Added citation for TIDES, sorted progs alphabetically

While reviewing Prasenjit's commits, I noticed that we had forgot to add
the citation for TIDES, also to make things clear, the program/library
build rules are now sorted alphabetically.

Finally, I noticed that after building the TiKZ PDF figures, it is crashing
(like on Prasenjit's computer). After looking around, I noticed its because
we were setting the of the `TEXINPUTS' environment variable to be the
installed TeX Live directory (which was ultimately redundant because by
default TeX will look into where it was installed). The important thing is
just that we remove any possible value the host system has, not to set new
directories.

4 files changed, 142 insertions, 107 deletions

diff --git a/reproduce/software/bibtex/tides.tex b/reproduce/software/bibtex/tides.tex
new file mode 100644
index 0000000..f902da0
--- /dev/null
+++ b/reproduce/software/bibtex/tides.tex
@@ -0,0 +1,19 @@
+%% Copyright (C) 2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+%%
+%% 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{tides,
+   author = {{Abad}, A. and {Barrio}, R. and {Belsa}, F. and {Rodriguez}, M},
+    title = "{Algorithm 924: TIDES, a Taylor Series Integrator for Differential EquationS}",
+  journal = {ACM TOMS},
+     year = 2012,
+    month = nov,
+   volume = 39,
+      eid = {5},
+    pages = {5:1},
+      doi = {10.1145/2382585.2382590},
+ keywords = {Taylor series method, automatic differentiation, high precision, numerical integration of ODEs, variational equations},
+}
diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.mk
index 6dca171..b9157f1 100644
--- a/reproduce/software/config/installation/TARGETS.mk
+++ b/reproduce/software/config/installation/TARGETS.mk
@@ -36,7 +36,7 @@
 
 
 # Programs and libraries.
-top-level-programs  = gnuastro tides
+top-level-programs  = gnuastro
 
 # Python libraries/modules.
-# top-level-python    = astropy
+top-level-python    = astropy
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 81e8512..706a179 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -844,7 +844,9 @@ $(ibidir)/libiconv: $(tdir)/libiconv-$(libiconv-version).tar.gz \
 $(ibidir)/git: $(tdir)/git-$(git-version).tar.xz \
 	       $(ibidir)/libiconv \
                $(ibidir)/curl	# Coreutils, so Git is built after it.
-	export LDFLAGS=-lcharset; \
+	if [ x$(on_mac_os) = xyes ]; then \
+	  export LDFLAGS="$$LDFLAGS -lcharset"; \
+	fi; \
 	$(call gbuild, $<, git-$(git-version), static, \
 	               --without-tcltk --with-shell=$(ibdir)/bash \
 	               --with-iconv=$(idir), V=1) \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index e2827e9..90fc060 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -135,7 +135,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz \
                         sextractor-$(sextractor-version).tar.lz \
                         swarp-$(swarp-version).tar.gz \
                         swig-$(swig-version).tar.gz \
-			tides-$(tides-version).tar.gz \
+                        tides-$(tides-version).tar.gz \
                         tiff-$(libtiff-version).tar.gz \
                         wcslib-$(wcslib-version).tar.bz2 \
                         yaml-$(yaml-version).tar.gz \
@@ -236,6 +236,11 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 
 
 
+
+
+
+
+
 # Libraries
 # ---------
 #
@@ -244,105 +249,6 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 # libraries. Therefore, we can't use the easy `.a' suffix for static
 # libraries as targets and there are different conventions for shared
 # library names.
-$(ibidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \
-                   $(ibidir)/curl
-
-        # CFITSIO hard-codes '@rpath' inside the shared library on
-        # Mac systems. So we need to change it to our library
-        # installation path. It doesn't affect GNU/Linux, so we'll
-        # just do it in any case to keep things clean.
-	topdir=$(pwd); cd $(ddir); tar xf $<
-	customtar=cfitsio-$(cfitsio-version)-custom.tar.gz
-	cd cfitsio-$(cfitsio-version)
-	sed configure -e's|@rpath|$(ildir)|g' > configure_tmp
-	mv configure_tmp configure
-	chmod +x configure
-	cd ..
-	tar cf $$customtar cfitsio-$(cfitsio-version)
-	cd $$topdir
-
-        # Continue the standard build on the customized tarball.
-	$(call gbuild, $$customtar, cfitsio-$(cfitsio-version), , \
-	               --enable-sse2 --enable-reentrant \
-	               --with-bzip2=$(idir), , make shared) \
-	&& rm $$customtar \
-	&& echo "CFITSIO $(cfitsio-version)" > $@
-
-$(ibidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz \
-                 $(ibidir)/freetype \
-                 $(ibidir)/libpng \
-                 $(ibidir)/pixman
-	$(call gbuild, $<, cairo-$(cairo-version), static, \
-	               --with-x=no) \
-	&& echo "Cairo $(cairo-version)" > $@
-
-$(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz
-	$(call gbuild, $<, gsl-$(gsl-version), static) \
-	&& echo "GNU Scientific Library $(gsl-version)" > $@
-
-$(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz
-        # In order to build single and double precission libraries of
-        # `fftw', installation of `fftw' is done twice. First time is to
-        # build single precission float libraries and second time is for
-        # building the default double precission float libraries
-	$(call gbuild, $<, fftw-$(fftw-version), static, \
-	               --enable-shared enable-threads \
-		       --enable-single --enable-type-prefix) \
-	&& $(call gbuild, $<, fftw-$(fftw-version), static, \
-	               --enable-shared --enable-threads \
-		       --enable-type-prefix) \
-	&& cp $(dtexdir)/fftw.tex $(ictdir)/ \
-	&& echo "FFTW $(fftw-version) \citep{fftw}" > $@
-
-# Freetype is necessary to install matplotlib
-$(ibidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \
-	                $(ibidir)/libpng
-	$(call gbuild, $<, freetype-$(freetype-version), static) \
-	&& echo "FreeType $(freetype-version)" > $@
-
-$(ibidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz  \
-                $(ibidir)/openmpi
-	export CC=mpicc; \
-	export FC=mpif90; \
-	$(call gbuild, $<, hdf5-$(hdf5-version), static, \
-	               --enable-parallel \
-	               --enable-fortran, -j$(numthreads) V=1) \
-	&& echo "HDF5 library $(hdf5-version)" > $@
-
-$(ibidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
-	$(call gbuild, $<, jpeg-9b, static) \
-	&& echo "Libjpeg $(libjpeg-version)" > $@
-
-$(ibidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz
-	$(call gbuild, $<, libpng-$(libpng-version), static) \
-	&& echo "Libpng $(libpng-version)" > $@
-
-$(ibidir)/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)" > $@
-
-$(ibidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz
-	$(call gbuild, $<, pixman-$(pixman-version), static) \
-	&& echo "Pixman $(pixman-version)" > $@
-
-$(ibidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
-                   $(ibidir)/libjpeg
-	$(call gbuild, $<, tiff-$(libtiff-version), static, \
-	               --disable-webp --disable-zstd) \
-	&& echo "Libtiff $(libtiff-version)" > $@
-
-$(ibidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz
-	$(call gbuild, $<, openmpi-$(openmpi-version), static, , \
-	               -j$(numthreads) V=1) \
-	&& echo "Open MPI $(openmpi-version)" > $@
-
 $(ibidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \
 	         $(tdir)/lapack-$(lapack-version).tar.gz
 
@@ -423,6 +329,96 @@ $(ibidir)/atlas: $(tdir)/atlas-$(atlas-version).tar.bz2 \
 	  echo "ATLAS $(atlas-version)" > $@; \
 	fi
 
+$(ibidir)/cfitsio: $(tdir)/cfitsio-$(cfitsio-version).tar.gz \
+                   $(ibidir)/curl
+
+        # CFITSIO hard-codes '@rpath' inside the shared library on
+        # Mac systems. So we need to change it to our library
+        # installation path. It doesn't affect GNU/Linux, so we'll
+        # just do it in any case to keep things clean.
+	topdir=$(pwd); cd $(ddir); tar xf $<
+	customtar=cfitsio-$(cfitsio-version)-custom.tar.gz
+	cd cfitsio-$(cfitsio-version)
+	sed configure -e's|@rpath|$(ildir)|g' > configure_tmp
+	mv configure_tmp configure
+	chmod +x configure
+	cd ..
+	tar cf $$customtar cfitsio-$(cfitsio-version)
+	cd $$topdir
+
+        # Continue the standard build on the customized tarball.
+	$(call gbuild, $$customtar, cfitsio-$(cfitsio-version), , \
+	               --enable-sse2 --enable-reentrant \
+	               --with-bzip2=$(idir), , make shared) \
+	&& rm $$customtar \
+	&& echo "CFITSIO $(cfitsio-version)" > $@
+
+$(ibidir)/cairo: $(tdir)/cairo-$(cairo-version).tar.xz \
+                 $(ibidir)/freetype \
+                 $(ibidir)/libpng \
+                 $(ibidir)/pixman
+	$(call gbuild, $<, cairo-$(cairo-version), static, \
+	               --with-x=no) \
+	&& echo "Cairo $(cairo-version)" > $@
+
+$(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz
+        # In order to build single and double precission libraries of
+        # `fftw', installation of `fftw' is done twice. First time is to
+        # build single precission float libraries and second time is for
+        # building the default double precission float libraries
+	$(call gbuild, $<, fftw-$(fftw-version), static, \
+	               --enable-shared enable-threads \
+		       --enable-single --enable-type-prefix) \
+	&& $(call gbuild, $<, fftw-$(fftw-version), static, \
+	               --enable-shared --enable-threads \
+		       --enable-type-prefix) \
+	&& cp $(dtexdir)/fftw.tex $(ictdir)/ \
+	&& echo "FFTW $(fftw-version) \citep{fftw}" > $@
+
+# Freetype is necessary to install matplotlib
+$(ibidir)/freetype: $(tdir)/freetype-$(freetype-version).tar.gz \
+	                $(ibidir)/libpng
+	$(call gbuild, $<, freetype-$(freetype-version), static) \
+	&& echo "FreeType $(freetype-version)" > $@
+
+$(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz
+	$(call gbuild, $<, gsl-$(gsl-version), static) \
+	&& echo "GNU Scientific Library $(gsl-version)" > $@
+
+$(ibidir)/hdf5: $(tdir)/hdf5-$(hdf5-version).tar.gz  \
+                $(ibidir)/openmpi
+	export CC=mpicc; \
+	export FC=mpif90; \
+	$(call gbuild, $<, hdf5-$(hdf5-version), static, \
+	               --enable-parallel \
+	               --enable-fortran, -j$(numthreads) V=1) \
+	&& echo "HDF5 library $(hdf5-version)" > $@
+
+$(ibidir)/libjpeg: $(tdir)/jpegsrc.$(libjpeg-version).tar.gz
+	$(call gbuild, $<, jpeg-9b, static) \
+	&& echo "Libjpeg $(libjpeg-version)" > $@
+
+$(ibidir)/libpng: $(tdir)/libpng-$(libpng-version).tar.xz
+	$(call gbuild, $<, libpng-$(libpng-version), static) \
+	&& echo "Libpng $(libpng-version)" > $@
+
+$(ibidir)/libtiff: $(tdir)/tiff-$(libtiff-version).tar.gz \
+                   $(ibidir)/libjpeg
+	$(call gbuild, $<, tiff-$(libtiff-version), static, \
+	               --disable-webp --disable-zstd) \
+	&& echo "Libtiff $(libtiff-version)" > $@
+
+$(ibidir)/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)" > $@
+
 $(ibidir)/openblas: $(tdir)/openblas-$(openblas-version).tar.gz
 	if [ x$(on_mac_os) = xyes ]; then \
 	  export CC=clang; \
@@ -436,15 +432,28 @@ $(ibidir)/openblas: $(tdir)/openblas-$(openblas-version).tar.gz
 	&& rm -rf OpenBLAS-$(openblas-version) \
 	&& echo "OpenBLAS $(openblas-version)" > $@
 
-$(ibidir)/yaml: $(tdir)/yaml-$(yaml-version).tar.gz
-	$(call gbuild, $<, yaml-$(yaml-version), static) \
-	&& echo "LibYAML $(yaml-version)" > $@
+$(ibidir)/openmpi: $(tdir)/openmpi-$(openmpi-version).tar.gz
+	$(call gbuild, $<, openmpi-$(openmpi-version), static, , \
+	               -j$(numthreads) V=1) \
+	&& echo "Open MPI $(openmpi-version)" > $@
 
+$(ibidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz
+	$(call gbuild, $<, pixman-$(pixman-version), static) \
+	&& echo "Pixman $(pixman-version)" > $@
 
 $(ibidir)/tides: $(tdir)/tides-$(tides-version).tar.gz
 	$(call gbuild, $<, tides-$(tides-version), static,\
 	               --with-gmp=$(idir) --with-mpfr=$(idir)) \
-	&& echo "TIDES $(tides-version)" > $@
+	&& cp $(dtexdir)/tides.tex $(ictdir)/ \
+	&& echo "TIDES $(tides-version) \citep{tides}" > $@
+
+$(ibidir)/yaml: $(tdir)/yaml-$(yaml-version).tar.gz
+	$(call gbuild, $<, yaml-$(yaml-version), static) \
+	&& echo "LibYAML $(yaml-version)" > $@
+
+
+
+
 
 # Libraries with special attention on Mac OS
 # ------------------------------------------
@@ -502,6 +511,11 @@ $(ibidir)/wcslib: $(tdir)/wcslib-$(wcslib-version).tar.bz2 \
 
 
 
+
+
+
+
+
 # Programs
 # --------
 #