Astropy installed in the pipeline

Astropy was added and one very important thing is that we have to
use the pypi tarball (https://pypi.org/) (which is bootstrapped)
and not the github tarball.

8 files changed, 209 insertions, 78 deletions

diff --git a/.file-metadata b/.file-metadata
index 5df4e17..1939902 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/.gitignore b/.gitignore
index f04b14e..5879789 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
 *.pdf
 *.out
 *.zip
+*.swp
 .nfs*
 mmap_*
 *.tar.gz
diff --git a/paper.tex b/paper.tex
index a36b3eb..16f6eb8 100644
--- a/paper.tex
+++ b/paper.tex
@@ -216,7 +216,9 @@ Scientific Library (GSL) \gslversion, GNU Tar \tarversion, GNU Wget
 Libjpeg \libjpegversion, Libtiff \libtiffversion, Metastore (forked)
 \metastoreversion, OpenSSL \opensslversion, Pkg-config \pkgconfigversion,
 Unzip \unzipversion, WCSLIB \wcslibversion, XZ Utils \xzversion, Zip
-\zipversion, and ZLib \zlibversion. The final paper was produced with
+\zipversion, and ZLib \zlibversion. We use Python {\pythonversion} with the
+following packages: Numpy {\numpyversion} and Astropy {\astropyversion}
+\citep{astropy2013, astropy2018}. The final paper was produced with
 \TeX{} Live \texliveversion, using the following packages: \TeX{}
 \textexversion, EC \texecversion, NewTX \texnewtxversion, Fontaxes
 \texfontaxesversion, Keyval, \texxkeyvalversion, Etoolbox
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index 0bea16a..f0774bc 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -1,52 +1,59 @@
 # Versions of the various dependnecies
 
 # Programs
-bash-version        = 5.0
-binutils-version    = 2.31.1
-bzip2-version       = 1.0.6
-cmake-version       = 3.12.4
-coreutils-version   = 8.30
-diffutils-version   = 3.7
-findutils-version   = 4.6.0.199-e3fc
-flock-version       = 0.2.3
-gawk-version        = 4.2.1
-gcc-version         = 8.2.0
-ghostscript-version = 9.26
-git-version         = 2.20.1
-gmp-version         = 6.1.2
-gnuastro-version    = 0.8
-grep-version        = 3.3
-gzip-version        = 1.10
-isl-version         = 0.18
-libtool-version     = 2.4.6
-libbsd-version      = 0.9.1
-lzip-version        = 1.20
-make-version        = 4.2.90
-metastore-version   = 1.1.2-23-fa9170b
-mpfr-version        = 4.0.1
-mpc-version         = 1.1.0
-ncurses-version     = 6.1
-numpy-version       = 1.16.1
-openssl-version     = 1.1.1a
-patchelf-version    = 0.9
-pkgconfig-version   = 0.29.2
-python-version      = 3.6.8
-readline-version    = 8.0
-sed-version         = 4.7
-tar-version         = 1.31
-unzip-version       = 6.0
-wget-version        = 1.20.1
-which-version       = 2.21
-xz-version          = 5.2.4
-zip-version         = 3.0
+bash-version               = 5.0
+binutils-version           = 2.31.1
+bzip2-version              = 1.0.6
+cmake-version              = 3.12.4
+coreutils-version          = 8.30
+diffutils-version          = 3.7
+findutils-version          = 4.6.0.199-e3fc
+flock-version              = 0.2.3
+gawk-version               = 4.2.1
+gcc-version                = 8.2.0
+ghostscript-version        = 9.26
+git-version                = 2.20.1
+gmp-version                = 6.1.2
+gnuastro-version           = 0.8
+grep-version               = 3.3
+gzip-version               = 1.10
+isl-version                = 0.18
+libtool-version            = 2.4.6
+libbsd-version             = 0.9.1
+lzip-version               = 1.20
+make-version               = 4.2.90
+metastore-version          = 1.1.2-23-fa9170b
+mpfr-version               = 4.0.1
+mpc-version                = 1.1.0
+ncurses-version            = 6.1
+openssl-version            = 1.1.1a
+patchelf-version           = 0.9
+pkgconfig-version          = 0.29.2
+python-version             = 3.6.8
+readline-version           = 8.0
+sed-version                = 4.7
+tar-version                = 1.31
+unzip-version              = 6.0
+wget-version               = 1.20.1
+which-version              = 2.21
+xz-version                 = 5.2.4
+zip-version                = 3.0
 
 # Libraries
-cfitsio-version     = 3.45
-curl-version        = 7.63.0
-gsl-version         = 2.5
-libjpeg-version     = v9b
-libtiff-version     = 4.0.10
-zlib-version        = 1.2.11
+cfitsio-version            = 3.45
+curl-version               = 7.63.0
+gsl-version                = 2.5
+libjpeg-version            = v9b
+libtiff-version            = 4.0.10
+zlib-version               = 1.2.11
+
+# Python packages
+# ---------------
+#
+# IMPORTANT: Fix url in `reproduce/src/make/dependencies.mk'
+# if changing the version
+astropy-version            = 3.1.1
+numpy-version              = 1.16.1
 
 # Special libraries
 # -----------------
@@ -55,5 +62,5 @@ zlib-version        = 1.2.11
 # the software build Makefiles (`reproduce/src/make/dependencies*.mk'). If
 # you change their version, also please change the explicit shared library
 # names also.
-libgit2-version     = 0.26.0
-wcslib-version      = 6.2
+libgit2-version            = 0.26.0
+wcslib-version             = 6.2
diff --git a/reproduce/src/make/dependencies-build-rules.mk b/reproduce/src/make/dependencies-build-rules.mk
index 0c7262e..2247518 100644
--- a/reproduce/src/make/dependencies-build-rules.mk
+++ b/reproduce/src/make/dependencies-build-rules.mk
@@ -103,6 +103,22 @@ 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.mk b/reproduce/src/make/dependencies.mk
index 52b65f4..a28de19 100644
--- a/reproduce/src/make/dependencies.mk
+++ b/reproduce/src/make/dependencies.mk
@@ -41,13 +41,12 @@ idir   = $(BDIR)/dependencies/installed
 ibdir  = $(BDIR)/dependencies/installed/bin
 ildir  = $(BDIR)/dependencies/installed/lib
 ilidir = $(BDIR)/dependencies/installed/lib/built
-pydir  = $(BDIR)/dependencies/installed/lib/python
 
 # Define the top-level programs to build (installed in `.local/bin').
-top-level-python   = numpy
-top-level-programs = astnoisechisel metastore flock zip
+top-level-python   = astropy
+top-level-programs = astnoisechisel metastore flock unzip zip
 all: $(ddir)/texlive-versions.tex                       \
-     $(foreach p, $(top-level-python),   $(pydir)/$(p)) \
+     $(foreach p, $(top-level-python),   $(ilidir)/$(p)) \
      $(foreach p, $(top-level-programs), $(ibdir)/$(p))
 
 # Other basic environment settings: We are only including the host
@@ -90,26 +89,27 @@ 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 = $(foreach t, cfitsio-$(cfitsio-version).tar.gz             \
-                        cmake-$(cmake-version).tar.gz                 \
-                        curl-$(curl-version).tar.gz                   \
-                        flock-$(flock-version).tar.xz                 \
-                        ghostscript-$(ghostscript-version).tar.gz     \
-                        git-$(git-version).tar.xz                     \
-                        gnuastro-$(gnuastro-version).tar.lz           \
-                        gsl-$(gsl-version).tar.gz                     \
-                        install-tl-unx.tar.gz                         \
-                        jpegsrc.$(libjpeg-version).tar.gz             \
-                        libbsd-$(libbsd-version).tar.xz               \
-                        libtool-$(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                \
-                        zip-$(zip-version).tar.gz                     \
-                        wcslib-$(wcslib-version).tar.bz2              \
+tarballs = $(foreach t, astropy-$(astropy-version).tar.gz                  \
+                        cfitsio-$(cfitsio-version).tar.gz                  \
+                        cmake-$(cmake-version).tar.gz                      \
+                        curl-$(curl-version).tar.gz                        \
+                        flock-$(flock-version).tar.xz                      \
+                        ghostscript-$(ghostscript-version).tar.gz          \
+                        git-$(git-version).tar.xz                          \
+                        gnuastro-$(gnuastro-version).tar.lz                \
+                        gsl-$(gsl-version).tar.gz                          \
+                        install-tl-unx.tar.gz                              \
+                        jpegsrc.$(libjpeg-version).tar.gz                  \
+                        libbsd-$(libbsd-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-$(libtiff-version).tar.gz                     \
+                        zip-$(zip-version).tar.gz                          \
+                        wcslib-$(wcslib-version).tar.bz2                   \
                       , $(tdir)/$(t) )
 $(tarballs): $(tdir)/%:
 	if [ -f $(DEPENDENCIES-DIR)/$* ]; then
@@ -122,7 +122,8 @@ $(tarballs): $(tdir)/%:
 
           # Set the top download link of the requested tarball.
 	  mergenames=1
-	  if [ $$n = cfitsio     ]; then
+	  if   [ $$n = astropy     ]; then w=https://files.pythonhosted.org/packages/eb/f7/1251bf6881861f24239efe0c24cbcfc4191ccdbb69ac3e9bb740d0c23352
+	  elif [ $$n = cfitsio     ]; then
 	    mergenames=0
 	    v=$$(echo $(cfitsio-version) | sed -e's/\.//'             \
 	              | awk '{l=length($$1);                          \
@@ -146,7 +147,7 @@ $(tarballs): $(tdir)/%:
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	  elif [ $$n = metastore   ]; then w=http://akhlaghi.org/src
-	  elif [ $$n = numpy       ]; then w=https://fossies.org/linux/misc
+	  elif [ $$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
@@ -483,10 +484,15 @@ $(ibdir)/zip: $(tdir)/zip-$(zip-version).tar.gz
 
 # Python packages
 # ---------------
-$(pydir)/numpy: $(tdir)/numpy-$(numpy-version).zip \
-                $(ibdir)/python3                   \
-                $(ibdir)/unzip
-	pip3 install $< --verbose
+$(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" > $@
+
+
 
 
 
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index ff06dcb..dfdf161 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -316,7 +316,6 @@ lvcheck = idir=$(BDIR)/dependencies/installed/include;                   \
 
 
 
-
 # Pipeline initialization results
 # -------------------------------
 #
@@ -413,3 +412,9 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 
         # TeX package versions
 	cat $(BDIR)/dependencies/texlive-versions.tex >> $@
+
+	# Python packages
+	$(call pvcheck, python3, $(python-version), Python, pythonversion)
+	echo "\newcommand{\\numpyversion}{$(numpy-version)}"     >> $@
+	echo "\newcommand{\\astropyversion}{$(astropy-version)}" >> $@
+
diff --git a/tex/src/references.tex b/tex/src/references.tex
index b3998a2..c8c2dd2 100644
--- a/tex/src/references.tex
+++ b/tex/src/references.tex
@@ -1,3 +1,64 @@
+@ARTICLE{astropy2018,
+   author = {{Astropy Collaboration} and {Price-Whelan}, A.~M. and {Sip{\H o}cz}, B.~M. and 
+	{G{\"u}nther}, H.~M. and {Lim}, P.~L. and {Crawford}, S.~M. and 
+	{Conseil}, S. and {Shupe}, D.~L. and {Craig}, M.~W. and {Dencheva}, N. and 
+	{Ginsburg}, A. and {VanderPlas}, J.~T. and {Bradley}, L.~D. and 
+	{P{\'e}rez-Su{\'a}rez}, D. and {de Val-Borro}, M. and {Aldcroft}, T.~L. and 
+	{Cruz}, K.~L. and {Robitaille}, T.~P. and {Tollerud}, E.~J. and 
+	{Ardelean}, C. and {Babej}, T. and {Bach}, Y.~P. and {Bachetti}, M. and 
+	{Bakanov}, A.~V. and {Bamford}, S.~P. and {Barentsen}, G. and 
+	{Barmby}, P. and {Baumbach}, A. and {Berry}, K.~L. and {Biscani}, F. and 
+	{Boquien}, M. and {Bostroem}, K.~A. and {Bouma}, L.~G. and {Brammer}, G.~B. and 
+	{Bray}, E.~M. and {Breytenbach}, H. and {Buddelmeijer}, H. and 
+	{Burke}, D.~J. and {Calderone}, G. and {Cano Rodr{\'{\i}}guez}, J.~L. and 
+	{Cara}, M. and {Cardoso}, J.~V.~M. and {Cheedella}, S. and {Copin}, Y. and 
+	{Corrales}, L. and {Crichton}, D. and {D'Avella}, D. and {Deil}, C. and 
+	{Depagne}, {\'E}. and {Dietrich}, J.~P. and {Donath}, A. and 
+	{Droettboom}, M. and {Earl}, N. and {Erben}, T. and {Fabbro}, S. and 
+	{Ferreira}, L.~A. and {Finethy}, T. and {Fox}, R.~T. and {Garrison}, L.~H. and 
+	{Gibbons}, S.~L.~J. and {Goldstein}, D.~A. and {Gommers}, R. and 
+	{Greco}, J.~P. and {Greenfield}, P. and {Groener}, A.~M. and 
+	{Grollier}, F. and {Hagen}, A. and {Hirst}, P. and {Homeier}, D. and 
+	{Horton}, A.~J. and {Hosseinzadeh}, G. and {Hu}, L. and {Hunkeler}, J.~S. and 
+	{Ivezi{\'c}}, {\v Z}. and {Jain}, A. and {Jenness}, T. and {Kanarek}, G. and 
+	{Kendrew}, S. and {Kern}, N.~S. and {Kerzendorf}, W.~E. and 
+	{Khvalko}, A. and {King}, J. and {Kirkby}, D. and {Kulkarni}, A.~M. and 
+	{Kumar}, A. and {Lee}, A. and {Lenz}, D. and {Littlefair}, S.~P. and 
+	{Ma}, Z. and {Macleod}, D.~M. and {Mastropietro}, M. and {McCully}, C. and 
+	{Montagnac}, S. and {Morris}, B.~M. and {Mueller}, M. and {Mumford}, S.~J. and 
+	{Muna}, D. and {Murphy}, N.~A. and {Nelson}, S. and {Nguyen}, G.~H. and 
+	{Ninan}, J.~P. and {N{\"o}the}, M. and {Ogaz}, S. and {Oh}, S. and 
+	{Parejko}, J.~K. and {Parley}, N. and {Pascual}, S. and {Patil}, R. and 
+	{Patil}, A.~A. and {Plunkett}, A.~L. and {Prochaska}, J.~X. and 
+	{Rastogi}, T. and {Reddy Janga}, V. and {Sabater}, J. and {Sakurikar}, P. and 
+	{Seifert}, M. and {Sherbert}, L.~E. and {Sherwood-Taylor}, H. and 
+	{Shih}, A.~Y. and {Sick}, J. and {Silbiger}, M.~T. and {Singanamalla}, S. and 
+	{Singer}, L.~P. and {Sladen}, P.~H. and {Sooley}, K.~A. and 
+	{Sornarajah}, S. and {Streicher}, O. and {Teuben}, P. and {Thomas}, S.~W. and 
+	{Tremblay}, G.~R. and {Turner}, J.~E.~H. and {Terr{\'o}n}, V. and 
+	{van Kerkwijk}, M.~H. and {de la Vega}, A. and {Watkins}, L.~L. and 
+	{Weaver}, B.~A. and {Whitmore}, J.~B. and {Woillez}, J. and 
+	{Zabalza}, V. and {Astropy Contributors}},
+    title = "{The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package}",
+  journal = {AJ},
+archivePrefix = "arXiv",
+   eprint = {1801.02634},
+ primaryClass = "astro-ph.IM",
+ keywords = {methods: data analysis, methods: miscellaneous, methods: statistical, reference systems },
+     year = 2018,
+    month = sep,
+   volume = 156,
+      eid = {123},
+    pages = {123},
+      doi = {10.3847/1538-3881/aabc4f},
+   adsurl = {http://adsabs.harvard.edu/abs/2018AJ....156..123A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
 @ARTICLE{bacon17,
    author = {{Bacon}, R. and {Conseil}, S. and {Mary}, D. and {Brinchmann}, J. and
 	{Shepherd}, M. and {Akhlaghi}, M. and {Weilbacher}, P.~M. and
@@ -43,3 +104,36 @@ archivePrefix = "arXiv",
    adsurl = {http://adsabs.harvard.edu/abs/2015ApJS..220....1A},
   adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
+
+
+
+
+@ARTICLE{astropy2013,
+   author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud}, E.~J. and
+	{Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and {Aldcroft}, T. and
+	{Davis}, M. and {Ginsburg}, A. and {Price-Whelan}, A.~M. and
+	{Kerzendorf}, W.~E. and {Conley}, A. and {Crighton}, N. and
+	{Barbary}, K. and {Muna}, D. and {Ferguson}, H. and {Grollier}, F. and
+	{Parikh}, M.~M. and {Nair}, P.~H. and {Unther}, H.~M. and {Deil}, C. and
+	{Woillez}, J. and {Conseil}, S. and {Kramer}, R. and {Turner}, J.~E.~H. and
+	{Singer}, L. and {Fox}, R. and {Weaver}, B.~A. and {Zabalza}, V. and
+	{Edwards}, Z.~I. and {Azalee Bostroem}, K. and {Burke}, D.~J. and
+	{Casey}, A.~R. and {Crawford}, S.~M. and {Dencheva}, N. and
+	{Ely}, J. and {Jenness}, T. and {Labrie}, K. and {Lim}, P.~L. and
+	{Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and {Refsdal}, B. and
+	{Servillat}, M. and {Streicher}, O.},
+    title = "{Astropy: A community Python package for astronomy}",
+  journal = {A\&A},
+archivePrefix = "arXiv",
+   eprint = {1307.6212},
+ primaryClass = "astro-ph.IM",
+ keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
+     year = 2013,
+    month = oct,
+   volume = 558,
+      eid = {A33},
+    pages = {A33},
+      doi = {10.1051/0004-6361/201322068},
+   adsurl = {http://adsabs.harvard.edu/abs/2013A\%26A...558A..33A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}