IMPORTANT: software config directly under reproduce/software/config

Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.

With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.

3 files changed, 16 insertions, 14 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 47a01a3..17bb47a 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -33,10 +33,10 @@
 
 
 # Top level environment
+include reproduce/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.conf
-include reproduce/software/config/installation/versions.conf
-include reproduce/software/config/installation/checksums.conf
+include reproduce/software/config/versions.conf
+include reproduce/software/config/checksums.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -1334,12 +1334,14 @@ $(ibidir)/gcc: | $(ibidir)/binutils \
 	  && cd ../.. \
 	  && tempname=$$odir/gcc-$(gcc-version)/build/rpath-temp-copy \
 	  && if [ "x$(on_mac_os)" != xyes ]; then \
-	       patchelf --add-needed $(ildir)/libiconv.so $(ildir)/libstdc++.so; \
 	       for f in $$(find $(idir)/libexec/gcc) $(ildir)/libstdc++*; do \
 	         isdynamic=$$(file $$f | grep "dynamically linked"); \
 	         if [ x"$$isdynamic" != x ]; then \
 	           cp $$f $$tempname; \
 	           patchelf --set-rpath $(ildir) $$tempname; \
+	           if [ "$$f" = $(ildir)/libstdc++.so ]; then \
+	             patchelf --add-needed $(ildir)/libiconv.so $$tempname; \
+	           fi; \
 	           mv $$tempname $$f; echo "corrected"; \
 	         fi; \
 	       done; \
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 6e01354..e62f02f 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -27,12 +27,12 @@
 
 
 # Top level environment
+include reproduce/software/config/LOCAL.conf
 include reproduce/software/make/build-rules.mk
-include reproduce/software/config/installation/LOCAL.conf
-include reproduce/software/config/installation/TARGETS.conf
-include reproduce/software/config/installation/versions.conf
-include reproduce/software/config/installation/checksums.conf
-include reproduce/software/config/installation/texlive-packages.conf
+include reproduce/software/config/TARGETS.conf
+include reproduce/software/config/versions.conf
+include reproduce/software/config/checksums.conf
+include reproduce/software/config/texlive-packages.conf
 
 lockdir = $(BDIR)/locks
 tdir    = $(BDIR)/software/tarballs
@@ -1240,7 +1240,7 @@ $(ibidir)/xlsxio: $(ibidir)/cmake \
 tlmirror=http://mirrors.rit.edu/CTAN/systems/texlive/tlnet
 
 # The core TeX Live system.
-$(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.conf \
+$(itidir)/texlive-ready-tlmgr: reproduce/software/config/texlive.conf \
                                | $(tdir)/install-tl-unx.tar.gz
 
         # Unpack, enter the directory, and install based on the given
@@ -1251,7 +1251,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
 	tar xf $(tdir)/install-tl-unx.tar.gz
 	cd install-tl-*
 	sed -e's|@installdir[@]|$(idir)|g' \
-	    $$topdir/reproduce/software/config/installation/texlive.conf \
+	    $$topdir/reproduce/software/config/texlive.conf \
 	    > texlive.conf
 
         # TeX Live's installation may fail due to any reason. But TeX Live
@@ -1292,7 +1292,7 @@ $(itidir)/texlive-ready-tlmgr: reproduce/software/config/installation/texlive.co
 #else
 #forbiber = $(ibidir)/libnsl
 #endif
-$(itidir)/texlive: reproduce/software/config/installation/texlive-packages.conf \
+$(itidir)/texlive: reproduce/software/config/texlive-packages.conf \
                    $(itidir)/texlive-ready-tlmgr \
                    $(forbiber)
 
diff --git a/reproduce/software/make/python.mk b/reproduce/software/make/python.mk
index a15841c..1ef1bf2 100644
--- a/reproduce/software/make/python.mk
+++ b/reproduce/software/make/python.mk
@@ -600,7 +600,7 @@ $(ipydir)/numpy: $(ibidir)/unzip \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
 	export CFLAGS="--std=c99 $$CFLAGS"; \
-	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
+	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \
 	$(call pybuild, unzip, numpy-$(numpy-version),$$conf, \
 	                Numpy $(numpy-version)) \
 	&& cp $(dtexdir)/numpy.tex $(ictdir)/ \
@@ -679,7 +679,7 @@ $(ipydir)/scipy: $(ipydir)/numpy \
 	else \
 	  export LDFLAGS="$(LDFLAGS) -shared"; \
 	fi; \
-	conf="$$(pwd)/reproduce/software/config/installation/numpy-scipy.cfg"; \
+	conf="$$(pwd)/reproduce/software/config/numpy-scipy.cfg"; \
 	$(call pybuild, tar xf, scipy-$(scipy-version),$$conf) \
 	&& cp $(dtexdir)/scipy.tex $(ictdir)/ \
 	&& echo "Scipy $(scipy-version) \citep{scipy2007,scipy2011}" > $@