 +320,13 @@ $(ibdir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz \
         # After searching in `bootstrap', I couldn't find `LIBS', only
         # `LDFLAGS'. So the extra libraries are being added to `LDFLAGS',
         # not `LIBS'.
+        #
+        # 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;                                                        \
 	cd $(ddir) && rm -rf cmake-$(cmake-version) &&             \
 	tar xf $< && cd cmake-$(cmake-version) &&                  \
 	./bootstrap --prefix=$(idir) --system-curl --system-zlib   \
@@ -456,12 +469,6 @@ endif
 	               $$staticopts, -j$(numthreads),                \
 	               make check -j$(numthreads))
 
-$(ibdir)/python3: $(tdir)/python-$(python-version).tar.gz
-	$(call gbuild, $<, Python-$(python-version))        \
-	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
-            {printf "%d.%d\n", $$1, $$2}')              \
-    && ln -s $(ildir)/python$$v $(ildir)/python
-
 $(ibdir)/unzip: $(tdir)/unzip-$(unzip-version).tar.gz
 	v=$$(echo $(unzip-version) | sed -e's/\.//')
 	$(call gbuild, $<, unzip$$v, static,,          \
@@ -482,20 +489,6 @@ $(ibdir)/zip: $(tdir)/zip-$(zip-version).tar.gz
 
 
 
-# Python packages
-# ---------------
-$(ilidir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
-                 $(ibdir)/python3
-	pip3 install $< --verbose && echo "numpy is built" > $@
-
-$(ilidir)/astropy: $(tdir)/astropy-$(astropy-version).tar.gz \
-                   $(ilidir)/numpy
-	pip3 install $< --verbose && echo "astropy is built" > $@
-
-
-
-
-
 # Since we want to avoid complicating the PATH, we are putting a symbolic
 # link of all the TeX Live executables in $(ibdir). But symbolic links are
 # hard to track for Make (as a target). Also, TeX in general is optional
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 71cdbb8..638338b 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -116,6 +116,19 @@ export LDFLAGS         := -L$(installdir)/lib
 export SHELL           := $(installdir)/bin/bash
 export CPPFLAGS        := -I$(installdir)/include
 
+# Python enviroment
+# So far we have found several other Python-related environment
+# variables which might interfere. So we are just removing all
+# of their values within the pipeline.
+export PYTHONPATH             := $(installdir)/lib/python/site-packages
+export PYTHONPATH3            := $(PYTHONPATH)
+export _LMFILES_              :=
+export PYTHONPATH2            :=
+export LOADEDMODULES          :=
+export MPI_PYTHON_SITEARCH    :=
+export MPI_PYTHON2_SITEARCH   :=
+export MPI_PYTHON3_SITEARCH   :=
+