Separate CFLAGS and LIBS for libcrystfel and main

9 files changed, 59 insertions, 23 deletions

diff --git a/Makefile.am b/Makefile.am
index cbf0aec6..6a81a78c 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -27,11 +27,11 @@ if HAVE_CAIRO
 bin_PROGRAMS += src/render_hkl
 endif
 
-AM_CFLAGS = -Wall
+AM_CFLAGS = -Wall @MAIN_CFLAGS@
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
 AM_CPPFLAGS += -I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
-LDADD += $(top_builddir)/libcrystfel/libcrystfel.la
+LDADD += $(top_builddir)/libcrystfel/libcrystfel.la @MAIN_LIBS@
 
 src_partial_sim_SOURCES = src/partial_sim.c
 
diff --git a/Makefile.in b/Makefile.in
index 8f6f65ed..32034377 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -438,6 +438,8 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
+LIBCRYSTFEL_CFLAGS = @LIBCRYSTFEL_CFLAGS@
+LIBCRYSTFEL_LIBS = @LIBCRYSTFEL_LIBS@
 LIBGNU_LIBDEPS = @LIBGNU_LIBDEPS@
 LIBGNU_LTLIBDEPS = @LIBGNU_LTLIBDEPS@
 LIBOBJS = @LIBOBJS@
@@ -446,6 +448,8 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+MAIN_CFLAGS = @MAIN_CFLAGS@
+MAIN_LIBS = @MAIN_LIBS@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 NEXT_AS_FIRST_DIRECTIVE_STDDEF_H = @NEXT_AS_FIRST_DIRECTIVE_STDDEF_H@
@@ -573,11 +577,11 @@ EXTRA_DIST = configure m4/gnulib-cache.m4 tests/first_merge_check \
 	scripts/indexed-filenames scripts/gen-sfs
 SUBDIRS = lib doc/reference libcrystfel
 ACLOCAL_AMFLAGS = -I m4
-AM_CFLAGS = -Wall
+AM_CFLAGS = -Wall @MAIN_CFLAGS@
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
 	-I$(top_srcdir)/lib
 LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@ \
-	$(top_builddir)/libcrystfel/libcrystfel.la
+	$(top_builddir)/libcrystfel/libcrystfel.la @MAIN_LIBS@
 src_partial_sim_SOURCES = src/partial_sim.c
 src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c \
 	$(am__append_3)
diff --git a/configure b/configure
index 2c68ae22..cec514dc 100755
--- a/configure
+++ b/configure
@@ -626,6 +626,10 @@ HTML_DIR
 GTKDOC_MKPDF
 GTKDOC_REBASE
 GTKDOC_CHECK
+LIBCRYSTFEL_LIBS
+MAIN_LIBS
+LIBCRYSTFEL_CFLAGS
+MAIN_CFLAGS
 HAVE_FFTW_FALSE
 HAVE_FFTW_TRUE
 HAVE_CAIRO_FALSE
@@ -14076,13 +14080,21 @@ $as_echo "$gl_cv_prog_c_ignore_unused_libraries" >&6; }
 
 
 
-CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread $GTK_CFLAGS"
-CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
-CFLAGS="$CFLAGS $GDK_pixbuf_CFLAGS $GDK_pixbuf_2_CFLAGS $FFTW_CFLAGS"
+MAIN_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread"
+MAIN_CFLAGS="$MAIN_CFLAGS $GTK_CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE "
+MAIN_CFLAGS="$MAIN_CFLAGS $libPNG_CFLAGS $Cairo_CFLAGS $GDK_pixbuf_CFLAGS"
+MAIN_CFLAGS="$MAIN_CFLAGS $GDK_pixbuf_2_CFLAGS $FFTW_CFLAGS"
 
-LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
-LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS $GDK_pixbuf_LIBS"
-LIBS="$LIBS $GDK_pixbuf_2_LIBS $TIMER_LIBS $FFTW_LIBS $LDFLAGS"
+
+LIBCRYSTFEL_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $FFTW_CFLAGS"
+
+
+MAIN_LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
+MAIN_LIBS="$MAIN_LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS $GDK_pixbuf_LIBS"
+MAIN_LIBS="$MAIN_LIBS $GDK_pixbuf_2_LIBS $TIMER_LIBS $FFTW_LIBS $LDFLAGS"
+
+
+LIBCRYSTFEL_LIBS="$LIBS $HDF5_LIBS $GSL_LIBS $FFTW_LIBS $LDFLAGS"
 
 
 
diff --git a/configure.ac b/configure.ac
index 1412eb7e..e9384f1e 100644
--- a/configure.ac
+++ b/configure.ac
@@ -253,14 +253,22 @@ AM_CONDITIONAL([HAVE_FFTW], test x$have_fftw = xtrue)
 gl_IGNORE_UNUSED_LIBRARIES
 
 
-CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread $GTK_CFLAGS"
-CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
-CFLAGS="$CFLAGS $GDK_pixbuf_CFLAGS $GDK_pixbuf_2_CFLAGS $FFTW_CFLAGS"
-
-LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
-LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS $GDK_pixbuf_LIBS"
-LIBS="$LIBS $GDK_pixbuf_2_LIBS $TIMER_LIBS $FFTW_LIBS $LDFLAGS"
-
+MAIN_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $OPENCL_CFLAGS -pthread"
+MAIN_CFLAGS="$MAIN_CFLAGS $GTK_CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE "
+MAIN_CFLAGS="$MAIN_CFLAGS $libPNG_CFLAGS $Cairo_CFLAGS $GDK_pixbuf_CFLAGS"
+MAIN_CFLAGS="$MAIN_CFLAGS $GDK_pixbuf_2_CFLAGS $FFTW_CFLAGS"
+AC_SUBST([MAIN_CFLAGS])
+
+LIBCRYSTFEL_CFLAGS="$CFLAGS $HDF5_CFLAGS $GSL_CFLAGS $FFTW_CFLAGS"
+AC_SUBST([LIBCRYSTFEL_CFLAGS])
+
+MAIN_LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
+MAIN_LIBS="$MAIN_LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS $GDK_pixbuf_LIBS"
+MAIN_LIBS="$MAIN_LIBS $GDK_pixbuf_2_LIBS $TIMER_LIBS $FFTW_LIBS $LDFLAGS"
+AC_SUBST([MAIN_LIBS])
+
+LIBCRYSTFEL_LIBS="$LIBS $HDF5_LIBS $GSL_LIBS $FFTW_LIBS $LDFLAGS"
+AC_SUBST([LIBCRYSTFEL_LIBS])
 
 GTK_DOC_CHECK([1.11],[--flavour no-tmpl])
 AC_CONFIG_MACRO_DIR(m4)
diff --git a/doc/reference/Makefile.in b/doc/reference/Makefile.in
index ae499829..5cdc8389 100644
--- a/doc/reference/Makefile.in
+++ b/doc/reference/Makefile.in
@@ -177,6 +177,8 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
+LIBCRYSTFEL_CFLAGS = @LIBCRYSTFEL_CFLAGS@
+LIBCRYSTFEL_LIBS = @LIBCRYSTFEL_LIBS@
 LIBGNU_LIBDEPS = @LIBGNU_LIBDEPS@
 LIBGNU_LTLIBDEPS = @LIBGNU_LTLIBDEPS@
 LIBOBJS = @LIBOBJS@
@@ -185,6 +187,8 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+MAIN_CFLAGS = @MAIN_CFLAGS@
+MAIN_LIBS = @MAIN_LIBS@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 NEXT_AS_FIRST_DIRECTIVE_STDDEF_H = @NEXT_AS_FIRST_DIRECTIVE_STDDEF_H@
diff --git a/lib/Makefile.in b/lib/Makefile.in
index 450eb180..4214d8b9 100644
--- a/lib/Makefile.in
+++ b/lib/Makefile.in
@@ -259,6 +259,8 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
+LIBCRYSTFEL_CFLAGS = @LIBCRYSTFEL_CFLAGS@
+LIBCRYSTFEL_LIBS = @LIBCRYSTFEL_LIBS@
 LIBGNU_LIBDEPS = @LIBGNU_LIBDEPS@
 LIBGNU_LTLIBDEPS = @LIBGNU_LTLIBDEPS@
 LIBOBJS = @LIBOBJS@
@@ -267,6 +269,8 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+MAIN_CFLAGS = @MAIN_CFLAGS@
+MAIN_LIBS = @MAIN_LIBS@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 NEXT_AS_FIRST_DIRECTIVE_STDDEF_H = @NEXT_AS_FIRST_DIRECTIVE_STDDEF_H@
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index e813699b..05532ab8 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -1,5 +1,5 @@
 lib_LTLIBRARIES = libcrystfel.la
-LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
+LDADD = $(top_builddir)/lib/libgnu.a @LIBCRYSTFEL_LIBS@
 
 libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/thread-pool.c src/image.c src/hdf5-file.c \
@@ -21,4 +21,4 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
 
 INCLUDES = "-I$(top_srcdir)/data"
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib
-AM_CPPFLAGS += -I$(top_srcdir)/lib
+AM_CPPFLAGS += -I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
diff --git a/libcrystfel/Makefile.in b/libcrystfel/Makefile.in
index e02c47a7..734021a7 100644
--- a/libcrystfel/Makefile.in
+++ b/libcrystfel/Makefile.in
@@ -232,6 +232,8 @@ INSTALL_SCRIPT = @INSTALL_SCRIPT@
 INSTALL_STRIP_PROGRAM = @INSTALL_STRIP_PROGRAM@
 LD = @LD@
 LDFLAGS = @LDFLAGS@
+LIBCRYSTFEL_CFLAGS = @LIBCRYSTFEL_CFLAGS@
+LIBCRYSTFEL_LIBS = @LIBCRYSTFEL_LIBS@
 LIBGNU_LIBDEPS = @LIBGNU_LIBDEPS@
 LIBGNU_LTLIBDEPS = @LIBGNU_LTLIBDEPS@
 LIBOBJS = @LIBOBJS@
@@ -240,6 +242,8 @@ LIBTOOL = @LIBTOOL@
 LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
+MAIN_CFLAGS = @MAIN_CFLAGS@
+MAIN_LIBS = @MAIN_LIBS@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 NEXT_AS_FIRST_DIRECTIVE_STDDEF_H = @NEXT_AS_FIRST_DIRECTIVE_STDDEF_H@
@@ -346,7 +350,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 lib_LTLIBRARIES = libcrystfel.la
-LDADD = $(top_builddir)/lib/libgnu.a @IGNORE_UNUSED_LIBRARIES_CFLAGS@
+LDADD = $(top_builddir)/lib/libgnu.a @LIBCRYSTFEL_LIBS@
 libcrystfel_la_SOURCES = src/reflist.c src/utils.c src/cell.c src/detector.c \
                          src/thread-pool.c src/image.c src/hdf5-file.c \
                          src/beam-parameters.c src/geometry.c src/statistics.c \
@@ -366,7 +370,7 @@ libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
 
 INCLUDES = "-I$(top_srcdir)/data"
 AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib \
-	-I$(top_srcdir)/lib
+	-I$(top_srcdir)/lib @LIBCRYSTFEL_CFLAGS@
 all: all-am
 
 .SUFFIXES:
diff --git a/libtool b/libtool
index 96efef8f..10548d94 100755
--- a/libtool
+++ b/libtool
@@ -138,7 +138,7 @@ lock_old_archive_extraction=no
 LTCC="gcc"
 
 # LTCC compiler flags.
-LTCFLAGS="-g -O2    -I/usr/local/cuda/include -pthread -pthread -I/usr/include/gtk-2.0 -I/usr/lib64/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12    -D_GNU_SOURCE -I/usr/include/libpng12   -pthread -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12    -pthread -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/libpng12 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include    "
+LTCFLAGS="-g -O2"
 
 # Take the output of nm and produce a listing of raw symbols and C names.
 global_symbol_pipe="sed -n -e 's/^.*[	 ]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[	 ][	 ]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'"