commit c8a867dc017f58a4ffbfb2d3d976506947e5d9d6
Author: Ronny Lorenz <ronny@tbi.univie.ac.at>
Date:   Mon May 13 08:22:42 2019 +0200

    SWIG: Fix install for wrappers generated by swig 4
    
    - We now default to install _RNA.*so files for Python2/3 into the RNA/
      subdirectory. This seems necessary to avoid problems when importing
      the RNA package, where the underlying loader changed from swig 3 to
      swig 4.
    - We also require swig 3.0.0 or later from now on to generate the
      wrapper code, and we drop the -modern flag

diff --git a/interfaces/Python/Makefile.am b/interfaces/Python/Makefile.am
index df279501..41be4c08 100644
--- a/interfaces/Python/Makefile.am
+++ b/interfaces/Python/Makefile.am
@@ -16,9 +16,8 @@ INTERFACE_FILES = $(SWIG_src) \
                   $(LANG_SPECIFIC_INTERFACE_FILES)
 
 pkgpy2execdir = $(py2execdir)/RNA
-pkgpy2cmoddir = $(py2execdir)
 
-pkgpy2cmod_LTLIBRARIES = _RNA.la
+pkgpy2exec_LTLIBRARIES = _RNA.la
 pkgpy2exec_DATA = RNA/__init__.py
 
 _RNA_la_SOURCES = $(INTERFACE_FILES) \
@@ -73,7 +72,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES)
 	$(swig_verbose)$(SWIG) -I$(top_srcdir)/src \
                   -I$(srcdir) -I$(builddir) \
                   $(RNA_CPPFLAGS) \
-                  -python -modern  -c++ \
+                  -python -c++ \
                   -o $(SWIG_wrapper) \
                   $(SWIG_main_src)
 
@@ -87,27 +86,33 @@ RNA/__init__.py: $(SWIG_module_name).py
 	$(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
   cp `test -f RNA.py || echo '$(srcdir)/'`RNA.py RNA/__init__.py
 
-_RNA$(PYTHON2_SO): _RNA.la
-	$(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) . ) && \
+RNA/_RNA$(PYTHON2_SO): _RNA.la
+	$(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
+  ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
+  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON2_SO) RNA ) && \
   rm -f libtoolconfig.tmp
 
-all-local:  _RNA$(PYTHON2_SO)
+CLEANFILES = \
+    RNA/_RNA$(PYTHON2_SO) \
+    RNA/__init__.py \
+    RNA/__init__.pyc
+
+all-local:  RNA/_RNA$(PYTHON2_SO)
 
 clean-local:
-	-rm -rf RNA _RNA$(PYTHON2_SO)
+	-rm -rf RNA
 
 # Remove the .la file - RNA.la is never linked against (it's a module)
 # and Python doesn't use libltdl.  Note that the library gets installed by
 # install-data, so that's where we need to hook.
 install-data-hook:
-	rm -f $(DESTDIR)$(pkgpy2cmoddir)/_RNA.la
+	rm -f $(DESTDIR)$(pkgpy2execdir)/_RNA.la
 
 # Because we don't install the .la file, "make uninstall" doesn't work and
 # we need to remove the file ourselves.
 uninstall-local:
-	eval `grep '^dlname=' $(pkgpy2cmod_LTLIBRARIES)` ; \
-	rm -f $(DESTDIR)$(pkgpy2cmoddir)/"$$dlname"
+	eval `grep '^dlname=' $(pkgpy2exec_LTLIBRARIES)` ; \
+	rm -f $(DESTDIR)$(pkgpy2execdir)/"$$dlname"
 
 ## remove all generated content
 maintainer-clean-local:
diff --git a/interfaces/Python3/Makefile.am b/interfaces/Python3/Makefile.am
index de9b049e..67824a99 100644
--- a/interfaces/Python3/Makefile.am
+++ b/interfaces/Python3/Makefile.am
@@ -17,10 +17,9 @@ INTERFACE_FILES = $(SWIG_src) \
                   $(LANG_SPECIFIC_INTERFACE_FILES)
 
 pkgpyexecdir = $(py3execdir)/RNA
-pkgpycmoddir = $(py3execdir)
 pkgpycachedir = $(pkgpyexecdir)/__pycache__
 
-pkgpycmod_LTLIBRARIES = _RNA.la
+pkgpyexec_LTLIBRARIES = _RNA.la
 pkgpyexec_DATA =  RNA/__init__.py
 pkgpycache_DATA = RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \
                   RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@
@@ -75,7 +74,7 @@ $(SWIG_wrapper): $(SWIG_src) $(INTERFACE_FILES)
                   -I$(srcdir) -I$(builddir) \
                   -DPY3 \
                   $(RNA_CPPFLAGS) \
-                  -python -modern -py3 -c++ \
+                  -python -py3 -c++ \
                   -o $(SWIG_wrapper) \
                   $(SWIG_main_src)
 
@@ -91,42 +90,43 @@ RNA/__init__.py: $(SWIG_module_name).py
 
 # We "import _RNA" first so that if we fail to import the glue library
 # we don't generate a broken .pyc or .pyo.
-RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py _RNA$(PYTHON3_SO)
+RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
 	$(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -c "import _RNA" ; \
   PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -c "import RNA" )
 
-RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py _RNA$(PYTHON3_SO)
+RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
 	$(AM_V_GEN)( PYTHONPATH="RNA:$$PYTHONPATH" $(PYTHON3) -O -c "import _RNA" ; \
   PYTHONPATH=".:$$PYTHONPATH" $(PYTHON3) -O -c "import RNA" )
 
-_RNA$(PYTHON3_SO): _RNA.la
-	$(AM_V_GEN)( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
-  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) . ) && \
+RNA/_RNA$(PYTHON3_SO): _RNA.la
+	$(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
+  ( $(LIBTOOL) --config > libtoolconfig.tmp ) && \
+  ( . ./libtoolconfig.tmp; cp $$objdir/_RNA$(PYTHON3_SO) RNA ) && \
   rm -f libtoolconfig.tmp
 
 CLEANFILES = \
-    _RNA$(PYTHON3_SO) \
+    RNA/_RNA$(PYTHON3_SO) \
     RNA/__init__.py \
     RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc \
     RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@\
     $(srcdir)/*.pyc
 
-all-local:  _RNA$(PYTHON3_SO)
+all-local:  RNA/_RNA$(PYTHON3_SO)
 
 clean-local:
-	-rm -rf RNA _RNA$(PYTHON3_SO)
+	-rm -rf RNA
 
 # Remove the .la file - RNA.la is never linked against (it's a module)
 # and Python doesn't use libltdl.  Note that the library gets installed by
 # install-data, so that's where we need to hook.
 install-data-hook:
-	rm -f $(DESTDIR)$(pkgpycmoddir)/_RNA.la
+	rm -f $(DESTDIR)$(pkgpyexecdir)/_RNA.la
 
 # Because we don't install the .la file, "make uninstall" doesn't work and
 # we need to remove the file ourselves.
 uninstall-local:
-	eval `grep '^dlname=' $(pkgpycmod_LTLIBRARIES)` ; \
-	rm -f $(DESTDIR)$(pkgpycmoddir)/"$$dlname"
+	eval `grep '^dlname=' $(pkgpyexec_LTLIBRARIES)` ; \
+	rm -f $(DESTDIR)$(pkgpyexecdir)/"$$dlname"
 
 ## remove all generated content
 maintainer-clean-local:
diff --git a/interfaces/RNA.i b/interfaces/RNA.i
index fb2260d6..6ae86641 100644
--- a/interfaces/RNA.i
+++ b/interfaces/RNA.i
@@ -1,4 +1,9 @@
+#ifdef SWIGPYTHON
+%module(moduleimport="from . import _RNA") RNA
+#else
 %module RNA
+#endif
+
 //%pragma(perl5)  modulecode="@EXPORT=qw(fold);"
 %pragma(perl5)  include="RNA.pod"
 
diff --git a/m4/ac_rna_swig.m4 b/m4/ac_rna_swig.m4
index 98583bed..29ea398f 100644
--- a/m4/ac_rna_swig.m4
+++ b/m4/ac_rna_swig.m4
@@ -9,13 +9,12 @@ AC_DEFUN([RNA_ENABLE_SWIG_INTERFACES],[
 
   AS_IF([test "x$with_swig" != "xno"],[
     wants_swig="yes"
-    AX_PKG_SWIG(2.0.0, [has_swig="yes"], [has_swig="no"])
+    AX_PKG_SWIG(3.0.0, [has_swig="yes"], [has_swig="no"])
   ],[
     wants_swig="no"
   ])
 
   AM_CONDITIONAL(HAS_SWIG, test "x$has_swig" != "xno")
-  
   RNA_ENABLE_SWIG_PERL
   RNA_ENABLE_SWIG_PYTHON
   RNA_ENABLE_SWIG_PYTHON3
@@ -55,10 +54,6 @@ AC_DEFUN([RNA_ENABLE_SWIG_PERL],[
       AC_MSG_ERROR([Perl is required to build.])
       [enable_perl_status="Perl is required to build."]
     fi
-#    AX_PERL_EXT_FLAGS([PERLXS_CFLAGS], [PERLXS_LDFLAGS])
-#    AX_PERL_EXT_LINK_CHECK([with_perl])
-#    AC_SUBST([PERLXS_CFLAGS])
-#    AC_SUBST([PERLXS_LDFLAGS])
   ])
 
   # prepare all files for perl interface