Make swig directory not recursive, but in parallel.

Makefile.am

@@ -1,4 +1,3 @@
-SUBDIRS = . $(MAYBE_SWIG)
 ACLOCAL_AMFLAGS = -I m4
 
 EXTRA_DIST = doc/jellyfish.pdf doc/jellyfish.man README LICENSE # jellyfish.spec
@@ -209,6 +208,11 @@ bin_test_all_LDADD = libgtest.la $(LDADD)
 YAGGO_SOURCES += unit_tests/test_main_cmdline.hpp
 noinst_HEADERS += unit_tests/test_main.hpp
 
+#################
+# SWIG bindings #
+#################
+include swig/Makefile.am
+
 include gtest.mk
 -include $(srcdir)/development.mk
 

configure.ac

@@ -108,35 +108,29 @@ AC_ARG_ENABLE([swig],
 AS_IF([test x$enable_swig = xyes],
       [AX_PKG_SWIG([3.0.0], [], [AC_MSG_ERROR([SWIG version 3 is required])])])
 AS_IF([test -n "$SWIG"],
-      [SWIG_ENABLE_CXX]
-      [maybe_swig=swig])
+      [SWIG_ENABLE_CXX])
 AM_CONDITIONAL([HAVE_SWIG], [test -n "$SWIG"])
 
 # Python binding setup
 AM_CONDITIONAL(PYTHON_BINDING, [test -n "$enable_python_binding" -a x$enable_python_binding != xno])
 AM_COND_IF([PYTHON_BINDING],
-           [AS_IF([test x$enable_python_binding != xyes], [PYTHON_SITE_PKG=$enable_python_binding])]
-           [AX_PYTHON_DEVEL]
-           [maybe_swig=swig])
+           [AS_IF([test x$enable_python_binding != xyes], [PYTHON_SITE_PKG=$enable_python_binding],
+                  [test "x$prefix" != xNONE], [PYTHON_SITE_PKG=$libdir/python])]
+           [AX_PYTHON_DEVEL])
 
 # Ruby binding setup
 AM_CONDITIONAL([RUBY_BINDING], [test -n "$enable_ruby_binding" -a x$enable_ruby_binding != xno])
 AM_COND_IF([RUBY_BINDING],
-           [AS_IF([test x$enable_ruby_binding != xyes], [RUBY_EXT_LIB=$enable_ruby_binding])]
-           [AX_RUBY_EXT]
-           [maybe_swig=swig])
+           [AS_IF([test x$enable_ruby_binding != xyes], [RUBY_EXT_LIB=$enable_ruby_binding],
+                  [test "x$prefix" != xNONE], [RUBY_EXT_LIB=$libdir/ruby])]
+           [AX_RUBY_EXT])
 
 # Perl binding setup
 AM_CONDITIONAL([PERL_BINDING], [test -n "$enable_perl_binding" -a x$enable_perl_binding != xno])
 AM_COND_IF([PERL_BINDING],
-           [AS_IF([test x$enable_perl_binding != xyes], [PERL_EXT_LIB=$enable_perl_binding])]
-           [AX_PERL_EXT]
-           [maybe_swig=swig])
-
-# Enable compilation of SWIG and bindings
-AC_SUBST([MAYBE_SWIG], [$maybe_swig])
-AS_IF([test -n "$maybe_swig"],
-      [AC_CONFIG_FILES([swig/Makefile])])
+           [AS_IF([test x$enable_perl_binding != xyes], [PERL_EXT_LIB=$enable_perl_binding],
+                  [test "x$prefix" != xNONE], [PERL_EXT_LIB=$libdir/perl])]
+           [AX_PERL_EXT])
 
 AC_OUTPUT
 

swig/Makefile.am

@@ -1,15 +1,13 @@
 # SWIG
-BUILT_SOURCES =
-CLEANFILES =
-EXTRA_DIST =
-SWIG_SRC = jellyfish.i hash_counter.i hash_set.i mer_dna.i mer_file.i string_mers.i
+SWIG_SRC = swig/jellyfish.i swig/hash_counter.i swig/hash_set.i	\
+           swig/mer_dna.i swig/mer_file.i swig/string_mers.i
 
 if HAVE_SWIG
 SWIG_V_GEN = $(swig_v_GEN_$(V))
 swig_v_GEN_ = $(swig_v_GEN_$(AM_DEFAULT_VERBOSITY))
 swig_v_GEN_0 = @echo "  SWIG    " $@;
 %/swig_wrap.cpp: $(SWIG_SRC)
-	$(SWIG_V_GEN)$(SWIG) -$* -I$(srcdir)/../include -o $@ $<
+	$(SWIG_V_GEN)$(SWIG) -$(notdir $*) -I$(srcdir)/../include -o $@ $<
 else
 %/swig_wrap.cc:
 	@echo >&2 SWIG >= 3.x.x not found. Make sure it is install and rerun configure
@@ -18,51 +16,51 @@ endif
 
 # Python support
 if PYTHON_BINDING
-PYTHON_BUILT = python/swig_wrap.cpp python/jellyfish.py
+PYTHON_BUILT = swig/python/swig_wrap.cpp swig/python/jellyfish.py
 BUILT_SOURCES += $(PYTHON_BUILT)
 
 pythonextdir = $(PYTHON_SITE_PKG)/jellyfish
-pythonext_SCRIPTS = python/__init__.pyc
-pythonext_LTLIBRARIES = python/_jellyfish.la
-python__jellyfish_la_SOURCES = python/swig_wrap.cpp $(SWIG_SRC)
-python__jellyfish_la_CPPFLAGS = $(PYTHON_CPPFLAGS) -I$(srcdir)/../include
-python__jellyfish_la_LDFLAGS = -module
-python__jellyfish_la_LIBADD = ../libjellyfish-2.0.la
+pythonext_SCRIPTS = swig/python/__init__.pyc
+pythonext_LTLIBRARIES = swig/python/_jellyfish.la
+swig_python__jellyfish_la_SOURCES = swig/python/swig_wrap.cpp $(SWIG_SRC)
+swig_python__jellyfish_la_CPPFLAGS = $(PYTHON_CPPFLAGS) -I$(srcdir)/include
+swig_python__jellyfish_la_LDFLAGS = -module
+swig_python__jellyfish_la_LIBADD = libjellyfish-2.0.la
 CLEANFILES += $(PYTHON_BUILT) $(pythonext_SCRIPTS)
 PYTHONC_V_GEN = $(pythonc_v_GEN_$(V))
 pythonc_v_GEN_ = $(pythonc_v_GEN_$(AM_DEFAULT_VERBOSITY))
 pythonc_v_GEN_0 = @echo "  PYTHONC " $@;
 %/__init__.pyc: %/jellyfish.py
 	$(PYTHONC_V_GEN)$(PYTHON) -c 'import py_compile, sys; py_compile.compile(sys.argv[1], sys.argv[2])' $< $@
-python/jellyfish.py: python/swig_wrap.cpp
+swig/python/jellyfish.py: swig/python/swig_wrap.cpp
 EXTRA_DIST += $(PYTHON_BUILT)
 endif
 
 # Ruby support
 if RUBY_BINDING
-RUBY_BUILT = ruby/swig_wrap.cpp
+RUBY_BUILT = swig/ruby/swig_wrap.cpp
 BUILT_SOURCES += $(RUBY_BUILT)
 rubyextdir = $(RUBY_EXT_LIB)
-rubyext_LTLIBRARIES = ruby/jellyfish.la
-ruby_jellyfish_la_SOURCES = ruby/swig_wrap.cpp $(SWIG_SRC)
-ruby_jellyfish_la_CPPFLAGS = $(RUBY_EXT_CFLAGS) -I$(srcdir)/../include
-ruby_jellyfish_la_LDFLAGS = -module
-ruby_jellyfish_la_LIBADD = ../libjellyfish-2.0.la
+rubyext_LTLIBRARIES = swig/ruby/jellyfish.la
+swig_ruby_jellyfish_la_SOURCES = swig/ruby/swig_wrap.cpp $(SWIG_SRC)
+swig_ruby_jellyfish_la_CPPFLAGS = $(RUBY_EXT_CFLAGS) -I$(srcdir)/include
+swig_ruby_jellyfish_la_LDFLAGS = -module
+swig_ruby_jellyfish_la_LIBADD = libjellyfish-2.0.la
 CLEANFILES += $(RUBY_BUILT)
 endif
 
 # Perl5 support
 if PERL_BINDING
-PERL_BUILT = perl5/swig_wrap.cpp perl5/jellyfish.pm
+PERL_BUILT = swig/perl5/swig_wrap.cpp swig/perl5/jellyfish.pm
 BUILT_SOURCES += $(PERL_BUILT)
 perlextdir = $(PERL_EXT_LIB)
-perlext_SCRIPTS = perl5/jellyfish.pm
-perlext_LTLIBRARIES = perl5/jellyfish.la
-perl5_jellyfish_la_SOURCES = perl5/swig_wrap.cpp $(SWIG_SRC)
-perl5_jellyfish_la_CPPFLAGS = $(PERL_EXT_CPPFLAGS) -I$(PERL_EXT_INC) -I$(srcdir)/../include
-perl5_jellyfish_la_LDFLAGS = -module
-perl5_jellyfish_la_LIBADD = ../libjellyfish-2.0.la
+perlext_SCRIPTS = swig/perl5/jellyfish.pm
+perlext_LTLIBRARIES = swig/perl5/jellyfish.la
+swig_perl5_jellyfish_la_SOURCES = swig/perl5/swig_wrap.cpp $(SWIG_SRC)
+swig_perl5_jellyfish_la_CPPFLAGS = $(PERL_EXT_CPPFLAGS) -I$(PERL_EXT_INC) -I$(srcdir)/include
+swig_perl5_jellyfish_la_LDFLAGS = -module
+swig_perl5_jellyfish_la_LIBADD = libjellyfish-2.0.la
 CLEANFILES += $(PERL5_BUILT)
-perl5/jellyfish.pm: perl5/swig_wrap.cpp
+swig/perl5/jellyfish.pm: swig/perl5/swig_wrap.cpp
 EXTRA_DIST += $(PERL_BUILT)
 endif