From 1d4c587489cbb17c7ae9f6c0d0d5d919690fafde Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Mon, 28 Oct 2019 15:19:34 +0000
Subject: HEALPix, Autoconf and Automake now in library

The tarball of HEALPix includes multiple languages and doesn't include the
ready-to-run GNU Build System by default, we actually have to build the
`./configure' script for the C/C++ libraries. So it was necessary to also
include GNU Autoconf and GNU Automake as prerequisites of HEALPix.

However, the official GNU Autoconf tarball (dating from 2012) doesn't build
on modern systems, so I just cloned it from its source and bootstrapped it
and built its modern tarball which we are using here.
---
 reproduce/software/bibtex/healpix.tex              | 18 +++++++
 .../software/config/installation/checksums.mk      |  4 ++
 reproduce/software/config/installation/versions.mk |  4 ++
 reproduce/software/make/basic.mk                   |  1 +
 reproduce/software/make/high-level.mk              | 63 +++++++++++++++++++++-
 reproduce/software/make/python.mk                  | 10 ++++
 6 files changed, 99 insertions(+), 1 deletion(-)
 create mode 100644 reproduce/software/bibtex/healpix.tex

(limited to 'reproduce/software')

diff --git a/reproduce/software/bibtex/healpix.tex b/reproduce/software/bibtex/healpix.tex
new file mode 100644
index 0000000..b9089be
--- /dev/null
+++ b/reproduce/software/bibtex/healpix.tex
@@ -0,0 +1,18 @@
+@ARTICLE{healpix,
+       author = {{G{\'o}rski}, K.~M. and {Hivon}, E. and {Banday}, A.~J. and {Wand
+        elt}, B.~D. and {Hansen}, F.~K. and {Reinecke}, M. and {Bartelmann}, M.},
+        title = "{HEALPix: A Framework for High-Resolution Discretization and Fast Analysis of Data Distributed on the Sphere}",
+      journal = {ApJ},
+     keywords = {Cosmology: Cosmic Microwave Background, Cosmology: Observations, Methods: Statistical, Astrophysics},
+         year = "2005",
+        month = "Apr",
+       volume = {622},
+       number = {2},
+        pages = {759},
+          doi = {10.1086/427976},
+archivePrefix = {arXiv},
+       eprint = {astro-ph/0409513},
+ primaryClass = {astro-ph},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2005ApJ...622..759G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
diff --git a/reproduce/software/config/installation/checksums.mk b/reproduce/software/config/installation/checksums.mk
index d1b900d..1fbe7dd 100644
--- a/reproduce/software/config/installation/checksums.mk
+++ b/reproduce/software/config/installation/checksums.mk
@@ -77,6 +77,8 @@ apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb
 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536
 astrometrynet-checksum = 35c268bf0a7068e01323b9bfccdf255c993df83c24b2e6026a00084c4ab87d031f1024205d0ed3aecc7e2a495d4bc0b0e67270d66679020b7cc2e4b2f30f5c4a
 atlas-checksum = bf17306f09f2aa973cb776e2c9eacfb2409ad4d95d19802e1c4e0597d0a099fccdb5eaafe273c2682a41e41a3c6fabc8bbba4ce03180cffea40ede5df1d1f56e
+autoconf-checksum = c25e834251bfc2befe822614caf1c80d7e1314a83e7173304abc235fd15a958b8db9fbc801e8ad98328dfd6d9dbc425bfbbefec500fa268992ae7bbf4fa5bc35
+automake-checksum = 47b0120a59e3e020529a6ce750297d7de1156fd2be38db5d101e50120f11b40c28741ecd5eacf2790a9e25386713dcf7717339cfa5d7943d0dbf47c417383448
 bison-checksum = 00d2b37187b93100ec4b220ce2752d12ccf68f9d0d39b380d375d36dd8a22aa1d6e60156918f95e4493f9531c5d42d8fad38fd807307b491c1ca7ca4177823d9
 boost-checksum = 4378e20f18db9f186ac0f38ad98c522526e0fe48a8deb968c41325e3f69e733be3298505e91ea713e79a9d9e741305fa879d289f74e6276e0ec7286f03be87fc
 cairo-checksum = 9eb27c4cf01c0b8b56f2e15e651f6d4e52c99d0005875546405b64f1132aed12fbf84727273f493d84056a13105e065009d89e94a8bfaf2be2649e232b82377f
@@ -91,6 +93,7 @@ ghostscript-checksum = 9ad7bd24b6d9b7d258e943783817be036a2e0234517baffa1016804ef
 gnuastro-checksum = 6ff8e86f2834a08acf94295ae022736a3f31afd3c66c0d74b012d98e53c2184c42d6d4558997a85b268c5e3ebb258041fe2db2478435788b26c0b94068dd892e
 gsl-checksum = 0be8240715f0b86aba2c63d9f12da4dba4719d4e350e9308d279e0dd3b2f0519ea26fd2e38a17f3e8cf43aacbaa2455207a7ca0d6c305f3b8725e8ece2250a74
 hdf5-checksum = f828ee9d63533effe1ad358230e5ce7b64c5016e49291d9533575f713cbfba496290fc0151fd9617898bdf36785984ddb38a9207f529d7702d4e23838fe050d8
+healpix-checksum = 29fe680d757bd94651bf029654257cb67286643aad510df4c2f0b06245174411376ec1beca64feebfac14a6fc0194525170635842916d79dcaddeddd9ac6f6c7
 help2man-checksum = 786a6bd4336c591cfeb0b4f2dc1429f6545e36514e7b238453c91368b8f531c46db2be025f02dc52e6dd8b971d6edbb4ff1a8e1b519f9253a3957ad7157790be
 imagemagick-checksum = ad4325df57769f9c4edf8ac71370cb9bb19e090e588d47eb0311e3f4895abd7a7edcbd2e7a495f21acd1daca97fa224bdf1fd978577588e45c11a7799c3d67f4
 imfit-checksum = 15edd2349232c1c8e611b31d3a46b0700112d274515f54d0a0085bb4bfa6d3d5f8a15cd926516e043a29ce841accf3534ae58dbfb952d858dc9445199c957096
@@ -148,6 +151,7 @@ flake8-checksum = a25076bb7f978ca23af0f2016b30bf5fe4680371b4c0939361a6f8c496f3c8
 future-checksum = c70565a660cf87c5e7e994bae0d4eb0b2b8b607ecb5ce65521c027bf0a39ce5699f0578413bd3c7edd5d01aeb1617de48dcea098a9e9021d8487a73007573030
 galsim-checksum = 11ecbfb9628cf85a4c25024c6f3a34bbdadf522f64e4e93e6428b545c65a48906a05eb7774d0faaacf52a48dddfd599bfc7cc7252ca854a18c3930f116533a3c
 h5py-checksum = 73b1f59e3e2b3eceebf7b97e49bd8f5199afafd7ef29917af05ff8415c2f2129a5c59db9658944370c9bcf8fc04ab26948ee27fc6fd948a22d19cace1ce8c853
+healpy-checksum = installed-with-healpix
 html5lib-checksum = 35939b4450893864da04e735ee5e0addacf1dd34bae6a6909c76572abf6bfded446a78a713dfde91c1485ba45867d7abeb6a45cf0545c16ea968707be7de5dd2
 idna-checksum = 8ca5cfe6350c51250bafdac7c6e4ddd54c4a5d6bf7acbcef896760a759868c8e9df1fdf550121d8512fa3eb316dcf031ec6058e03b4f66eadee21b63e2187d33
 jeepney-checksum = 43083994a7c6af84a5a68d3ff8f6dc4d9129ce9fa55517838fb62d9f62bb78bdf52067649d0b95d08d689b7d7475cb9b2a956662e265a776ad42dcf4ccc0ab63
diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk
index 20e6632..278baf0 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.mk
@@ -75,6 +75,8 @@ apr-version = 1.7.0
 apr-util-version = 1.6.1
 astrometrynet-version = 0.77
 atlas-version = 3.10.3
+autoconf-version = 2.69.200-babc
+automake-version = 1.16.1
 bison-version = 3.4.2
 boost-version = 1.71.0
 cairo-version = 1.16.0
@@ -90,6 +92,7 @@ ghostscript-version = 9.27
 gnuastro-version = 0.10
 gsl-version = 2.6
 hdf5-version = 1.10.5
+healpix-version = 3.50
 help2man-version = 1.47.11
 imagemagick-version = 7.0.8-67
 imfit-version = 1.6.1
@@ -143,6 +146,7 @@ flake8-version = 3.7.8
 future-version = 0.18.1
 galsim-version = 2.2.1
 h5py-version = 2.9.0
+healpy-version = installed-with-healpix
 html5lib-version = 1.0.1
 idna-version = 2.8
 jeepney-version = 0.4
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index b0b757f..65bdf1e 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -904,6 +904,7 @@ $(ibidir)/glibtool: $(tdir)/libtool-$(libtool-version).tar.xz \
                     | $(ibidir)/m4
 	$(call gbuild, $<, libtool-$(libtool-version), static, \
                        --program-prefix=g) \
+	&& ln -s $(ibdir)/glibtoolize $(ibdir)/libtoolize \
 	&& echo "GNU Libtool $(libtool-version)" > $@
 
 $(ibidir)/grep: $(tdir)/grep-$(grep-version).tar.xz \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 36e88ef..7ee7062 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -136,6 +136,8 @@ tarballs = $(foreach t, apr-$(apr-version).tar.gz \
                         apr-util-$(apr-util-version).tar.gz \
                         astrometry.net-$(astrometrynet-version).tar.gz \
                         atlas-$(atlas-version).tar.bz2 \
+                        autoconf-$(autoconf-version).tar.lz \
+                        automake-$(automake-version).tar.gz \
                         bison-$(bison-version).tar.xz \
                         boost-$(boost-version).tar.gz \
                         cairo-$(cairo-version).tar.xz \
@@ -150,6 +152,7 @@ tarballs = $(foreach t, apr-$(apr-version).tar.gz \
                         gnuastro-$(gnuastro-version).tar.lz \
                         gsl-$(gsl-version).tar.gz \
                         hdf5-$(hdf5-version).tar.gz \
+                        healpix-$(healpix-version).tar.gz \
                         help2man-$(help2man-version).tar.xz \
                         imagemagick-$(imagemagick-version).tar.xz \
                         imfit-$(imfit-version).tar.gz \
@@ -194,7 +197,9 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  mergenames=0
 	  c=$(atlas-checksum)
 	  w=https://sourceforge.net/projects/math-atlas/files/Stable/$(atlas-version)/atlas$(atlas-version).tar.bz2/download
-	elif [ $$n = bison       ]; then c=$(bison-checksum); w=http://ftp.gnu.org/gnu/bison/
+	elif [ $$n = autoconf    ]; then c=$(autoconf-checksum); w=http://akhlaghi.org/reproduce-software
+	elif [ $$n = automake    ]; then c=$(automake-checksum); w=http://ftp.gnu.org/gnu/automake
+	elif [ $$n = bison       ]; then c=$(bison-checksum); w=http://ftp.gnu.org/gnu/bison
 	elif [ $$n = boost       ]; then
 	  mergenames=0
 	  c=$(boost-checksum)
@@ -228,6 +233,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	  c=$(hdf5-checksum)
 	  majorver=$$(echo $(hdf5-version) | sed -e 's/\./ /g' | awk '{printf("%d.%d", $$1, $$2)}')
 	  w=https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$$majorver/hdf5-$(hdf5-version)/src/$*
+	elif [ $$n = healpix     ]; then c=$(healpix-checksum); w=http://akhlaghi.org/reproduce-software
 	elif [ $$n = help        ]; then c=$(help2man-checksum); w=http://ftp.gnu.org/gnu/help2man
 	elif [ $$n = imagemagick ]; then c=$(imagemagick-checksum); w=http://akhlaghi.org/reproduce-software
 	elif [ $$n = imfit       ]; then
@@ -519,6 +525,53 @@ $(ibidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz  \
 	               --enable-fortran, -j$(numthreads) V=1) \
 	&& echo "HDF5 library $(hdf5-version)" > $@
 
+# HEALPix includes the source of its C, C++, Python (and several other
+# languages) libraries within one tarball. We will include the Python
+# installation only when any other Python module is requested (in
+# `TARGETS.mk').
+#
+# Note that the default `./configure' script is an interactive script which
+# is hard to automate. So we need to go into the `autotools' directory of
+# the `C' and `cxx' directories and configure the GNU Build System (with
+# `autoreconf', which uses `autoconf' and `automake') to easily build the
+# HEALPix C/C++ libraries in batch mode.
+ifeq ($(strip $(top-level-python)),)
+healpix-python-dep =
+else
+healpix-python-dep = $(ipydir)/matplotlib $(ipydir)/astropy
+endif
+$(ibidir)/healpix: $(tdir)/healpix-$(healpix-version).tar.gz \
+                   $(healpix-python-dep) \
+                   $(ibidir)/autoconf \
+                   $(ibidir)/automake \
+                   $(ibidir)/cfitsio
+	if [ x"$(healpix-python-dep)" = x ]; then
+	   pycommand1="echo no-healpy-because-no-other-python"
+	   pycommand2="echo no-healpy-because-no-other-python"
+	else
+	   pycommand1="python setup.py build"
+	   pycommand2="python setup.py install"
+	fi
+	rm -rf $(ddir)/Healpix_$(healpix-version)
+	topdir=$(pwd); cd $(ddir); tar xf $<
+	cd Healpix_$(healpix-version)/src/C/autotools/ \
+	&& autoreconf --install \
+	&& ./configure --prefix=$(idir) \
+	&& make V=1 -j$(numthreads) SHELL=$(ibdir)/bash \
+	&& make install \
+	&& cd ../../cxx/autotools/ \
+	&& autoreconf --install \
+	&& ./configure --prefix=$(idir) \
+	&& make V=1 -j$(numthreads) SHELL=$(ibdir)/bash \
+	&& make install \
+	&& cd ../../healpy \
+	&& $$pycommand1 \
+	&& $$pycommand2 \
+	&& cd $$topdir \
+	&& rm -rf $(ddir)/Healpix_$(healpix-version) \
+	&& cp $(dtexdir)/healpix.tex $(ictdir)/ \
+	&& echo "HEALPix $(healpix-version) \citep{healpix}" > $@
+
 $(ibidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
 	$(call gbuild, $<, jpeg-9b, static) \
 	&& echo "Libjpeg $(libjpeg-version)" > $@
@@ -705,6 +758,14 @@ $(ibidir)/astrometrynet: $(tdir)/astrometry.net-$(astrometrynet-version).tar.gz
 	&& cp $(dtexdir)/astrometrynet.tex $(ictdir)/ \
 	&& echo "Astrometry.net $(astrometrynet-version) \citep{astrometrynet}" > $@
 
+$(ibidir)/autoconf: $(tdir)/autoconf-$(autoconf-version).tar.lz
+	$(call gbuild, $<, autoconf-$(autoconf-version), static, ,V=1) \
+	&& echo "GNU Autoconf $(autoconf-version)" > $@
+
+$(ibidir)/automake: $(tdir)/automake-$(automake-version).tar.gz
+	$(call gbuild, $<, automake-$(automake-version), static, ,V=1) \
+	&& echo "GNU Automake $(automake-version)" > $@
+
 $(ibidir)/bison: $(tdir)/bison-$(bison-version).tar.xz \
                  $(ibidir)/help2man
 	$(call gbuild, $<, bison-$(bison-version), static, ,V=1) \
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index b7cbc9b..14e7b75 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -455,6 +455,16 @@ $(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
 	$(call pybuild, tar xf, $<, h5py-$(h5py-version), ,\
 	                h5py $(h5py-version))
 
+# `healpy' is actually installed as part of the HEALPix package. It will be
+# installed with its C/C++ libraries if any other Python library is
+# requested with HEALPix. So actually calling for `healpix' (when `healpix'
+# is requested) is not necessary. But some users might not know about this
+# and just ask for `healpy'. To avoid confusion in such cases, we'll just
+# set `healpy' to be dependent on `healpix' and not download any tarball
+# for it, or write anything in the final target.
+$(ipydir)/healpy: $(ibidir)/healpix
+	touch $@
+
 $(ipydir)/html5lib: $(tdir)/html5lib-$(html5lib-version).tar.gz  \
                     $(ipydir)/webencodings \
                     $(ipydir)/six
-- 
cgit v1.2.1