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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
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