From ba0895b5299512e5028429e9e0111ab9944899cc Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 26 Apr 2016 16:45:33 +0200
Subject: Add SIRT plugin

---
 build/linux/Makefile.in | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index f10f482..14027e1 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -399,8 +399,10 @@ ifeq ($(python),yes)
 install-python: py
 	$(INSTALL_SH) -m 755 -d @prefix@/python
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra
+	$(INSTALL_SH) -m 755 -d @prefix@/python/astra/plugins
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.so @prefix@/python/astra
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.py @prefix@/python/astra
+	$(INSTALL_SH) -m 644 python/finalbuild/astra/plugins/*.py @prefix@/python/astra/plugins
 	$(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/
 	@echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
 	@echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH"
-- 
cgit v1.2.3


From 64a48bea80b909311351dc3b1345a17c693ddb69 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 28 Sep 2016 14:58:41 +0200
Subject: Add experimental support for Octave

Based on initial patch by @kalvdans.
---
 build/linux/Makefile.in  | 51 +++++++++++++++++++++++++++++++++++++++++++++++-
 build/linux/configure.ac | 23 ++++++++++++++++++++++
 2 files changed, 73 insertions(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 14027e1..076cfd1 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -5,6 +5,7 @@ boostutf=@HAVEBOOSTUTF@
 
 
 MATLAB_ROOT=@MATLAB_ROOT@
+octave=@HAVEOCTAVE@
 
 TARGETS=libastra.la
 
@@ -16,6 +17,10 @@ ifeq ($(python),yes)
 TARGETS+=py
 endif
 
+ifeq ($(octave),yes)
+TARGETS+=oct
+endif
+
 all: $(TARGETS)
 
 prefix=@prefix@
@@ -46,6 +51,16 @@ LIBS      += -lcudart -lcufft
 NVCC       = @NVCC@
 endif
 
+ifeq ($(octave),yes)
+OCTLDFLAGS:=$(LDFLAGS)
+CPPFLAGS += @OCTAVE_CPPFLAGS@
+ifeq ($(cuda),yes)
+OCTFLAGS=-DASTRA_CUDA
+else
+OCTFLAGS=
+endif
+endif
+
 ifeq ($(matlab),yes)
 CPPFLAGS+=-I$(MATLAB_ROOT)/extern/include -DMATLAB_MEX_FILE
 CXXFLAGS+=-fopenmp
@@ -259,6 +274,20 @@ ifeq ($(python),yes)
 MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX)
 endif
 
+OCTAVE_CXX_OBJECTS=\
+	matlab/mex/octave_support.o
+
+OCTAVE_MEX=\
+	matlab/mex/astra_mex_algorithm_c.mex \
+	matlab/mex/astra_mex_data2d_c.mex \
+	matlab/mex/astra_mex_c.mex \
+	matlab/mex/astra_mex_matrix_c.mex \
+	matlab/mex/astra_mex_projector_c.mex \
+	matlab/mex/astra_mex_projector3d_c.mex \
+	matlab/mex/astra_mex_log_c.mex \
+	matlab/mex/astra_mex_data3d_c.mex \
+	matlab/mex/astra_mex_direct_c.mex
+
 OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./
 DEPDIRS = $(addsuffix $(DEPDIR),$(OBJECT_DIRS))
 -include $(wildcard $(addsuffix /*.d,$(DEPDIRS)))
@@ -294,6 +323,13 @@ python-root-install: libastra.la
 endif
 
 
+ifeq ($(octave),yes)
+oct: $(OCTAVE_MEX)
+
+%.mex: %.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS) libastra.la
+	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) -L.libs -lastra --output $* $*.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
+endif
+
 libastra.la: $(ALL_OBJECTS)
 	./libtool --mode=link --tag=CXX $(LD) -rpath $(LIBDIR) -o $@ $(LDFLAGS) $(LIBS) $+
 
@@ -374,7 +410,7 @@ distclean: clean
 	rm -rf $(srcdir)/autom4te.cache
 	rm -f $(srcdir)/configure Makefile
 
-install: install-libraries install-matlab install-python
+install: install-libraries install-matlab install-python install-octave
 
 install-libraries: libastra.la
 	$(INSTALL_SH) -m 755 -d @libdir@
@@ -413,6 +449,19 @@ else
 install-python:
 endif
 
+ifeq ($(octave),yes)
+# TODO: This install location doesn't work well for /usr or /usr/local
+install-octave: $(OCTAVE_MEX)
+	$(INSTALL_SH) -m 755 -d @prefix@/octave
+	$(INSTALL_SH) -m 755 -d @prefix@/octave/mex
+	$(INSTALL_SH) -m 755 -d @prefix@/octave/tools
+	$(INSTALL_SH) -m 644 $(OCTAVE_MEX) @prefix@/octave/mex
+	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m @prefix@/octave/tools
+# TODO: docs
+else
+install-octave:
+endif
+
 
 Makefile: $(srcdir)/Makefile.in config.status
 	CONFIG_HEADERS= CONFIG_LINKS= CONFIG_FILES=$@ $(SHELL) ./config.status
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 630b08d..0d80cec 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -175,6 +175,28 @@ fi
 
 AC_SUBST(HAVEMATLAB)
 
+# octave
+
+AC_ARG_ENABLE(octave, [[  --disable-octave      disable Octave support]])
+if test x"$enable_octave" != xno; then
+  AC_PATH_PROG([HAVEOCTAVE], [octave-config], [no], [$PATH])
+  AC_MSG_CHECKING([for octave])
+  if test x"HAVEOCTAVE" != xno -a $HAVEMATLAB = yes; then
+    HAVEOCTAVE=no
+    AC_MSG_RESULT([no (since Matlab support is enabled)])
+  else
+    if test x"$HAVEOCTAVE" != xno; then
+      OCTAVE_CPPFLAGS="-I`octave-config -p OCTINCLUDEDIR`"
+      AC_SUBST(OCTAVE_CPPFLAGS)
+      HAVEOCTAVE=yes
+    fi
+    AC_MSG_RESULT($HAVEOCTAVE)
+  fi
+else
+  HAVEOCTAVE=no
+fi
+AC_SUBST(HAVEOCTAVE)
+
 # python
 
 AC_ARG_WITH(python, [[  --with-python=path      path of Python binary (optional)]],,)
@@ -271,6 +293,7 @@ echo
 echo "Summary of ASTRA Toolbox build options:"
 echo "  CUDA   : $HAVECUDA"
 echo "  Matlab : $HAVEMATLAB"
+echo "  Octave : $HAVEOCTAVE"
 echo "  Python : $HAVEPYTHON"
 echo
 echo "  prefix : $prefix"
-- 
cgit v1.2.3


From d93769add0fc322c051614d610f1aa645cb859da Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 21 Nov 2016 10:29:38 +0100
Subject: Add install-octave to .PHONY

---
 build/linux/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 076cfd1..50afc1c 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -474,7 +474,7 @@ $(srcdir)/configure: $(srcdir)/configure.ac
 	@echo "configure.ac has been changed. Regenerating configure script"
 	cd $(srcdir) && $(SHELL) ./autogen.sh
 
-.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python
+.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python install-octave
 
 # don't remove intermediate files:
 .SECONDARY:
-- 
cgit v1.2.3


From 6282fbe29bd2a8594bbc589e3996030e882b84f5 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 21 Nov 2016 12:16:40 +0100
Subject: Show NVCCFLAGS help

---
 build/linux/configure.ac | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 0d80cec..96be24c 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -141,6 +141,8 @@ if test x"$HAVECUDA" = xyes; then
   AC_MSG_RESULT([$NVCCARCHS])
 fi
 
+AC_ARG_VAR(NVCCFLAGS, [CUDA nvcc flags])
+
 
 AC_SUBST(HAVECUDA)
 AC_SUBST(LDFLAGS_CUDA)
-- 
cgit v1.2.3


From fab3c9ab472f1044f8aaf5d08f398f08995ba338 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 21 Nov 2016 13:27:46 +0100
Subject: Separate python build and install steps

---
 build/linux/Makefile.in | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 50afc1c..865a936 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -309,14 +309,10 @@ endif
 ifeq ($(python),yes)
 py: libastra.la
 	$(MKDIR) python/build
-	$(MKDIR) python/finalbuild
 	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \
-	--install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \
-	--install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild
+	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build
 
-python-root-install: libastra.la
-	$(MKDIR) python/build
+python-root-install: py
 	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
 	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install
 
@@ -433,6 +429,11 @@ endif
 ifeq ($(python),yes)
 # TODO: This install location doesn't work well for /usr or /usr/local
 install-python: py
+	$(MKDIR) python/finalbuild
+	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
+	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \
+	--install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \
+	--install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild
 	$(INSTALL_SH) -m 755 -d @prefix@/python
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra/plugins
-- 
cgit v1.2.3


From 88ef7076c710c4482d923d1f8a33ec0dec031d7f Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 21 Nov 2016 16:59:34 +0100
Subject: Update tested cuda compute capabilities

---
 build/linux/configure.ac | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 96be24c..7ccc8f5 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -133,9 +133,9 @@ fi
 AC_ARG_WITH(cuda_compute, [[  --with-cuda-compute=archs  comma separated list of CUDA compute models (optional)]],,)
 if test x"$HAVECUDA" = xyes; then
   AC_MSG_CHECKING([for nvcc archs])
-  dnl 10 11 12 13 20 30 32 35 37 50
+  dnl 10 11 12 13 20 21 30 32 35 37 50 52 53 60 61
   if test x"$with_cuda_compute" = x; then
-    with_cuda_compute="10,12,20,30,35,50"
+    with_cuda_compute="20,30,35,50,60"
   fi
   ASTRA_FIND_NVCC_ARCHS([$with_cuda_compute],NVCCFLAGS_EXTRA,NVCCARCHS)
   AC_MSG_RESULT([$NVCCARCHS])
-- 
cgit v1.2.3


From 7e10c16eee71c608a1dba1dd2fec8471567f6b61 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 21 Nov 2016 17:00:50 +0100
Subject: Overhaul package installation

There are now three ways of installing from configure/make:

./configure --with-install-type=prefix (default)

libraries go into @libdir@
matlab tools/mex go into @datadir@/astra/matlab
octave tools/mex go into @datadir@/astra/octave
python module goes into site-packages

./configure --with-install-type=dir

libraries go into @prefix@/lib
matlab tools/mex go into @prefix@/matlab
octave tools/mex go into @prefix@/octave
python module goes into @prefix@/python

./configure --with-install-type=module

matlab tools/mex go into @prefix@/matlab
octave tools/mex go into @prefix@/octave
python module goes into site-packages
library is installed along with the matlab/octave/python module(s), with rpath
---
 build/linux/Makefile.in  | 183 +++++++++++++++++++++++++++++------------------
 build/linux/configure.ac |  12 +++-
 2 files changed, 125 insertions(+), 70 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 865a936..1c7088e 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -1,12 +1,19 @@
+install_type=@INSTALL_TYPE@
+
 cuda=@HAVECUDA@
 matlab=@HAVEMATLAB@
 python=@HAVEPYTHON@
 boostutf=@HAVEBOOSTUTF@
 
-
 MATLAB_ROOT=@MATLAB_ROOT@
 octave=@HAVEOCTAVE@
 
+MKDIR=mkdir -p
+CXX=@CXX@
+LD=@CXX@
+SHELL=@SHELL@
+INSTALL_SH=$(SHELL) $(srcdir)/install-sh
+
 TARGETS=libastra.la
 
 ifeq ($(matlab),yes)
@@ -25,6 +32,7 @@ all: $(TARGETS)
 
 prefix=@prefix@
 exec_prefix=@exec_prefix@
+datarootdir=@datarootdir@
 
 srcdir=@srcdir@
 abs_top_builddir=@abs_top_builddir@
@@ -43,6 +51,8 @@ LDFLAGS+=-g
 
 CPPFLAGS+=@CPPFLAGS_OS@
 
+BOOSTUTF_LIBS=@LIBS_BOOSTUTF@
+
 ifeq ($(cuda),yes)
 CPPFLAGS  += @CPPFLAGS_CUDA@ -DASTRA_CUDA
 NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I$(srcdir)/../.. -I$(srcdir)/../../include -DASTRA_CUDA
@@ -51,58 +61,38 @@ LIBS      += -lcudart -lcufft
 NVCC       = @NVCC@
 endif
 
-ifeq ($(octave),yes)
-OCTLDFLAGS:=$(LDFLAGS)
-CPPFLAGS += @OCTAVE_CPPFLAGS@
-ifeq ($(cuda),yes)
-OCTFLAGS=-DASTRA_CUDA
-else
-OCTFLAGS=
-endif
-endif
-
 ifeq ($(matlab),yes)
+# TODO: Do we also want -fopenmp for octave?
 CPPFLAGS+=-I$(MATLAB_ROOT)/extern/include -DMATLAB_MEX_FILE
 CXXFLAGS+=-fopenmp
 LDFLAGS+=-fopenmp
 endif
 
+# MODLDFLAGS are the base LDFLAGS for matlab, octave, python modules
+MODLDFLAGS=$(LDFLAGS) -L$(abs_top_builddir)/.libs
+ifeq ($(install_type),module)
+MODLDFLAGS+=-Wl,-rpath,'\$$ORIGIN'
+endif
+
 ifeq ($(python),yes)
 PYTHON      = @PYTHON@
-PYLIBDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; import six; six.print_(get_config_var("LIBDIR"))')
-PYINCDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())')
+PYLIBDIR := $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; import six; six.print_(get_config_var("LIBDIR"))')
+PYINCDIR := $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())')
 PYLIBVER = `basename $(PYINCDIR)`
 CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR)
 PYCPPFLAGS  := $(CPPFLAGS)
 PYCPPFLAGS  += -I../include
-PYLDFLAGS = $(LDFLAGS)
-PYLDFLAGS   += -L$(abs_top_builddir)/.libs
+PYLDFLAGS = $(MODLDFLAGS)
 endif
 
 # This is below where PYCPPFLAGS copies CPPFLAGS.  The python code is built
 # from a different directory, so these relative includes would be wrong.
 CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include
 
-BOOST_CPPFLAGS=
-BOOST_LDFLAGS=
-
-BOOSTUTF_LIBS=@LIBS_BOOSTUTF@
-
-
-CPPFLAGS+=$(BOOST_CPPFLAGS)
-LDFLAGS+=$(BOOST_LDFLAGS)
-
-
-MKDIR=mkdir -p
-CXX=@CXX@
-LD=@CXX@
-SHELL=@SHELL@
-INSTALL_SH=$(SHELL) $(srcdir)/install-sh
-
 ifeq ($(matlab),yes)
 MEXFLAGS  = -cxx
-MEXLDFLAGS='$$LDFLAGS $(LDFLAGS)'
-MEXLIBS   = -L.libs -lut
+MEXLDFLAGS=\$$LDFLAGS $(MODLDFLAGS)
+MEXLIBS   = -lut
 MEXSUFFIX = @MEXSUFFIX@
 MEX       = @MEX@
 
@@ -111,13 +101,23 @@ MEXFLAGS += -DASTRA_CUDA
 endif
 
 ifeq ($(python),yes)
-MEXPYLDFLAGS='$$LDFLAGS $(LDFLAGS) -L$(PYLIBDIR)'
+# TODO: Why PYLIBDIR?
+MEXPYLDFLAGS=\$$LDFLAGS $(MODLDFLAGS) -L$(PYLIBDIR)
 MEXPYLIBS=$(MEXLIBS) -l$(PYLIBVER)
 endif
 
 endif
 
-LIBDIR=/usr/local/lib
+
+ifeq ($(octave),yes)
+OCTLDFLAGS:=$(MODLDFLAGS)
+CPPFLAGS += @OCTAVE_CPPFLAGS@
+ifeq ($(cuda),yes)
+OCTFLAGS=-DASTRA_CUDA
+else
+OCTFLAGS=
+endif
+endif
 
 DEPDIR=.deps
 
@@ -293,28 +293,28 @@ DEPDIRS = $(addsuffix $(DEPDIR),$(OBJECT_DIRS))
 -include $(wildcard $(addsuffix /*.d,$(DEPDIRS)))
 LIBDIRS = $(addsuffix .libs,./ src/ cuda/2d/ cuda/3d/)
 
+SONAME=$(shell . ${abs_top_builddir}/libastra.la; echo $$dlname)
 
 ifeq ($(matlab),yes)
 mex: $(MATLAB_MEX)
 
 %.$(MEXSUFFIX): %.o $(MATLAB_CXX_OBJECTS) libastra.la
-	$(MEX) LDFLAGS=$(MEXLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS)
+	$(MEX) LDFLAGS="$(MEXLDFLAGS)" $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS)
 
 ifeq ($(python),yes)
 matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX): matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) libastra.la
-	$(MEX) LDFLAGS=$(MEXPYLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS)
+	$(MEX) LDFLAGS="$(MEXPYLDFLAGS)" $(MEXFLAGS) $(LIBS) $(MEXPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS)
 endif
 endif
 
 ifeq ($(python),yes)
 py: libastra.la
 	$(MKDIR) python/build
-	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build
-
-python-root-install: py
-	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install
+# TODO: Avoid writing into source dir
+	ln -s $(abs_top_builddir)/.libs/$(SONAME) $(srcdir)/../../python/astra
+# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
+	cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS='${PYLDFLAGS}' $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build
+	rm $(srcdir)/../../python/astra/$(SONAME)
 
 endif
 
@@ -327,7 +327,7 @@ oct: $(OCTAVE_MEX)
 endif
 
 libastra.la: $(ALL_OBJECTS)
-	./libtool --mode=link --tag=CXX $(LD) -rpath $(LIBDIR) -o $@ $(LDFLAGS) $(LIBS) $+
+	./libtool --mode=link --tag=CXX $(LD) -rpath @libdir@ -o $@ $(LDFLAGS) $(LIBS) $+
 
 %.o: %.cpp
 	$(MKDIR) $(*D)/$(DEPDIR)
@@ -406,32 +406,64 @@ distclean: clean
 	rm -rf $(srcdir)/autom4te.cache
 	rm -f $(srcdir)/configure Makefile
 
-install: install-libraries install-matlab install-python install-octave
-
 install-libraries: libastra.la
 	$(INSTALL_SH) -m 755 -d @libdir@
 	./libtool --mode=install $(INSTALL_SH) -m 644 libastra.la @libdir@
 	./libtool --mode=finish @libdir@
 
-ifeq ($(matlab),yes)
-# TODO: This install location doesn't work well for /usr or /usr/local
-install-matlab: $(MATLAB_MEX)
-	$(INSTALL_SH) -m 755 -d @prefix@/matlab
-	$(INSTALL_SH) -m 755 -d @prefix@/matlab/mex
-	$(INSTALL_SH) -m 755 -d @prefix@/matlab/tools
-	$(INSTALL_SH) -m 644 $(MATLAB_MEX) @prefix@/matlab/mex
-	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m @prefix@/matlab/tools
-# TODO: docs
+
+# ------------------------
+# INSTALLATION
+# ------------------------
+
+ifeq ($(install_type),prefix)
+# libraries into @libdir@, python into site-packages, mex into @datadir@
+install: install-libraries install-matlab python-root-install install-octave
+
+PYPKGDATA=
+MATLABBASE=@datadir@/astra/matlab
+OCTAVEBASE=@datadir@/astra/octave
+endif
+
+ifeq ($(install_type),dir)
+# everything into @prefix@
+install: install-libraries install-matlab install-python install-octave
+
+PYPKGDATA=
+MATLABBASE=@prefix@/matlab
+OCTAVEBASE=@prefix@/octave
+PYTHONBASE=@prefix@/python
+endif
+
+ifeq ($(install_type),module)
+# python into site-packages, mex into @datadir@
+# library copied into python/mex directories
+# modules built with rpath=$ORIGIN
+install: install-matlab python-root-install install-octave
+
+PYPKGDATA=$(SONAME)
+MATLABBASE=@prefix@/matlab
+OCTAVEBASE=@prefix@/octave
+
+install-matlab-so: libastra.la
+	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/mex
+	$(INSTALL_SH) -m 644 $(abs_top_builddir)/.libs/$(SONAME) $(MATLABBASE)/mex
+install-octave-so: libastra.la
+	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/mex
+	$(INSTALL_SH) -m 644 $(abs_top_builddir)/.libs/$(SONAME) $(OCTAVEBASE)/mex
 else
-install-matlab:
+install-matlab-so:
+install-octave-so:
 endif
 
+
+
 ifeq ($(python),yes)
 # TODO: This install location doesn't work well for /usr or /usr/local
 install-python: py
 	$(MKDIR) python/finalbuild
 	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-	cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \
+	cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \
 	--install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \
 	--install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild
 	$(INSTALL_SH) -m 755 -d @prefix@/python
@@ -441,23 +473,36 @@ install-python: py
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.py @prefix@/python/astra
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/plugins/*.py @prefix@/python/astra/plugins
 	$(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/
-	@echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
-	@echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH"
-	@echo "and @libdir@ to your LD_LIBRARY_PATH."
-	@echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
 # TODO: docs
+
+python-root-install: py
+# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
+	cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install
 else
+python-root-install:
 install-python:
 endif
 
+ifeq ($(matlab),yes)
+install-matlab: $(MATLAB_MEX) install-matlab-so
+	$(INSTALL_SH) -m 755 -d $(MATLABBASE)
+	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/mex
+	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/tools
+	$(INSTALL_SH) -m 644 $(MATLAB_MEX) $(MATLABBASE)/mex
+	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m $(MATLABBASE)/tools
+# TODO: docs
+else
+install-matlab:
+endif
+
+
 ifeq ($(octave),yes)
-# TODO: This install location doesn't work well for /usr or /usr/local
-install-octave: $(OCTAVE_MEX)
-	$(INSTALL_SH) -m 755 -d @prefix@/octave
-	$(INSTALL_SH) -m 755 -d @prefix@/octave/mex
-	$(INSTALL_SH) -m 755 -d @prefix@/octave/tools
-	$(INSTALL_SH) -m 644 $(OCTAVE_MEX) @prefix@/octave/mex
-	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m @prefix@/octave/tools
+install-octave: $(OCTAVE_MEX) install-octave-so
+	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)
+	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/mex
+	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/tools
+	$(INSTALL_SH) -m 644 $(OCTAVE_MEX) $(OCTAVEBASE)/mex
+	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m $(OCTAVEBASE)/tools
 # TODO: docs
 else
 install-octave:
@@ -475,7 +520,7 @@ $(srcdir)/configure: $(srcdir)/configure.ac
 	@echo "configure.ac has been changed. Regenerating configure script"
 	cd $(srcdir) && $(SHELL) ./autogen.sh
 
-.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python install-octave
+.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python install-octave install-matlab-so install-octave-so
 
 # don't remove intermediate files:
 .SECONDARY:
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 7ccc8f5..26fa215 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -24,7 +24,7 @@ dnl
 dnl -----------------------------------------------------------------------
 dnl $Id$
 
-AC_INIT(astra_toolbox, 1.7.1)
+AC_INIT(astra, 1.7.1)
 AC_CONFIG_SRCDIR([Makefile.in])
 LT_INIT([disable-static])
 
@@ -274,6 +274,15 @@ AC_SUBST(CPPFLAGS_OS)
 VPATH_SRCDIR="$srcdir"
 AC_SUBST(VPATH_SRCDIR)
 
+
+# Installation type
+AC_ARG_WITH(install-type, [[  --with-install-type=prefix|module|dir  type of installation (default prefix)]],,with_install_type=prefix)
+
+INSTALL_TYPE=$with_install_type
+AC_SUBST(INSTALL_TYPE)
+
+
+
 # TODO:
 
 # Detection of tools:
@@ -299,4 +308,5 @@ echo "  Octave : $HAVEOCTAVE"
 echo "  Python : $HAVEPYTHON"
 echo
 echo "  prefix : $prefix"
+echo "  install: $with_install_type"
 echo
-- 
cgit v1.2.3


From bb01a88b5176c13c6881489887ec789dd10849a0 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 09:45:51 +0100
Subject: Build astra_mex_plugin for octave

---
 build/linux/Makefile.in | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 1c7088e..ecc3903 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -117,6 +117,12 @@ OCTFLAGS=-DASTRA_CUDA
 else
 OCTFLAGS=
 endif
+ifeq ($(python),yes)
+OCTPYLIBS=-l$(PYLIBVER)
+else
+OCTPYLIBS=
+endif
+
 endif
 
 DEPDIR=.deps
@@ -270,10 +276,6 @@ MATLAB_MEX=\
 	matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) \
 	matlab/mex/astra_mex_direct_c.$(MEXSUFFIX)
 
-ifeq ($(python),yes)
-MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX)
-endif
-
 OCTAVE_CXX_OBJECTS=\
 	matlab/mex/octave_support.o
 
@@ -288,6 +290,12 @@ OCTAVE_MEX=\
 	matlab/mex/astra_mex_data3d_c.mex \
 	matlab/mex/astra_mex_direct_c.mex
 
+ifeq ($(python),yes)
+MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX)
+OCTAVE_MEX+=matlab/mex/astra_mex_plugin_c.mex
+endif
+
+
 OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./
 DEPDIRS = $(addsuffix $(DEPDIR),$(OBJECT_DIRS))
 -include $(wildcard $(addsuffix /*.d,$(DEPDIRS)))
@@ -323,7 +331,12 @@ ifeq ($(octave),yes)
 oct: $(OCTAVE_MEX)
 
 %.mex: %.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS) libastra.la
-	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) -L.libs -lastra --output $* $*.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
+	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) -lastra --output $* $*.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
+
+ifeq ($(python),yes)
+matlab/mex/astra_mex_plugin_c.mex: matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS) libastra.la
+	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) $(OCTPYLIBS) -lastra --output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
+endif
 endif
 
 libastra.la: $(ALL_OBJECTS)
-- 
cgit v1.2.3


From a71a219ae5e0faded0c6161e17d8e17d39b01883 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 09:46:05 +0100
Subject: Disable octave interface by default

---
 build/linux/configure.ac | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 26fa215..785b698 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -179,8 +179,8 @@ AC_SUBST(HAVEMATLAB)
 
 # octave
 
-AC_ARG_ENABLE(octave, [[  --disable-octave      disable Octave support]])
-if test x"$enable_octave" != xno; then
+AC_ARG_ENABLE(octave, [[  --enable-octave         enable Octave support]])
+if test x"$enable_octave" = xyes; then
   AC_PATH_PROG([HAVEOCTAVE], [octave-config], [no], [$PATH])
   AC_MSG_CHECKING([for octave])
   if test x"HAVEOCTAVE" != xno -a $HAVEMATLAB = yes; then
-- 
cgit v1.2.3


From e69de5d1f5c80c58f9351617bb9ea117fcc6cad3 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 15:24:22 +0100
Subject: Clean up linking against libpython for oct/mex

---
 build/linux/Makefile.in | 17 ++++-------------
 1 file changed, 4 insertions(+), 13 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index ecc3903..d760a8e 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -83,6 +83,7 @@ CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR)
 PYCPPFLAGS  := $(CPPFLAGS)
 PYCPPFLAGS  += -I../include
 PYLDFLAGS = $(MODLDFLAGS)
+MODPYLIBS=-l$(PYLIBVER)
 endif
 
 # This is below where PYCPPFLAGS copies CPPFLAGS.  The python code is built
@@ -100,12 +101,6 @@ ifeq ($(cuda),yes)
 MEXFLAGS += -DASTRA_CUDA
 endif
 
-ifeq ($(python),yes)
-# TODO: Why PYLIBDIR?
-MEXPYLDFLAGS=\$$LDFLAGS $(MODLDFLAGS) -L$(PYLIBDIR)
-MEXPYLIBS=$(MEXLIBS) -l$(PYLIBVER)
-endif
-
 endif
 
 
@@ -117,14 +112,10 @@ OCTFLAGS=-DASTRA_CUDA
 else
 OCTFLAGS=
 endif
-ifeq ($(python),yes)
-OCTPYLIBS=-l$(PYLIBVER)
-else
-OCTPYLIBS=
-endif
 
 endif
 
+
 DEPDIR=.deps
 
 BASE_OBJECTS=\
@@ -311,7 +302,7 @@ mex: $(MATLAB_MEX)
 
 ifeq ($(python),yes)
 matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX): matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) libastra.la
-	$(MEX) LDFLAGS="$(MEXPYLDFLAGS)" $(MEXFLAGS) $(LIBS) $(MEXPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS)
+	$(MEX) LDFLAGS="$(MEXLDFLAGS)" $(MEXFLAGS) $(LIBS) $(MEXLIBS) $(MODPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS)
 endif
 endif
 
@@ -335,7 +326,7 @@ oct: $(OCTAVE_MEX)
 
 ifeq ($(python),yes)
 matlab/mex/astra_mex_plugin_c.mex: matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS) libastra.la
-	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) $(OCTPYLIBS) -lastra --output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
+	mkoctfile --mex $(OCTFLAGS) $(OCTLDFLAGS) $(LIBS) $(MODPYLIBS) -lastra --output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS) $(OCTAVE_CXX_OBJECTS)
 endif
 endif
 
-- 
cgit v1.2.3


From bc03dad9393d6fd9aad1ba22c98c223edecc918b Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 16:25:24 +0100
Subject: Show installation paths at end of configure

---
 build/linux/configure.ac | 49 +++++++++++++++++++++++++++++++++++++++++-------
 1 file changed, 42 insertions(+), 7 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 785b698..e562e77 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -302,11 +302,46 @@ AC_OUTPUT
 
 echo
 echo "Summary of ASTRA Toolbox build options:"
-echo "  CUDA   : $HAVECUDA"
-echo "  Matlab : $HAVEMATLAB"
-echo "  Octave : $HAVEOCTAVE"
-echo "  Python : $HAVEPYTHON"
-echo
-echo "  prefix : $prefix"
-echo "  install: $with_install_type"
+echo "  CUDA  : $HAVECUDA"
+echo "  Matlab: $HAVEMATLAB"
+echo "  Octave: $HAVEOCTAVE"
+echo "  Python: $HAVEPYTHON"
 echo
+echo "Installation type: $with_install_type"
+case $with_install_type in
+  prefix)
+    echo   "  Library     : "$(eval echo `eval echo $libdir`)
+    if test $HAVEMATLAB = yes; then
+      echo "  Matlab files: "$(eval echo `eval echo $datadir`)"/astra/matlab"
+    fi
+    if test $HAVEOCTAVE = yes; then
+      echo "  Octave files: "$(eval echo `eval echo $datadir`)"/astra/octave"
+    fi
+    if test $HAVEPYTHON = yes; then
+      echo "  Python files to site-packages"
+    fi
+    ;;
+  dir)
+    echo   "  Library     : "$(eval echo `eval echo $libdir`)
+    if test $HAVEMATLAB = yes; then
+      echo "  Matlab files: $prefix/matlab"
+    fi
+    if test $HAVEOCTAVE = yes; then
+      echo "  Octave files: $prefix/octave"
+    fi
+    if test $HAVEPYTHON = yes; then
+      echo "  Python files: $prefix/python"
+    fi
+    ;;
+  module)
+    echo   "  Library into Matlab/Octave/Python module directories"
+    if test $HAVEMATLAB = yes; then
+      echo "  Matlab files: $prefix/matlab"
+    fi
+    if test $HAVEOCTAVE = yes; then
+      echo "  Octave files: $prefix/octave"
+    fi
+    if test $HAVEPYTHON = yes; then
+      echo "  Python files to site-packages"
+    fi
+esac
-- 
cgit v1.2.3


From bbda2ad4d12a839701737a98e210cef489d62177 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 17:26:27 +0100
Subject: Avoid six for PYINCDIR in Makefile.in

---
 build/linux/Makefile.in | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index d760a8e..d248947 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -76,8 +76,7 @@ endif
 
 ifeq ($(python),yes)
 PYTHON      = @PYTHON@
-PYLIBDIR := $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; import six; six.print_(get_config_var("LIBDIR"))')
-PYINCDIR := $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())')
+PYINCDIR := $(shell $(PYTHON) -c 'from __future__ import print_function; from distutils.sysconfig import get_python_inc; print(get_python_inc())')
 PYLIBVER = `basename $(PYINCDIR)`
 CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR)
 PYCPPFLAGS  := $(CPPFLAGS)
-- 
cgit v1.2.3


From 19e79122e3f58f22e96a003cc494e38ff255bb0d Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 17:30:08 +0100
Subject: Rename python-root-install to install-python-site-packages

---
 build/linux/Makefile.in | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index d248947..0ca136a 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -421,7 +421,7 @@ install-libraries: libastra.la
 
 ifeq ($(install_type),prefix)
 # libraries into @libdir@, python into site-packages, mex into @datadir@
-install: install-libraries install-matlab python-root-install install-octave
+install: install-libraries install-matlab install-python-site-packages install-octave
 
 PYPKGDATA=
 MATLABBASE=@datadir@/astra/matlab
@@ -442,7 +442,7 @@ ifeq ($(install_type),module)
 # python into site-packages, mex into @datadir@
 # library copied into python/mex directories
 # modules built with rpath=$ORIGIN
-install: install-matlab python-root-install install-octave
+install: install-matlab install-python-site-packages install-octave
 
 PYPKGDATA=$(SONAME)
 MATLABBASE=@prefix@/matlab
@@ -478,11 +478,11 @@ install-python: py
 	$(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/
 # TODO: docs
 
-python-root-install: py
+install-python-site-packages: py
 # Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
 	cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install
 else
-python-root-install:
+install-python-site-packages:
 install-python:
 endif
 
@@ -523,7 +523,7 @@ $(srcdir)/configure: $(srcdir)/configure.ac
 	@echo "configure.ac has been changed. Regenerating configure script"
 	cd $(srcdir) && $(SHELL) ./autogen.sh
 
-.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python install-octave install-matlab-so install-octave-so
+.PHONY: all mex test clean distclean install install-libraries py install-python-site-packages install-python install-octave install-matlab-so install-octave-so
 
 # don't remove intermediate files:
 .SECONDARY:
-- 
cgit v1.2.3


From e72b97ccd734c8bc8c4cb3cbedbb053fb0cd0849 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 22 Nov 2016 17:30:23 +0100
Subject: Remove resolved TODO

---
 build/linux/Makefile.in | 1 -
 1 file changed, 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 0ca136a..d1ce5fb 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -462,7 +462,6 @@ endif
 
 
 ifeq ($(python),yes)
-# TODO: This install location doesn't work well for /usr or /usr/local
 install-python: py
 	$(MKDIR) python/finalbuild
 	# Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-- 
cgit v1.2.3


From 496d07d50118bd080e573686f65ed16e39be8f5b Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 23 Nov 2016 10:54:36 +0100
Subject: Make shared objects 755

---
 build/linux/Makefile.in | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index d1ce5fb..ae43afa 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -450,10 +450,10 @@ OCTAVEBASE=@prefix@/octave
 
 install-matlab-so: libastra.la
 	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/mex
-	$(INSTALL_SH) -m 644 $(abs_top_builddir)/.libs/$(SONAME) $(MATLABBASE)/mex
+	$(INSTALL_SH) -m 755 $(abs_top_builddir)/.libs/$(SONAME) $(MATLABBASE)/mex
 install-octave-so: libastra.la
 	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/mex
-	$(INSTALL_SH) -m 644 $(abs_top_builddir)/.libs/$(SONAME) $(OCTAVEBASE)/mex
+	$(INSTALL_SH) -m 755 $(abs_top_builddir)/.libs/$(SONAME) $(OCTAVEBASE)/mex
 else
 install-matlab-so:
 install-octave-so:
@@ -471,7 +471,7 @@ install-python: py
 	$(INSTALL_SH) -m 755 -d @prefix@/python
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra
 	$(INSTALL_SH) -m 755 -d @prefix@/python/astra/plugins
-	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.so @prefix@/python/astra
+	$(INSTALL_SH) -m 755 python/finalbuild/astra/*.so @prefix@/python/astra
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/*.py @prefix@/python/astra
 	$(INSTALL_SH) -m 644 python/finalbuild/astra/plugins/*.py @prefix@/python/astra/plugins
 	$(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/
@@ -490,7 +490,7 @@ install-matlab: $(MATLAB_MEX) install-matlab-so
 	$(INSTALL_SH) -m 755 -d $(MATLABBASE)
 	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/mex
 	$(INSTALL_SH) -m 755 -d $(MATLABBASE)/tools
-	$(INSTALL_SH) -m 644 $(MATLAB_MEX) $(MATLABBASE)/mex
+	$(INSTALL_SH) -m 755 $(MATLAB_MEX) $(MATLABBASE)/mex
 	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m $(MATLABBASE)/tools
 # TODO: docs
 else
@@ -503,7 +503,7 @@ install-octave: $(OCTAVE_MEX) install-octave-so
 	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)
 	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/mex
 	$(INSTALL_SH) -m 755 -d $(OCTAVEBASE)/tools
-	$(INSTALL_SH) -m 644 $(OCTAVE_MEX) $(OCTAVEBASE)/mex
+	$(INSTALL_SH) -m 755 $(OCTAVE_MEX) $(OCTAVEBASE)/mex
 	$(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m $(OCTAVEBASE)/tools
 # TODO: docs
 else
-- 
cgit v1.2.3


From eeffd2d9748b8912b384a5764b808f5bfc850ade Mon Sep 17 00:00:00 2001
From: Holger Kohr <h.kohr@cwi.nl>
Date: Wed, 23 Nov 2016 10:21:55 +0100
Subject: Separate C++ and python builds & make conda work nicely

- make builder (= advanced user or us ourselves) choose compilers
  and CUDA
- add a check for the C++11 flag for nvcc to work around the
  infamous boost bug if necessary
- use conda boost to build the C++ library
- simplify python bindings conda recipe to only build the bindings;
  the C++ library is now a build and runtime dependency
- add runtime dependencies to python bindings recipe
- some small adjustments to builder.py
---
 build/linux/configure.ac | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index e562e77..3a2a92b 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -228,8 +228,8 @@ if test x"$with_python" != x -a x"$with_python" != xno; then
   AC_MSG_CHECKING(for Cython module)
   ASTRA_TRY_PYTHON([
 import Cython
-from distutils.version import LooseVersion
-assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13"))
+from pkg_resources import parse_version
+assert(parse_version(Cython.__version__) >= parse_version("0.13"))
 ],,HAVEPYTHON=no)
   if test x$HAVEPYTHON = xno; then
     AC_MSG_RESULT(no)
-- 
cgit v1.2.3


From 71db6331f8dd0d5abbeee92977af01293be4f427 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 28 Nov 2016 15:54:07 +0100
Subject: Update headers (website+2016)

---
 build/linux/configure.ac | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 3a2a92b..2f992ad 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -1,9 +1,9 @@
 dnl -----------------------------------------------------------------------
-dnl Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
-dnl            2014-2015, CWI, Amsterdam
+dnl Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+dnl            2014-2016, CWI, Amsterdam
 dnl
 dnl Contact: astra@uantwerpen.be
-dnl Website: http://sf.net/projects/astra-toolbox
+dnl Website: http://www.astra-toolbox.com/
 dnl
 dnl This file is part of the ASTRA Toolbox.
 dnl
@@ -22,7 +22,6 @@ dnl You should have received a copy of the GNU General Public License
 dnl along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 dnl
 dnl -----------------------------------------------------------------------
-dnl $Id$
 
 AC_INIT(astra, 1.7.1)
 AC_CONFIG_SRCDIR([Makefile.in])
-- 
cgit v1.2.3


From 77f2cedaac088da5107dcfb37ae62d8f3a56f335 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 5 Dec 2016 14:44:09 +0100
Subject: Update version to 1.8

---
 build/linux/configure.ac | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 2f992ad..46c84a5 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -23,7 +23,7 @@ dnl along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
 dnl
 dnl -----------------------------------------------------------------------
 
-AC_INIT(astra, 1.7.1)
+AC_INIT(astra, 1.8.0)
 AC_CONFIG_SRCDIR([Makefile.in])
 LT_INIT([disable-static])
 
-- 
cgit v1.2.3


From ca1a9aaf9435d13cda5b33faa9084e03a42457cb Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 18 Jan 2017 17:07:23 +0100
Subject: Avoid 'echo -e' for improved sh portability

This fixes the CUDA .d file fixup for macOS.
---
 build/linux/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index ae43afa..5dfb75e 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -358,7 +358,7 @@ endif
 	@rm -f $(*D)/$(DEPDIR)/$(*F).d2
 	@# Generate empty targets for all dependencies listed in the .d file.
 	@# This mimics gcc's -MP option.
-	@for x in `cat $(*D)/$(DEPDIR)/$(*F).d`; do if test a$$x != a: -a a$$x != a\\; then echo -e "\n$$x:\n" >> $(*D)/$(DEPDIR)/$(*F).d; fi; done
+	@for x in `cat $(*D)/$(DEPDIR)/$(*F).d`; do if test a$$x != a: -a a$$x != a\\; then (echo; echo "$$x:") >> $(*D)/$(DEPDIR)/$(*F).d; fi; done
 	@# Generate a fake libtool .lo file
 	@echo "# $*.lo - a libtool object file" > $*.lo
 	@echo "# Generated by" `./libtool --version | head -n 1` >> $*.lo
-- 
cgit v1.2.3


From bf5475783f2a1bdcddf8426fea136f3b09c61859 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Thu, 19 Jan 2017 12:13:35 +0100
Subject: Add small portability comment about CUDA 5.5

---
 build/linux/Makefile.in | 1 +
 1 file changed, 1 insertion(+)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 5dfb75e..3894a8a 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -353,6 +353,7 @@ ifeq ($(gen_static_libs),yes)
 	@$(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o >/dev/null 2>&1
 endif
 	@# Generate a .d file, and change the target name in it from .o to .lo
+	@# CUDA 5.5's nvcc doesn't have the -MT option we would like to use.
 	@$(NVCC) $(NVCCFLAGS) -M $(<) -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d2
 	@sed '1s/\.o :/.lo :/' < $(*D)/$(DEPDIR)/$(*F).d2 > $(*D)/$(DEPDIR)/$(*F).d
 	@rm -f $(*D)/$(DEPDIR)/$(*F).d2
-- 
cgit v1.2.3


From 03c3e5b5043cc8cba9aceeb8641d497edd1be7cf Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 8 Feb 2017 11:27:24 +0100
Subject: Clean up symlink after failed python build

---
 build/linux/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 3894a8a..371b656 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -311,7 +311,7 @@ py: libastra.la
 # TODO: Avoid writing into source dir
 	ln -s $(abs_top_builddir)/.libs/$(SONAME) $(srcdir)/../../python/astra
 # Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++.
-	cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS='${PYLDFLAGS}' $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build
+	(cd $(srcdir)/../../python; ASTRA_INSTALL_LIBRARY_AS_DATA=$(PYPKGDATA) CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS='${PYLDFLAGS}' $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build) || (rm $(srcdir)/../../python/astra/$(SONAME); false)
 	rm $(srcdir)/../../python/astra/$(SONAME)
 
 endif
-- 
cgit v1.2.3


From d85a660f064e8130b27e11c7fd762221c754c315 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Thu, 26 Jan 2017 14:57:57 +0100
Subject: Start work on CFloat32Data3DGPU to allow persistent/external GPU
 memory

---
 build/linux/Makefile.in | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 371b656..9066f0a 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -199,7 +199,10 @@ CUDA_CXX_OBJECTS=\
 	src/CudaFDKAlgorithm3D.lo \
 	src/CudaSirtAlgorithm3D.lo \
 	src/CudaBackProjectionAlgorithm3D.lo \
-	src/CudaForwardProjectionAlgorithm3D.lo
+	src/CudaForwardProjectionAlgorithm3D.lo \
+	src/Float32Data3DGPU.lo \
+	src/Float32ProjectionData3DGPU.lo \
+	src/Float32VolumeData3DGPU.lo
 
 CUDA_OBJECTS=\
 	cuda/2d/algo.lo \
-- 
cgit v1.2.3


From e4ca9eb2bf7371fa9c1ac8951d298c989cb5aa28 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 23 Jan 2017 11:58:19 +0100
Subject: Let autogen.sh use either glibtoolize or libtoolize on macOS

This is necessary since conda's libtool installs libtoolize on macOS.
---
 build/linux/autogen.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/autogen.sh b/build/linux/autogen.sh
index 544fdeb..bb3b5cc 100755
--- a/build/linux/autogen.sh
+++ b/build/linux/autogen.sh
@@ -12,8 +12,11 @@ if test $? -ne 0; then
   exit 1
 fi
 
-case `uname` in Darwin*) LIBTOOLIZEBIN=glibtoolize ;;
-  *) LIBTOOLIZEBIN=libtoolize ;; esac
+case `uname` in
+  Darwin*)
+    test -x "`which glibtoolize 2>/dev/null`" && LIBTOOLIZEBIN=glibtoolize || LIBTOOLIZEBIN=libtoolize ;;
+  *)
+    LIBTOOLIZEBIN=libtoolize ;; esac
 
 $LIBTOOLIZEBIN --install --force > /dev/null 2>&1
 if test $? -ne 0; then
-- 
cgit v1.2.3


From 0f6c2fdc899b19000c3fcfa3f4e2129dd16a44ce Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 23 Jan 2017 12:32:10 +0100
Subject: Change lib/lib64 logic

macOS CUDA uses lib even on 64 bit
---
 build/linux/configure.ac | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 46c84a5..43cb1a8 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -102,14 +102,7 @@ if test x"$NVCC" != xno; then
   HAVECUDA=yes
   BACKUP_CUDA_LDFLAGS="$LDFLAGS"
   if test x"$with_cuda" != x -a x"$with_cuda" != xyes; then
-    case $host_cpu in
-    x86_64)
-      LDFLAGS_CUDA="-L$with_cuda/lib64"
-      ;;
-    *)
-      LDFLAGS_CUDA="-L$with_cuda/lib"
-      ;;
-    esac
+    test -d $with_cuda/lib64 && LDFLAGS_CUDA="-L$with_cuda/lib64" || LDFLAGS_CUDA="-L$with_cuda/lib"
     CPPFLAGS_CUDA="-I$with_cuda/include"
     LDFLAGS="$LDFLAGS $LDFLAGS_CUDA"
   fi
-- 
cgit v1.2.3


From 99718ef1734c0db06034127da703f70a1c30f1a3 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Fri, 3 Feb 2017 16:57:54 +0100
Subject: Disable openmp on macOS

---
 build/linux/Makefile.in  | 3 +++
 build/linux/configure.ac | 3 +++
 2 files changed, 6 insertions(+)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 9066f0a..ae3dec8 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -4,6 +4,7 @@ cuda=@HAVECUDA@
 matlab=@HAVEMATLAB@
 python=@HAVEPYTHON@
 boostutf=@HAVEBOOSTUTF@
+macos=@IS_MACOS@
 
 MATLAB_ROOT=@MATLAB_ROOT@
 octave=@HAVEOCTAVE@
@@ -64,9 +65,11 @@ endif
 ifeq ($(matlab),yes)
 # TODO: Do we also want -fopenmp for octave?
 CPPFLAGS+=-I$(MATLAB_ROOT)/extern/include -DMATLAB_MEX_FILE
+ifeq ($(macos),no)
 CXXFLAGS+=-fopenmp
 LDFLAGS+=-fopenmp
 endif
+endif
 
 # MODLDFLAGS are the base LDFLAGS for matlab, octave, python modules
 MODLDFLAGS=$(LDFLAGS) -L$(abs_top_builddir)/.libs
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 43cb1a8..813b462 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -251,13 +251,16 @@ AC_CANONICAL_HOST
 case $host_os in
   darwin* )
         CPPFLAGS_OS="-stdlib=libstdc++ -mmacosx-version-min=10.6"
+        IS_MACOS=yes
         ;;
     *)
         CPPFLAGS_OS=""
+        IS_MACOS=no
         ;;
 esac
 
 AC_SUBST(CPPFLAGS_OS)
+AC_SUBST(IS_MACOS)
 
 # For some reason, some older versions of autoconf produce a config.status
 # that disables all lines looking like VPATH=@srcdir@
-- 
cgit v1.2.3


From a3336fc3445fca283be97528d60f2f55501491b0 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Fri, 3 Feb 2017 16:58:36 +0100
Subject: Use @loader_path to make mex files find libastra.0.dylib in cwd

---
 build/linux/Makefile.in | 6 ++++++
 1 file changed, 6 insertions(+)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index ae3dec8..0120d60 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -304,6 +304,12 @@ mex: $(MATLAB_MEX)
 
 %.$(MEXSUFFIX): %.o $(MATLAB_CXX_OBJECTS) libastra.la
 	$(MEX) LDFLAGS="$(MEXLDFLAGS)" $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS)
+ifeq ($(install_type),module)
+ifeq ($(macos),yes)
+	@# tell macOS dynamic loader to look in mex directory for libastra.0.dylib
+	install_name_tool -change `otool -DX .libs/$(SONAME)` @loader_path/$(SONAME) $@
+endif
+endif
 
 ifeq ($(python),yes)
 matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX): matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) libastra.la
-- 
cgit v1.2.3


From f5c25084f09a8f35c4e3d01eb84de984778ae8a9 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Fri, 3 Feb 2017 16:58:56 +0100
Subject: Set stdlib to libstdc++ on macOS consistently

---
 build/linux/Makefile.in  | 3 ++-
 build/linux/configure.ac | 9 ++++++---
 2 files changed, 8 insertions(+), 4 deletions(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 0120d60..1c0c56a 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -50,7 +50,8 @@ CXXFLAGS+=-g -O3 -Wall -Wshadow
 LIBS+=-lpthread
 LDFLAGS+=-g
 
-CPPFLAGS+=@CPPFLAGS_OS@
+CXXFLAGS+=@CXXFLAGS_OS@
+LDFLAGS+=@LDFLAGS_OS@
 
 BOOSTUTF_LIBS=@LIBS_BOOSTUTF@
 
diff --git a/build/linux/configure.ac b/build/linux/configure.ac
index 813b462..b95d94f 100644
--- a/build/linux/configure.ac
+++ b/build/linux/configure.ac
@@ -250,16 +250,19 @@ AC_SUBST(HAVEPYTHON)
 AC_CANONICAL_HOST
 case $host_os in
   darwin* )
-        CPPFLAGS_OS="-stdlib=libstdc++ -mmacosx-version-min=10.6"
+        CXXFLAGS_OS="-stdlib=libstdc++ -mmacosx-version-min=10.6"
+        LDFLAGS_OS="-stdlib=libstdc++"
         IS_MACOS=yes
         ;;
     *)
-        CPPFLAGS_OS=""
+        CXXFLAGS_OS=""
+        LDFLAGS_OS=""
         IS_MACOS=no
         ;;
 esac
 
-AC_SUBST(CPPFLAGS_OS)
+AC_SUBST(CXXFLAGS_OS)
+AC_SUBST(LDFLAGS_OS)
 AC_SUBST(IS_MACOS)
 
 # For some reason, some older versions of autoconf produce a config.status
-- 
cgit v1.2.3


From 00a1c6118b2d64b867c8e640c295462bcccfc7c9 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Fri, 8 Sep 2017 15:03:55 +0200
Subject: Add macOS note

---
 build/linux/Makefile.in | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'build/linux')

diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in
index 1c0c56a..c83e9f0 100644
--- a/build/linux/Makefile.in
+++ b/build/linux/Makefile.in
@@ -308,7 +308,9 @@ mex: $(MATLAB_MEX)
 ifeq ($(install_type),module)
 ifeq ($(macos),yes)
 	@# tell macOS dynamic loader to look in mex directory for libastra.0.dylib
-	install_name_tool -change `otool -DX .libs/$(SONAME)` @loader_path/$(SONAME) $@
+	@# CHECKME: some versions of otool return a two-line output for otool -DX?
+	@# (xcode 8.2.1 / macos 10.11.6 ?)
+	install_name_tool -change `otool -DX .libs/$(SONAME) | tail -n 1` @loader_path/$(SONAME) $@
 endif
 endif
 
-- 
cgit v1.2.3