Imported some recent/parallel work, conflicts fixed

Especially because of the new convention regarding backslashes, there were
many conflicts that are now fixed. But none were substantial.

8 files changed, 114 insertions, 62 deletions

diff --git a/.file-metadata b/.file-metadata
index a86e94c..c22144e 100644
--- a/.file-metadata
+++ b/.file-metadata
diff --git a/configure b/configure
index e99776b..000ec4f 100755
--- a/configure
+++ b/configure
@@ -884,42 +884,80 @@ fi
 #
 # On some GNU/Linux distros, the C compiler is broken into `multilib' (for
 # 32-bit and 64-bit support, with their own headers). On these systems,
-# `sys/cdefs.h' is not available by default. So if the user hasn't manually
-# installed it before this configure script, GCC won't build. We are thus
-# explicitly testing a small C program here to see if the host's C compiler
-# won't have any problems in building GCC.
+# `/usr/include/sys/cdefs.h' and `/usr/lib/libc.a' are not available by
+# default. So GCC will crash with different ugly errors! The only solution
+# is that user manually installs the `multilib' part as root, before
+# running the configure script.
+#
+# Note that `sys/cdefs.h' may be available in other directories (for
+# example `/usr/include/x86_64-linux-gnu/') that are automatically included
+# in an installed GCC. HOWEVER during the build of GCC, all those other
+# directories are ignored. So even if they exist, they are useless.
+warningsleep=0
 if [ $host_cc = 0 ]; then
-    tfile=$sdir/gcc-cdefs-test.c;
-    echo "#include <sys/cdefs.h>"     > $tfile;
-    echo "int main(void){return 0;}" >> $tfile;
-    if gcc $tfile -o $sdir/gcc-cdefs-test &> /dev/null; then
-        rm $sdir/gcc-cdefs-test*;
-    else
+    if ! [ -f /usr/include/sys/cdefs.h ]; then
         host_cc=1
-    fi;
-    rm -f $tfile;
+        warningsleep=1
+        cat <<EOF
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+This system doesn't have '/usr/include/sys/cdefs.h'. Because of this, the
+project can't build its custom GCC to ensure better reproducibility. We
+strongly recommend installing the proper package (for your operating
+system) that installs this necessary file. For example on some Debian-based
+GNU/Linux distros, you need these two packages: 'gcc-multilib' and
+'g++-multilib'.
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+EOF
+    fi
 
-    if [ $host_cc = 1 ]; then
+    if [ -f /usr/lib/libc.a ] || [ -f /usr/lib64/libc.a ]; then
+        # This is just a place holder
+        host_cc=$host_cc
+    else
+        host_cc=1
+        warningsleep=1
         cat <<EOF
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!         Warning        !!!!!!!!!!!!!!!!!!!!!!
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
-This system's C compiler (called with 'gcc') can't include
-'sys/cdefs.h. Because of this, the project can't build its custom GCC to
-ensure better reproducibility. We strongly recommend installing the proper
-package (for your operating system) that installs this necessary file. For
-example on some Debian-based GNU/Linux distros, you need these two
-packages: 'gcc-multilib' and 'g++-multilib'.
-
-However, since GCC is pretty low-level, this configuration script will
-continue in 5 seconds and use your system's C compiler (it won't build a
-custom GCC). But please consider installing the necessary package(s) to
-complete your C compiler, then re-run './configure'.
+This system doesn't have '/usr/lib/libc.a' or '/usr/lib64/libc.a'. Because
+of this, the project can't build its custom GCC to ensure better
+reproducibility. We strongly recommend installing the proper package (for
+your operating system) that installs this necessary file.
+
+Some possible solutions:
+  1. On some Debian-based GNU/Linux distros, these two packages may fix the
+     problem: 'gcc-multilib' and 'g++-multilib'.
+  2. (BE CAREFUL!) If you have '/usr/lib/x86_64-linux-gnu' but don't have
+     '/usr/lib64', then running the following command might fix this
+     particular problem by making a symbolic link.
+         $ sudo ln -s /usr/lib/x86_64-linux-gnu /usr/lib64
+     After the configure script is finished, delete the link with 'rm
+     /usr/lib64' (you won't need it any more as far as this project is
+     concerned).
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
 
 EOF
+    fi
+
+    if [ $warningsleep = 1 ]; then
+        cat <<EOF
+
+PLEASE SEE THE WARNINGS ABOVE.
+
+Since GCC is pretty low-level, this configuration script will continue in 5
+seconds and use your system's C compiler (it won't build a custom GCC). But
+please consider installing the necessary package(s) to complete your C
+compiler, then re-run './configure'.
+
+EOF
         sleep 5
     fi
 fi
diff --git a/reproduce/software/config/installation/TARGETS.mk b/reproduce/software/config/installation/TARGETS.mk
index 4b1ff2e..b9157f1 100644
--- a/reproduce/software/config/installation/TARGETS.mk
+++ b/reproduce/software/config/installation/TARGETS.mk
@@ -1,6 +1,7 @@
 # Necessary high-level software to build in this project.
 #
 # Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# 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
diff --git a/reproduce/software/config/installation/numpy-scipy.cfg b/reproduce/software/config/installation/numpy-scipy.cfg
index 4b7a7b0..03038ed 100644
--- a/reproduce/software/config/installation/numpy-scipy.cfg
+++ b/reproduce/software/config/installation/numpy-scipy.cfg
@@ -8,6 +8,7 @@
 # should leave out sections that your package does not use.
 #
 # Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# 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
diff --git a/reproduce/software/config/installation/versions.mk b/reproduce/software/config/installation/versions.mk
index df2b4fa..5c7743d 100644
--- a/reproduce/software/config/installation/versions.mk
+++ b/reproduce/software/config/installation/versions.mk
@@ -83,10 +83,10 @@ gsl-version                = 2.5
 hdf5-version               = 1.10.5
 libffi-version             = 3.2.1
 libjpeg-version            = v9b
+libpng-version             = 1.6.37
 libtiff-version            = 4.0.10
 libtool-version            = 2.4.6
 libxml2-version            = 2.9.9
-netpbm-version             = 10.47.72
 openblas-version           = 0.3.5
 openmpi-version            = 4.0.1
 pixman-version             = 0.38.0
@@ -159,8 +159,8 @@ webencodings-version       = 0.5.1
 # during their build and must be accounted for.
 #
 # Special notes:
-#   - `libpng' is downgraded: the current installation of `netpbm' requires
-#     a version less than 1.5.
+#   - `netpbm' questions in the configure steps maybe change with different
+#   or new versions.
 
 # Basic/low-level
 bzip2-version              = 1.0.6
@@ -168,5 +168,5 @@ bzip2-version              = 1.0.6
 # Optional/high-level
 lapack-version             = 3.8.0
 libgit2-version            = 0.26.0
-libpng-version             = 1.4.22
+netpbm-version             = 10.86.99
 wcslib-version             = 6.2
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index f2442ff..05161e9 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -16,6 +16,7 @@
 # ------------------------------------------------------------------------
 #
 # Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # This Makefile is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by the
@@ -806,7 +807,8 @@ $(ibidir)/git: $(tdir)/git-$(git-version).tar.xz \
 	&& echo "Git $(git-version)" > $@
 
 $(ibidir)/gmp: $(tdir)/gmp-$(gmp-version).tar.lz \
-               $(ibidir)/bash
+               $(ibidir)/bash                    \
+               $(ibidir)/m4
 	$(call gbuild, $<, gmp-$(gmp-version), static, , , make check)  \
 	&& echo "GNU Multiple Precision Arithmetic Library $(gmp-version)" > $@
 
@@ -1038,7 +1040,7 @@ $(ibidir)/gcc: $(gcc-prerequisites) \
 	  rm -f $(ibdir)/gcc* $(ibdir)/g++ $(ibdir)/gfortran $(ibdir)/gcov*;\
 	  rm -rf $(ildir)/gcc $(ildir)/libcc* $(ildir)/libgcc*; \
 	  rm -rf $(ildir)/libgfortran* $(ildir)/libstdc* rm $(idir)/x86_64*;\
-	                                                                    \
+	                                 \
 	  ln -fs $(ildir) $(idir)/lib64; \
 	                                 \
 	  cd $(ddir); \
@@ -1076,7 +1078,7 @@ $(ibidir)/gcc: $(gcc-prerequisites) \
 	           patchelf --set-rpath $(ildir) $$f; \
 	         fi; \
 	       done; \
-	     fi; \
-	  ln -sf $(ibdir)/gcc $(ibdir)/cc \
+	     fi \
+	  && ln -sf $(ibdir)/gcc $(ibdir)/cc \
 	  && echo "GNU Compiler Collection (GCC) $(gcc-version)" > $@; \
 	fi
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index c930814..85120bd 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -9,6 +9,7 @@
 # ------------------------------------------------------------------------
 #
 # Copyright (C) 2018-2019 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # This Makefile is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by the
@@ -123,7 +124,7 @@ tarballs = $(foreach t, astrometry.net-$(astrometrynet-version).tar.gz \
                         libpng-$(libpng-version).tar.xz \
                         libgit2-$(libgit2-version).tar.gz \
                         libxml2-$(libxml2-version).tar.gz \
-                        netpbm-$(netpbm-version).tgz \
+                        netpbm-$(netpbm-version).tar.gz \
                         openmpi-$(openmpi-version).tar.gz \
                         openblas-$(openblas-version).tar.gz \
                         pixman-$(pixman-version).tar.gz \
@@ -183,9 +184,7 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	    mergenames=0
 	    w=https://github.com/libgit2/libgit2/archive/v$(libgit2-version).tar.gz
 	  elif [ $$n = libxml      ]; then w=ftp://xmlsoft.org/libxml2
-	  elif [ $$n = netpbm      ]; then
-	    mergenames=0
-		w=https://sourceforge.net/projects/netpbm/files/super_stable/$(netpbm-version)/netpbm-$(netpbm-version).tgz/download
+	  elif [ $$n = netpbm      ]; then w=http://akhlaghi.org/src
 	  elif [ $$n = openblas    ]; then
 	    mergenames=0
 	    w=https://github.com/xianyi/OpenBLAS/archive/v$(openblas-version).tar.gz
@@ -207,13 +206,13 @@ $(tarballs): $(tdir)/%: | $(lockdir)
 	    exit 1
 	  fi
 
-	  # Download the requested tarball. Note that some packages may not
-	  # follow our naming convention (where the package name is merged
-	  # with its version number). In such cases, `w' will be the full
-	  # address, not just the top directory address. But since we are
-	  # storing all the tarballs in one directory, we want it to have
-	  # the same naming convention, so we'll download it to a temporary
-	  # name, then rename that.
+      # Download the requested tarball. Note that some packages may not
+      # follow our naming convention (where the package name is merged
+      # with its version number). In such cases, `w' will be the full
+      # address, not just the top directory address. But since we are
+      # storing all the tarballs in one directory, we want it to have
+      # the same naming convention, so we'll download it to a temporary
+      # name, then rename that.
 	  if [ $$mergenames = 1 ]; then  tarballurl=$$w/"$*"
 	  else                           tarballurl=$$w
 	  fi
@@ -279,7 +278,7 @@ $(ibidir)/gsl: $(tdir)/gsl-$(gsl-version).tar.gz
 
 $(ibidir)/fftw: $(tdir)/fftw-$(fftw-version).tar.gz
 	$(call gbuild, $<, fftw-$(fftw-version), static, \
-	               --enable-shared) \
+	               --enable-shared --enable-single) \
 	&& cp $(dtexdir)/fftw.tex $(ictdir)/ \
 	&& echo "FFTW $(fftw-version) \citep{fftw}" > $@
 
@@ -314,7 +313,7 @@ $(ibidir)/libxml2: $(tdir)/libxml2-$(libxml2-version).tar.gz
        # If you really need the Python bindings, try the
        # --with-python-install-dir=DIR option
 	$(call gbuild, $<, libxml2-$(libxml2-version), static, \
-                   --without-python)                       \
+	               --without-python)                       \
 	&& echo "Libxml2 $(libxml2-version)" > $@
 
 $(ibidir)/pixman: $(tdir)/pixman-$(pixman-version).tar.gz
@@ -500,9 +499,17 @@ $(ibidir)/astrometrynet: $(tdir)/astrometry.net-$(astrometrynet-version).tar.gz
                          $(ipydir)/numpy \
                          $(ibidir)/swig \
                          $(ibidir)/gsl
+        # We are modifying the Makefile in two steps because on Mac OS
+        # system we do not have `/proc/cpuinfo' nor `free'. Since this is
+        # only for the `report.txt', this changes do not causes problems in
+        # running `astrometrynet'
 	cd $(ddir) \
+	&& rm -rf astrometry.net-$(astrometrynet-version) \
 	&& if ! tar xf $<; then echo; echo "Tar error"; exit 1; fi \
 	&& cd astrometry.net-$(astrometrynet-version) \
+	&& sed -e 's|cat /proc/cpuinfo|echo "Ignoring CPU info"|' \
+	       -e 's|-free|echo "Ignoring RAM info"|' Makefile > Makefile.tmp \
+	&& mv Makefile.tmp Makefile \
 	&& make \
 	&& make py \
 	&& make extra \
@@ -594,7 +601,7 @@ $(ibidir)/netpbm: $(tdir)/netpbm-$(netpbm-version).tgz \
                   $(ibidir)/libpng \
                   $(ibidir)/unzip
 	if [ x$(on_mac_os) = xyes ]; then \
-	  answers='\n\n\n\n\n\n\n\n\n\n\n\nnone\n\n\n'; \
+	  answers='\n\n$(ildir)\n\n\n\n\n\n$(ildir)/include\n\n$(ildir)/include\n\n$(ildir)/include\nnone\n\n'; \
 	else \
 	  answers='\n\n\n\ny\n\n\n\n\n\n\n\n\n\n\n\n\n'; \
 	fi; \
@@ -608,7 +615,7 @@ $(ibidir)/netpbm: $(tdir)/netpbm-$(netpbm-version).tgz \
 	&& rm -rf $(ddir)/$$unpackdir/install \
 	&& make package pkgdir=$(ddir)/$$unpackdir/install \
 	&& printf "$(ddir)/$$unpackdir/install\n$(idir)\n\n\nN\n\n\n\n\nN\n\n" \
-	        | ./installnetpbm \
+	          | ./installnetpbm \
 	&& cd .. \
 	&& rm -rf $$unpackdir \
 	&& echo "Netpbm $(netpbm-version)" > $@
@@ -619,9 +626,9 @@ $(ibidir)/netpbm: $(tdir)/netpbm-$(netpbm-version).tgz \
 # the option --enable-openblas and it worked (same issue happened with
 # `sextractor'.
 $(ibidir)/scamp: $(tdir)/scamp-$(scamp-version).tar.lz \
-                      $(ibidir)/cdsclient \
-                      $(ibidir)/openblas \
-                      $(ibidir)/fftw
+                 $(ibidir)/cdsclient \
+                 $(ibidir)/openblas \
+                 $(ibidir)/fftw
 	$(call gbuild, $<, scamp-$(scamp-version), static, \
                    --enable-threads --enable-openblas \
                    --with-fftw-libdir=$(idir) \
@@ -639,19 +646,19 @@ $(ibidir)/sextractor: $(tdir)/sextractor-$(sextractor-version).tar.lz \
                       $(ibidir)/openblas \
                       $(ibidir)/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}" > $@
+	               --enable-threads --enable-openblas \
+	               --with-openblas-libdir=$(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 \
                  $(ibidir)/fftw
 	$(call gbuild, $<, swarp-$(swarp-version), static, \
-                   --enable-threads) \
-    && cp $(dtexdir)/swarp.tex $(ictdir)/ \
-    && echo "SWarp $(swarp-version) \citep{swarp}" > $@
+                       --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
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index 4c407f6..1a7be56 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -350,7 +350,9 @@ $(ipydir)/h5py: $(tdir)/h5py-$(h5py-version).tar.gz \
                 $(ipydir)/pypkgconfig \
                 $(ipydir)/setuptools \
                 $(ipydir)/cython \
-                $(ibidir)/hdf5
+                $(ipydir)/numpy \
+                $(ibidir)/hdf5 \
+                $(ipydir)/six
                 #$(ipydir)/mpi4py # AFTER its problem is fixed.
         #export HDF5_MPI=ON;       # AFTER its problem is fixed.
 	export HDF5_DIR=$(ildir); \
@@ -496,8 +498,9 @@ $(ipydir)/setuptools_scm: $(tdir)/setuptools_scm-$(setuptools_scm-version).tar.g
 	$(call pybuild, tar xf, $<, setuptools_scm-$(setuptools_scm-version), ,\
 	                Setuptools-scm $(setuptools_scm-version))
 
-$(ipydir)/sip_tpv: $(tdir)/sip_tpv-$(sip_tpv-version).tar.gz   \
-                  $(ipydir)/mpmath \
+$(ipydir)/sip_tpv: $(tdir)/sip_tpv-$(sip_tpv-version).tar.gz \
+                  $(ipydir)/astropy \
+                  $(ipydir)/numpy \
                   $(ipydir)/sympy
 	$(call pybuild, tar xf, $<, sip_tpv-$(sip_tpv-version), ,) \
 	&& cp $(dtexdir)/sip_tpv.tex $(ictdir)/ \