Imported recent work on several astronomy packages

With this commit, Raul's work on the installation of several astronomy
software is implemented in the main template.

10 files changed, 286 insertions, 30 deletions

diff --git a/configure b/configure
index 2fa80ea..55ce4dc 100755
--- a/configure
+++ b/configure
@@ -1106,7 +1106,7 @@ hasentry=0
 bibfiles="$ictdir/*"
 for f in $bibfiles; do if [ -f $f ]; then hasentry=1; break; fi; done;
 
-# Make sure we start with an empty file.
+# Make sure we start with an empty output file.
 pkgbib=$mtexdir/dependencies-bib.tex
 echo "" > $pkgbib
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 5378ee3..549b7c0 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -90,7 +90,7 @@ $(mtexdir)/project.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s)
 # recipe and the `paper.pdf' recipe. But if `tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
-$(texbdir)/paper.bbl: tex/src/references.tex                         \
+$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
                       | $(tikzdir) $(texbdir) $(mtexdir)/project.tex
         # If `$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
diff --git a/reproduce/software/bibtex/astrometrynet.tex b/reproduce/software/bibtex/astrometrynet.tex
new file mode 100644
index 0000000..8bbaceb
--- /dev/null
+++ b/reproduce/software/bibtex/astrometrynet.tex
@@ -0,0 +1,20 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{astrometrynet,
+	doi = {10.1088/0004-6256/139/5/1782},
+	url = {https://doi.org/10.1088%2F0004-6256%2F139%2F5%2F1782},
+	year = 2010,
+	month = {mar},
+	publisher = {{IOP} Publishing},
+	volume = {139},
+	number = {5},
+	pages = {1782},
+	author = {Dustin Lang and David W. Hogg and Keir Mierle and Michael Blanton and Sam Roweis},
+	title = {{ASTROMETRY}.{NET}: {BLIND} {ASTROMETRIC} {CALIBRATION} {OF} {ARBITRARY} {ASTRONOMICAL} {IMAGES}},
+	journal = {AJ}
+}
diff --git a/reproduce/software/bibtex/scamp.tex b/reproduce/software/bibtex/scamp.tex
new file mode 100644
index 0000000..8d825d7
--- /dev/null
+++ b/reproduce/software/bibtex/scamp.tex
@@ -0,0 +1,18 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{scamp,
+   author = {{Bertin}, E.},
+    title = "{Automatic Astrometric and Photometric Calibration with SCAMP}",
+     year = 2006,
+   journal= {ASPConf},
+   volume = 351,
+    month = jul,
+    pages = {112},
+   adsurl = {http://cdsads.u-strasbg.fr/abs/2006ASPC..351..112B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff --git a/reproduce/software/bibtex/sextractor.tex b/reproduce/software/bibtex/sextractor.tex
new file mode 100644
index 0000000..90d3eff
--- /dev/null
+++ b/reproduce/software/bibtex/sextractor.tex
@@ -0,0 +1,18 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@article{sextractor,
+    author = {{Bertin, E.} and {Arnouts, S.}},
+    title = {SExtractor: Software for source extraction},
+    DOI= "10.1051/aas:1996164",
+    url= "https://doi.org/10.1051/aas:1996164",
+    journal = {AASS},
+    year = 1996,
+    volume = 117,
+    number = 2,
+    pages = "393",
+}
diff --git a/reproduce/software/bibtex/swarp.tex b/reproduce/software/bibtex/swarp.tex
new file mode 100644
index 0000000..3ff9b91
--- /dev/null
+++ b/reproduce/software/bibtex/swarp.tex
@@ -0,0 +1,18 @@
+%% Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
+%%
+%% Copying and distribution of this file, with or without modification,
+%% are permitted in any medium without royalty provided the copyright
+%% notice and this notice are preserved.  This file is offered as-is,
+%% without any warranty.
+
+@ARTICLE{swarp,
+   author = {{Bertin}, E. and {Mellier}, Y. and {Radovich}, M. and {Missonnier}, G. and
+    {Didelon}, P. and {Morin}, B.},
+  journal = {ASPConf},
+    title = "{The TERAPIX Pipeline}",
+     year = {2002},
+   volume = {281},
+    pages = {228},
+   adsurl = {http://adsabs.harvard.edu/abs/2002ASPC..281..228B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk
index 149f9ae..5761165 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.mk
@@ -17,9 +17,12 @@
 # <http://www.gnu.org/licenses/>.
 
 # C/C++ programs and libraries.
+astrometrynet-version      = 0.77
 atlas-version              = 3.10.3
 bash-version               = 5.0
 binutils-version           = 2.31.1
+cairo-version              = 1.16.0
+cdsclient-version          = 3.84
 cfitsio-version            = 3.45
 cmake-version              = 3.14.2
 coreutils-version          = 8.31
@@ -44,9 +47,9 @@ isl-version                = 0.18
 libbsd-version             = 0.9.1
 libffi-version             = 3.2.1
 libjpeg-version            = v9b
-libpng-version             = 1.6.36
 libtiff-version            = 4.0.10
 libtool-version            = 2.4.6
+libxml2-version            = 2.9.9
 lzip-version               = 1.20
 m4-version                 = 1.4.18
 make-version               = 4.2.90
@@ -54,14 +57,20 @@ metastore-version          = 1.1.2-23-fa9170b
 mpfr-version               = 4.0.2
 mpc-version                = 1.1.0
 ncurses-version            = 6.1
+netpbm-version             = 10.47.72
 openblas-version           = 0.3.5
 openmpi-version            = 4.0.1
 openssl-version            = 1.1.1a
 patchelf-version           = 0.9
+pixman-version             = 0.38.0
 pkgconfig-version          = 0.29.2
 python-version             = 3.7.3
 readline-version           = 8.0
+scamp-version              = 2.6.7
 sed-version                = 4.7
+sextractor-version         = 2.25.0
+swarp-version              = 2.38.0
+swig-version               = 3.0.12
 tar-version                = 1.32
 unzip-version              = 6.0
 wget-version               = 1.20.3
@@ -75,10 +84,12 @@ zlib-version               = 1.2.11
 #
 # When updating the version of these libraries, please look into the build
 # rule first: In one way or another, the version string becomes necessary
-# during their build and must be accounted for.
+# during their build and must be accounted for. In particular:
+#  `libpng' is downgraded because `netpbm' requires `libpng' version < 1.5
 bzip2-version              = 1.0.6
 lapack-version             = 3.8.0
 libgit2-version            = 0.26.0
+libpng-version             = 1.4.22
 wcslib-version             = 6.2
 
 # Python packages
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index cfa05d2..6e6550e 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -830,6 +830,7 @@ ifeq ($(host_cc),1)
 gcc-prerequisites =
 else
 gcc-prerequisites = $(tdir)/gcc-$(gcc-version).tar.xz \
+                    $(ibidir)/binutils                \
                     $(ilidir)/isl                     \
                     $(ilidir)/mpc
 endif
@@ -854,6 +855,8 @@ $(ibidir)/gcc: $(gcc-prerequisites)   \
 	  $(call makelink,gcc);                                            \
 	  $(call makelink,g++,mandatory);                                  \
 	  $(call makelink,gfortran,mandatory);                             \
+	  $(call makelink,strip,mandatory);                                \
+	  ln -sf $$(which gcc) $(ibdir)/cc;                                \
 	  ccinfo=$$(gcc --version | awk 'NR==1');                          \
 	  echo "C compiler (""$$ccinfo"")" > $@;                           \
 	else                                                               \
@@ -898,6 +901,7 @@ $(ibidir)/gcc: $(gcc-prerequisites)   \
 	           patchelf --set-rpath $(ildir) $$f;                      \
 	         fi;                                                       \
 	       done;                                                       \
-	     fi                                                            \
+	     fi;                                                           \
+	  ln -sf $(ibdir)/gcc $(ibdir)/cc                                  \
 	  && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@;     \
 	fi
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index f7b1f4f..cff2ff8 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -50,9 +50,18 @@ ipydir  = $(BDIR)/software/installed/version-info/python
 # high level software depend on it. The current rule for ATLAS is tested
 # successfully on Mac (only static) and GNU/Linux (shared and static). But,
 # since it takes a few hours to build, it is not currently a target.
-top-level-libraries = # atlas
-top-level-python    = astroquery matplotlib
-top-level-programs  = gnuastro metastore
+
+# About available software/libraries: currently the template has rules for
+# installing software that are widely used in science, and in particular in
+# astrophysics.  However, not all of these software will be used for all
+# people interested in this template.  Due to that, we put some of what we
+# consider the main software as optional software of the template (to see a
+# complete list of all software/libraries, look at the version number
+# Makefile). If that software is needed, just remove the comment `#' to
+# install it.
+top-level-libraries =                       # atlas
+top-level-programs  = gnuastro metastore    # astrometrynet scamp sextractor swarp
+top-level-python    = numpy                 # astropy astroquery matplotlib scipy
 all: $(foreach p, $(top-level-libraries), $(ilidir)/$(p)) \
      $(foreach p, $(top-level-programs),  $(ibidir)/$(p)) \
      $(foreach p, $(top-level-python),    $(ipydir)/$(p)) \
@@ -114,8 +123,11 @@ include reproduce/software/make/python.mk
 # 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 = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
+tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz     \
                         atlas-$(atlas-version).tar.bz2                     \
+                        cairo-$(cairo-version).tar.xz                      \
+                        cdsclient-$(cdsclient-version).tar.gz              \
+                        cfitsio-$(cfitsio-version).tar.gz                  \
                         cmake-$(cmake-version).tar.gz                      \
                         curl-$(curl-version).tar.gz                        \
                         freetype-$(freetype-version).tar.gz                \
@@ -131,9 +143,16 @@ tarballs = $(foreach t, cfitsio-$(cfitsio-version).tar.gz                  \
                         libbsd-$(libbsd-version).tar.xz                    \
                         libpng-$(libpng-version).tar.xz                    \
                         libgit2-$(libgit2-version).tar.gz                  \
+                        libxml2-$(libxml2-version).tar.gz                  \
                         metastore-$(metastore-version).tar.gz              \
+                        netpbm-$(netpbm-version).tgz                       \
                         openmpi-$(openmpi-version).tar.gz                  \
                         openblas-$(openblas-version).tar.gz                \
+                        pixman-$(pixman-version).tar.gz                    \
+                        scamp-$(scamp-version).tar.lz                      \
+                        sextractor-$(sextractor-version).tar.lz            \
+                        swarp-$(swarp-version).tar.gz                      \
+                        swig-$(swig-version).tar.gz                        \
                         tiff-$(libtiff-version).tar.gz                     \
                         wcslib-$(wcslib-version).tar.bz2                   \
                       , $(tdir)/$(t) )
@@ -157,9 +176,12 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	                                 : (l==2 ? "%d00\n"           \
                                             : "%d000\n") ), $$1)}')
 	    w=https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio$$v.tar.gz
+	  elif [ $$n = astrometry  ]; then w=http://astrometry.net/downloads
 	  elif [ $$n = atlas       ]; then
 	    mergenames=0
 	    w=https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
+	  elif [ $$n = cairo       ]; then w=https://www.cairographics.org/releases
+	  elif [ $$n = cdsclient   ]; then w=http://cdsarc.u-strasbg.fr/ftp/pub/sw
 	  elif [ $$n = cmake       ]; then
 	    mergenames=0
 	    majv=$$(echo $(cmake-version) \
@@ -185,7 +207,11 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  elif [ $$n = libgit      ]; then
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
+	  elif [ $$n = libxml      ]; then w=ftp://xmlsoft.org/libxml2
 	  elif [ $$n = metastore   ]; then w=http://akhlaghi.org/src
+	  elif [ $$n = netpbm      ]; then
+	    mergenames=0
+		w=https://sourceforge.net/projects/netpbm/files/super_stable/$(netpbm-version)/netpbm-$(netpbm-version).tgz/download
 	  elif [ $$n = openblas    ]; then
 	    mergenames=0
 	    w=https://github.com/xianyi/OpenBLAS/archive/v$(openblas-version).tar.gz
@@ -193,6 +219,11 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	    mergenames=0
 	    majorver=$$(echo $(openmpi-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
 	    w=https://download.open-mpi.org/release/open-mpi/v$$majorver/$*
+	  elif [ $$n = pixman      ]; then w=https://www.cairographics.org/releases
+	  elif [ $$n = scamp       ]; then w=http://akhlaghi.org/src
+	  elif [ $$n = sextractor  ]; then w=http://akhlaghi.org/src
+	  elif [ $$n = swarp       ]; then w=https://www.astromatic.net/download/swarp
+	  elif [ $$n = swig        ]; then w=https://sourceforge.net/projects/swig/files/swig/swig-$(swig-version)
 	  elif [ $$n = tiff        ]; then w=https://download.osgeo.org/libtiff
 	  elif [ $$n = wcslib      ]; then w=ftp://ftp.atnf.csiro.au/pub/software/wcslib
 	  else
@@ -261,6 +292,13 @@ $(ilidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \
 	&& rm $$customtar                                \
 	&& echo "CFITSIO $(cfitsio-version)" > $@
 
+$(ilidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz    \
+                 $(ilidir)/freetype                       \
+                 $(ilidir)/libpng                         \
+                 $(ilidir)/pixman
+	$(call gbuild, $<, cairo-$(cairo-version), static)    \
+	&& echo "Cairo $(cairo-version)" > $@
+
 $(ilidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz
 	$(call gbuild, $<, gsl-$(gsl-version), static) \
 	&& echo "GNU Scientific Library $(gsl-version)" > $@
@@ -277,7 +315,7 @@ $(ilidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \
 	$(call gbuild, $<, freetype-$(freetype-version), static) \
 	&& echo "FreeType $(freetype-version)" > $@
 
-$(ilidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz \
+$(ilidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz  \
                 $(ilidir)/openmpi
 	export CC=mpicc;                                 \
 	export FC=mpif90;                                \
@@ -298,6 +336,21 @@ $(ilidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz
 	$(call gbuild, $<, libpng-$(libpng-version), static) \
 	&& echo "Libpng $(libpng-version)" > $@
 
+$(ilidir)/libxml2: $(tdir)/libxml2-$(libxml2-version).tar.gz
+       # The libxml2 tarball also contains Python bindings which are built and
+       # installed to a system directory by default. If you don't need the Python
+       # bindings, the easiest solution is to compile without Python support:
+       # ./configure --without-python
+       # If you really need the Python bindings, try the
+       # --with-python-install-dir=DIR option
+	$(call gbuild, $<, libxml2-$(libxml2-version), static, \
+                   --without-python)                       \
+	&& echo "Libxml2 $(libxml2-version)" > $@
+
+$(ilidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz
+	$(call gbuild, $<, pixman-$(pixman-version), static) \
+	&& echo "Pixman $(pixman-version)" > $@
+
 $(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
                    $(ilidir)/libjpeg
 	$(call gbuild, $<, tiff-$(libtiff-version), static, \
@@ -306,7 +359,7 @@ $(ilidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
 
 $(ilidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz
 	$(call gbuild, $<, openmpi-$(openmpi-version), static, , V=1) \
-	&& echo "OpenMPI $(openmpi-version)" > $@
+	&& echo "Open MPI $(openmpi-version)" > $@
 
 $(ilidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \
 	         $(tdir)/lapack-$(lapack-version).tar.gz
@@ -463,6 +516,51 @@ $(ilidir)/wcslib: $(tdir)/wcslib-$(wcslib-version).tar.bz2 \
 # Programs
 # --------
 #
+# Astrometry-net contains a lot of programs. We need to specify the
+# installation directory and the Python executable (by default it will look
+# for /usr/bin/python)
+$(ibidir)/astrometrynet: $(tdir)/astrometry.net-$(astrometrynet-version).tar.gz \
+                         $(ilidir)/cairo                                        \
+                         $(ilidir)/cfitsio                                      \
+                         $(ilidir)/gsl                                          \
+                         $(ilidir)/libjpeg                                      \
+                         $(ilidir)/libpng                                       \
+                         $(ibidir)/netpbm                                       \
+                         $(ipydir)/numpy                                        \
+                         $(ibidir)/python                                       \
+                         $(ibidir)/swig                                         \
+                         $(ilidir)/wcslib
+	cd $(ddir)                                                            \
+    && if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi            \
+    && cd astrometry.net-$(astrometrynet-version)                         \
+    && make                                                               \
+    && make py                                                            \
+    && make extra                                                         \
+    && make install INSTALL_DIR=$(idir) PYTHON_SCRIPT="$(ibdir)/python"   \
+    && cd ..                                                              \
+    && rm -rf astrometry.net-$(astrometrynet-version)                     \
+    && cp $(dtexdir)/astrometrynet.tex $(ictdir)/                         \
+    && echo "Astrometry.net $(astrometrynet-version) \citep{astrometrynet}" > $@
+
+# cdsclient is a set of software written in c to interact with astronomical
+# database servers. It is a dependency of `scamp' to be able to download
+# reference catalogues.
+# NOTE: we do not use a convencional `gbuild' installation because the
+# programs are scripts and we need to touch them before installing.
+# Otherwise this software will be re-built each time the configure step is
+# invoked.
+$(ibidir)/cdsclient: $(tdir)/cdsclient-$(cdsclient-version).tar.gz
+	cd $(ddir)                                                    \
+	&& tar xf $<                                                  \
+	&& cd cdsclient-$(cdsclient-version)                          \
+	&& touch *                                                    \
+	&& ./configure --prefix=$(idir)                               \
+	&& make                                                       \
+	&& make install                                               \
+	&& cd ..                                                      \
+	&& rm -rf cdsclient-$(cdsclient-version)                      \
+	&& echo "cdsclient $(cdsclient-version)" > $@
+
 # CMake can be built with its custom `./bootstrap' script.
 $(ibidir)/cmake: $(tdir)/cmake-$(cmake-version).tar.gz \
                  $(ibidir)/curl
@@ -613,16 +711,84 @@ endif
 	&& cp $(dtexdir)/gnuastro.tex $(ictdir)/                 \
 	&& echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
-
-
-
-
-
-
-
-
-
-
+# Netpbm is a prerequisite of Astrometry-net, it contains a lot of programs.
+# This program has a crazy dialogue installation which is override using the
+# printf statment. Each `\n' is a new question that the installation process
+# ask to the user. We give all answers with a pipe to the scripts (configure
+# and install). The questions are different depending on the system (tested
+# on GNU/Linux and Mac OS).
+$(ibidir)/netpbm: $(tdir)/netpbm-$(netpbm-version).tgz   \
+                  $(ilidir)/libjpeg                      \
+                  $(ilidir)/libpng                       \
+                  $(ilidir)/libtiff                      \
+                  $(ilidir)/libxml2                      \
+                  $(ibidir)/unzip
+	if [ x$(on_mac_os) = xyes ]; then                                      \
+      answers='\n\n\n\n\n\n\n\n\n\n\n\nnone\n\n\n';                        \
+    else                                                                   \
+      answers='\n\n\n\ny\n\n\n\n\n\n\n\n\n\n\n\n\n';                       \
+    fi;                                                                    \
+    cd $(ddir)                                                             \
+    && unpackdir=netpbm-$(netpbm-version)                                  \
+    && rm -rf $$unpackdir                                                  \
+    && if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi             \
+    && cd $$unpackdir                                                      \
+    && printf "$$answers" | ./configure                                    \
+    && make                                                                \
+    && rm -rf $(ddir)/$$unpackdir/install                                  \
+    && make package pkgdir=$(ddir)/$$unpackdir/install                     \
+    && printf "$(ddir)/$$unpackdir/install\n$(idir)\n\n\nN\n\n\n\n\nN\n\n" \
+              | ./installnetpbm                                            \
+    && cd ..                                                               \
+    && rm -rf $$unpackdir                                                  \
+    && echo "Netpbm $(netpbm-version)" > $@
+
+# SCAMP documentation says ATLAS is a mandatory prerequisite for using
+# SCAMP. We have ATLAS into the project but there are some problems with the
+# libraries that are not yet solved. However, we tried to install it with
+# the option --enable-openblas and it worked (same issue happened with
+# `sextractor'.
+$(ibidir)/scamp: $(tdir)/scamp-$(scamp-version).tar.lz                \
+                      $(ilidir)/fftw                                  \
+                      $(ilidir)/openblas                              \
+                      $(ibidir)/cdsclient
+	$(call gbuild, $<, scamp-$(scamp-version), static,                \
+                   --enable-threads --enable-openblas                 \
+                   --with-fftw-libdir=$(idir)                         \
+                   --with-fftw-incdir=$(idir)/include                 \
+                   --with-openblas-libdir=$(ildir)                    \
+                   --with-openblas-incdir=$(idir)/include)            \
+	&& cp $(dtexdir)/scamp.tex $(ictdir)/                             \
+    && echo "SCAMP $(scamp-version) \citep{scamp}" > $@
+
+# Sextractor crashes complaining about not linking with some ATLAS
+# libraries. But we can override this issue since we have Openblas
+# installed, it is just necessary to explicity tell sextractor to use it in
+# the configuration step.
+$(ibidir)/sextractor: $(tdir)/sextractor-$(sextractor-version).tar.lz \
+                      $(ilidir)/openblas                              \
+                      $(ilidir)/fftw
+	$(call gbuild, $<, sextractor-$(sextractor-version), static,      \
+                   --enable-threads --enable-openblas                 \
+                   --with-openblas-libdir=$(ildir)                    \
+                   --with-openblas-incdir=$(idir)/include)            \
+    && ln -fs $(ibdir)/sex $(ibdir)/sextractor                        \
+    && cp $(dtexdir)/sextractor.tex $(ictdir)/                        \
+    && echo "Sextractor $(sextractor-version) \citep{sextractor}" > $@
+
+$(ibidir)/swarp: $(tdir)/swarp-$(swarp-version).tar.gz \
+                 $(ilidir)/fftw
+	$(call gbuild, $<, swarp-$(swarp-version), static, \
+                   --enable-threads)                   \
+    && cp $(dtexdir)/swarp.tex $(ictdir)/              \
+    && echo "SWarp $(swarp-version) \citep{swarp}" > $@
+
+$(ibidir)/swig: $(tdir)/swig-$(swig-version).tar.gz
+	# Option --without-pcre was a suggestion once the configure step was
+	# tried and it failed. It was not recommended but it works!
+	# pcr is a dependency of swig
+	$(call gbuild, $<, swig-$(swig-version), static, --without-pcre) \
+	&& echo "Swig $(swig-version)" > $@
 
 
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 5ec99f0..22c6284 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -214,13 +214,13 @@ $(pytarballs): $(tdir)/%:
 # 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))        \
+	$(call gbuild, $<, libffi-$(libffi-version)) \
 	echo "Libffi $(libffi-version)" > $@
 
-$(ibidir)/python3: $(tdir)/python-$(python-version).tar.gz \
-                   $(ilidir)/libffi
-        # On Mac systems, the build complains about `clang' specific
-        # features, so we can't use our own GCC build here.
+$(ibidir)/python: $(tdir)/python-$(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++;                               \
@@ -231,7 +231,8 @@ $(ibidir)/python3: $(tdir)/python-$(python-version).tar.gz \
 	       --enable-shared)                             \
 	&& v=$$(echo $(python-version) | awk 'BEGIN{FS="."} \
 	    {printf "%d.%d\n", $$1, $$2}')                  \
-	&& ln -s $(ildir)/python$$v $(ildir)/python         \
+	&& ln -sf $(ildir)/python$$v $(ildir)/python        \
+	&& ln -sf $(ibdir)/python$$v $(ibdir)/python        \
 	&& rm -rf $(ipydir)                                 \
 	&& mkdir $(ipydir)                                  \
 	&& echo "Python $(python-version)" > $@
@@ -259,8 +260,8 @@ pybuild = cd $(ddir); rm -rf $(3);                            \
 	       -e 's|@INCDIR[@]|'"$(idir)/include"'|'             \
 	       $(4) > site.cfg;                                   \
 	 fi;                                                      \
-	 python3 setup.py build                                   \
-	 && python3 setup.py install                              \
+	 python setup.py build                                    \
+	 && python setup.py install                               \
 	 && cd ..                                                 \
 	 && rm -rf $(3)                                           \
 	 && echo "$(5)" > $@
@@ -475,7 +476,7 @@ $(ipydir)/secretstorage: $(tdir)/secretstorage-$(secretstorage-version).tar.gz \
 	                SecretStorage $(secretstorage-version))
 
 $(ipydir)/setuptools: $(tdir)/setuptools-$(setuptools-version).zip \
-                      $(ibidir)/python3                            \
+                      $(ibidir)/python                             \
                       $(ibidir)/unzip
 	$(call pybuild, unzip, $<, setuptools-$(setuptools-version), ,\
 	                Setuptools $(setuptools-version))