Clean up Makefile.am files

Add global variables to configure.ac, to avoid unnecessary multiple
definitions.

configure.ac

@@ -22,6 +22,7 @@ AC_CONFIG_SRCDIR(src)
 AM_INIT_AUTOMAKE
 AM_PROG_CC_C_O
 AM_CONFIG_HEADER(config.h)
+AC_CONFIG_MACRO_DIR([m4])
 
 AC_ISC_POSIX
 AC_SUBST(CXXFLAGS,$CXXFLAGS)
@@ -242,6 +243,28 @@ AC_DEFINE_UNQUOTED([COPYRIGHT],
 AC_DEFINE([GIT_COMMIT], "esyscmd(git show | head -n 1 | sed 's/commit //' |  grep -o -e '.\{8\}' | head -n 1 |tr -d '\n')", [git HEAD commit hash])
 AC_DEFINE([GIT_COMMIT_DATE], "esyscmd(git log -1 | head -n 3 | grep 'Date:' | sed s/'Date:   '// | tr -d '\n')", [git HEAD commit date])
 
+# set some automake variables
+
+# CPP flags for submodules
+[MOD_CPPFLAGS="-I\$(srcdir) -I\$(srcdir)/.. -I\$(srcdir)/../boost-workaround \
+-DHAVE_CONFIG_H"]
+AC_SUBST(MOD_CPPFLAGS)
+
+# default directory for submodules
+[MOD_DIR="${pythondir}/graph_tool"]
+AC_SUBST(MOD_DIR)
+
+# default LIBADD flags for submodules
+[MOD_LIBADD="${PYTHON_LDFLAGS} ${BOOST_LDFLAGS} ${OPENMP_LDFLAGS}\
+-lboost_python  -lboost_iostreams -lexpat"]
+AC_SUBST(MOD_LIBADD)
+
+# needed for typeinfo objects to work across DSO boundaries.
+# see http://gcc.gnu.org/faq.html#dso
+[MOD_LDFLAGS="-module  -avoid-version  -export-dynamic  -no-undefined\
+-Wl,-E"]
+AC_SUBST(MOD_LDFLAGS)
+
 AC_OUTPUT([
 Makefile
 src/Makefile

src/graph/clustering/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-AM_CPPFLAGS =\
-    -I$(srcdir)/.. \
-    -I$(srcdir)/../../boost-workaround \
-    -DHAVE_CONFIG_H
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
 
-AM_CFLAGS=$(AM_CXXFLAGS)
+AM_CFLAGS = $(AM_CXXFLAGS)
 
 libgraph_tool_clusteringdir = $(pythondir)/graph_tool/clustering
 
@@ -13,6 +10,10 @@ libgraph_tool_clustering_LTLIBRARIES = libgraph_tool_clustering.la
 
 libgraph_tool_clustering_la_includedir = $(pythondir)/graph_tool/include
 
+libgraph_tool_clustering_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_clustering_la_LDFLAGS = $(MOD_LDFLAGS)
+
 libgraph_tool_clustering_la_SOURCES = \
     graph_clustering.cc \
     graph_extended_clustering.cc
@@ -20,20 +21,3 @@ libgraph_tool_clustering_la_SOURCES = \
 libgraph_tool_clustering_la_include_HEADERS = \
     graph_clustering.hh \
     graph_extended_clustering.hh
-
-libgraph_tool_clustering_la_LIBADD = \
-    $(PYTHON_LDFLAGS) \
-    $(BOOST_LDFLAGS) \
-    $(OPENMP_LDFLAGS) \
-    -lboost_python \
-    -lboost_iostreams \
-    -lexpat
-
-# needed for typeinfo objects to work across DSO boundaries.
-# see http://gcc.gnu.org/faq.html#dso
-libgraph_tool_clustering_la_LDFLAGS = \
-    -module \
-    -avoid-version \
-    -export-dynamic \
-    -no-undefined \
-    -Wl,-E

src/graph/correlations/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-AM_CPPFLAGS =\
-    -I$(srcdir)/.. \
-    -I$(srcdir)/../../boost-workaround \
-    -DHAVE_CONFIG_H
-
-AM_CFLAGS=$(AM_CXXFLAGS)
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
+AM_CFLAGS = $(AM_CXXFLAGS)
 
 libgraph_tool_correlationsdir = $(pythondir)/graph_tool/correlations
 
@@ -13,6 +9,10 @@ libgraph_tool_correlations_LTLIBRARIES = libgraph_tool_correlations.la
 
 libgraph_tool_correlations_la_includedir = $(pythondir)/graph_tool/include
 
+libgraph_tool_correlations_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_correlations_la_LDFLAGS = $(MOD_LDFLAGS)
+
 libgraph_tool_correlations_la_SOURCES = \
     graph_assortativity.cc \
     graph_correlations.cc \
@@ -26,20 +26,3 @@ libgraph_tool_correlations_la_SOURCES = \
 libgraph_tool_correlations_la_include_HEADERS = \
     graph_assortativity.hh \
     graph_correlations.hh
-
-libgraph_tool_correlations_la_LIBADD = \
-    $(PYTHON_LDFLAGS) \
-    $(BOOST_LDFLAGS) \
-    $(OPENMP_LDFLAGS) \
-    -lboost_python \
-    -lboost_iostreams \
-    -lexpat
-
-# needed for typeinfo objects to work across DSO boundaries.
-# see http://gcc.gnu.org/faq.html#dso
-libgraph_tool_correlations_la_LDFLAGS = \
-    -module \
-    -avoid-version \
-    -export-dynamic \
-    -no-undefined \
-    -Wl,-E

src/graph/generation/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-AM_CPPFLAGS =\
-    -I$(srcdir)/.. \
-    -I$(srcdir)/../../boost-workaround \
-    -DHAVE_CONFIG_H
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
 
-AM_CXXFLAGS =\
-    -Wall \
-    $(PYTHON_CPPFLAGS) \
-    $(BOOST_CPPFLAGS)
-
-AM_CFLAGS=$(AM_CXXFLAGS)
+AM_CXXFLAGS = $(CXXFLAGS)
 
 libgraph_tool_generationdir = $(pythondir)/graph_tool/generation
 
@@ -18,25 +10,12 @@ libgraph_tool_generation_LTLIBRARIES = libgraph_tool_generation.la
 
 libgraph_tool_generation_la_includedir = $(pythondir)/graph_tool/include
 
+libgraph_tool_generation_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_generation_la_LDFLAGS = $(MOD_LDFLAGS)
+
 libgraph_tool_generation_la_SOURCES = \
     graph_generation.cc
 
 libgraph_tool_generation_la_include_HEADERS = \
     graph_generation.hh
-
-libgraph_tool_generation_la_LIBADD = \
-    $(PYTHON_LDFLAGS) \
-    $(BOOST_LDFLAGS) \
-    $(OPENMP_LDFLAGS) \
-    -lboost_python \
-    -lboost_iostreams \
-    -lexpat
-
-# needed for typeinfo objects to work across DSO boundaries.
-# see http://gcc.gnu.org/faq.html#dso
-libgraph_tool_generation_la_LDFLAGS = \
-    -module \
-    -avoid-version \
-    -export-dynamic \
-    -no-undefined \
-    -Wl,-E

src/graph/misc/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-AM_CPPFLAGS =\
-    -I$(srcdir) -I$(srcdir)/.. \
-    -I$(srcdir)/../boost-workaround \
-    -DHAVE_CONFIG_H
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
 
 AM_CFLAGS=$(AM_CXXFLAGS)
 
-libgraph_tool_miscdir = $(pythondir)/graph_tool/misc
+libgraph_tool_miscdir = $(MOD_DIR)/misc
 
 libgraph_tool_misc_LTLIBRARIES = libgraph_tool_misc.la
 
-libgraph_tool_misc_la_includedir = $(pythondir)/graph_tool/include
+libgraph_tool_misc_la_includedir = $(MOD_DIR)/include
+
+libgraph_tool_misc_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_misc_la_LDFLAGS = $(MOD_LDFLAGS)
 
 libgraph_tool_misc_la_SOURCES = \
     graph_rewiring.cc \
@@ -19,20 +20,3 @@ libgraph_tool_misc_la_SOURCES = \
 
 libgraph_tool_misc_la_include_HEADERS = \
     graph_rewiring.hh
-
-libgraph_tool_misc_la_LIBADD = \
-    $(PYTHON_LDFLAGS) \
-    $(BOOST_LDFLAGS) \
-    $(OPENMP_LDFLAGS) \
-    -lboost_python \
-    -lboost_iostreams \
-    -lexpat
-
-# needed for typeinfo objects to work across DSO boundaries.
-# see http://gcc.gnu.org/faq.html#dso
-libgraph_tool_misc_la_LDFLAGS = \
-    -module \
-    -avoid-version \
-    -export-dynamic \
-    -no-undefined \
-    -Wl,-E

src/graph/util/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-AM_CPPFLAGS =\
-    -I$(srcdir) -I$(srcdir)/.. \
-    -I$(srcdir)/../boost-workaround \
-    -DHAVE_CONFIG_H
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
 
-AM_CFLAGS=$(AM_CXXFLAGS)
+AM_CFLAGS = $(AM_CXXFLAGS)
 
 libgraph_tool_utildir = $(pythondir)/graph_tool/util
 
@@ -13,26 +10,13 @@ libgraph_tool_util_LTLIBRARIES = libgraph_tool_util.la
 
 libgraph_tool_util_la_includedir = $(pythondir)/graph_tool/include
 
+libgraph_tool_util_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_util_la_LDFLAGS = $(MOD_LDFLAGS)
+
 libgraph_tool_util_la_SOURCES = \
     graph_search.cc \
     graph_util_bind.cc
 
 libgraph_tool_util_la_include_HEADERS = \
     graph_search.hh
-
-libgraph_tool_util_la_LIBADD = \
-    $(PYTHON_LDFLAGS) \
-    $(BOOST_LDFLAGS) \
-    $(OPENMP_LDFLAGS) \
-    -lboost_python \
-    -lboost_iostreams \
-    -lexpat
-
-# needed for typeinfo objects to work across DSO boundaries.
-# see http://gcc.gnu.org/faq.html#dso
-libgraph_tool_util_la_LDFLAGS = \
-    -module \
-    -avoid-version \
-    -export-dynamic \
-    -no-undefined \
-    -Wl,-E

src/graph_tool/Makefile.am

@@ -7,44 +7,44 @@ graph_tool_PYTHON = \
     io.py \
     all.py
 
-graph_tooldir = $(pythondir)/graph_tool
+graph_tooldir = $(MOD_DIR)
 
 graph_tool_run_action_PYTHON = \
     run_action/__init__.py \
     run_action/inline.py \
     run_action/run_action_template.hh
-graph_tool_run_actiondir = $(pythondir)/graph_tool/run_action
+graph_tool_run_actiondir = $(MOD_DIR)/run_action
 
 graph_tool_test_PYTHON = \
     test/__init__.py \
     test/basic.py \
     test/properties.py
-graph_tool_testdir = $(pythondir)/graph_tool/test
+graph_tool_testdir = $(MOD_DIR)/test
 
 graph_tool_generation_PYTHON = \
     generation/__init__.py
-graph_tool_generationdir = $(pythondir)/graph_tool/generation
+graph_tool_generationdir = $(MOD_DIR)/generation
 
 graph_tool_correlations_PYTHON = \
     correlations/__init__.py
-graph_tool_correlationsdir = $(pythondir)/graph_tool/correlations
+graph_tool_correlationsdir = $(MOD_DIR)/correlations
 
 graph_tool_stats_PYTHON = \
     stats/__init__.py
-graph_tool_statsdir = $(pythondir)/graph_tool/stats
+graph_tool_statsdir = $(MOD_DIR)/stats
 
 graph_tool_clustering_PYTHON = \
     clustering/__init__.py
-graph_tool_clusteringdir = $(pythondir)/graph_tool/clustering
+graph_tool_clusteringdir = $(MOD_DIR)/clustering
 
 graph_tool_draw_PYTHON = \
     draw/__init__.py
-graph_tool_drawdir = $(pythondir)/graph_tool/draw
+graph_tool_drawdir = $(MOD_DIR)/draw
 
 graph_tool_util_PYTHON = \
     util/__init__.py
-graph_tool_utildir = $(pythondir)/graph_tool/util
+graph_tool_utildir = $(MOD_DIR)/util
 
 graph_tool_misc_PYTHON = \
     misc/__init__.py
-graph_tool_miscdir = $(pythondir)/graph_tool/misc
+graph_tool_miscdir = $(MOD_DIR)/misc