From 3c7d59a46ca2940435258cb2bc1050aea5fd0b87 Mon Sep 17 00:00:00 2001
From: Raul Infante-Sainz <infantesainz@gmail.com>
Date: Wed, 17 Apr 2019 14:32:40 +0100
Subject: SExtractor is now included into the project

With this commit, we add SExtractor to be installed into the project. It
is a widely used program to detect object and build catalogues from
astronomical images.

We had some problems when installing it because it could not link with
some ATLAS libraries. But, since we have OpenBLAS installed, we can use
it to override the problem with ATLAS.
---
 .file-metadata                                     | Bin 6194 -> 6282 bytes
 reproduce/software/bibtex/sextractor.tex           |  18 ++++++++++++++++++
 reproduce/software/config/installation/versions.mk |   1 +
 reproduce/software/make/high-level.mk              |  19 ++++++++++++++++++-
 4 files changed, 37 insertions(+), 1 deletion(-)
 create mode 100644 reproduce/software/bibtex/sextractor.tex

diff --git a/.file-metadata b/.file-metadata
index 1c09605..bbda38e 100644
Binary files a/.file-metadata and b/.file-metadata differ
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/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk
index 270eb97..b7de983 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.mk
@@ -66,6 +66,7 @@ pkgconfig-version          = 0.29.2
 python-version             = 3.7.3
 readline-version           = 8.0
 sed-version                = 4.7
+sextractor-version         = 2.25.0
 swarp-version              = 2.38.0
 swig-version               = 3.0.12
 tar-version                = 1.32
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 144057e..59287c6 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -51,7 +51,7 @@ ipydir  = $(BDIR)/software/installed/version-info/python
 # 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-programs  = astrometrynet gnuastro metastore swarp
+top-level-programs  = astrometrynet gnuastro metastore sextractor swarp
 top-level-python    = astroquery matplotlib
 all: $(foreach p, $(top-level-libraries), $(ilidir)/$(p)) \
      $(foreach p, $(top-level-programs),  $(ibidir)/$(p)) \
@@ -139,6 +139,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometry-version).tar.gz        \
                         openmpi-$(openmpi-version).tar.gz                  \
                         openblas-$(openblas-version).tar.gz                \
                         pixman-$(pixman-version).tar.gz                    \
+                        sextractor-$(sextractor-version).tar.lz            \
                         swarp-$(swarp-version).tar.gz                      \
                         swig-$(swig-version).tar.gz                        \
                         tiff-$(libtiff-version).tar.gz                     \
@@ -207,6 +208,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	    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 = 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 [ $$n = tiff        ]; then w=https://download.osgeo.org/libtiff
@@ -712,6 +714,21 @@ $(ibidir)/netpbm: $(tdir)/netpbm-$(netpbm-version).tgz   \
     && rm -rf $$unpackdir                                                  \
     && echo "Netpbm $(netpbm-version)" > $@
 
+# 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, \
-- 
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