## @configure_input@ ## ## @file Makefile.in ## @brief Makefile template for libSBML Java bindings ## @author Mike Hucka ## @author Ben Kovitz ## @author Akiya Jouraku ## ## # ----------------------------------------------------------------------------- # Configuration variables # ----------------------------------------------------------------------------- # Some of the following are substituted automatically by `configure'. If # you are looking at "Makefile", do not edit these values; instead, run the # configure script at the top level of the src tree. It will recreate # "Makefile". include @top_srcdir@/config/makefile-common-vars.mk # `srcdir' points to the current directory, but should be set by configure. # `subdir' must be set manually to the relative dir under srcdir. Don't # set `subdir' to an absolute path, or some make actions will fail. srcdir = @srcdir@ thisdir = src/bindings/java # In the normal core C++/C libSBML code, `sources' are used by the default # rules to determine what needs to be compiled. In these language # bindings, the variable is not used by default rules, and everything is # handled explicitly below. However, to maintain some resemblance to the # other libSBML build organization, we still use the name `sources'. sources = libsbml_wrap.cpp libsbml_wrap.h javadoc.i extra_sources = libsbml.i \ local.cpp \ local.i \ local-doc-extras.i \ local-downcast-extension-layout.i \ local-downcast-extension.i.in \ local-downcast-astplugins.i.in \ local-downcast-converters.i.in \ local-downcast-converters-layout.i \ local-downcast-namespaces-layout.i \ local-downcast-namespaces.i.in \ local-packages-layout.i \ local-packages.i.in \ local-downcast-extension-l3v2extendedmath.i \ local-downcast-astplugins-l3v2extendedmath.i \ local-downcast-namespaces-l3v2extendedmath.i \ local-packages-l3v2extendedmath.i \ # The SWIG interface files should not need to be regenerated for recipients # of the libSBML distributions; only developers should need to regenerate # them. The conditions for this are handled later below. swig_sources = $(extra_sources) ../swig/libsbml.h ../swig/libsbml.i # Variables `subdirs', `headers', `sources', `libraries', `extra_CPPFLAGS', # `extra_CXXFLAGS', `extra_LDFLAGS' and `distfiles' are used by the default # rules in `makefile-common-actions.mk' included at the end. extra_CPPFLAGS = $(JAVA_CPPFLAGS) -I../swig SWIGFLAGS += $(JAVA_CPPFLAGS) -I../swig extra_LDFLAGS = $(JAVA_LDFLAGS) extra_LIBS = $(JAVA_LIBS) ifdef USE_EXPAT extra_CPPFLAGS += @EXPAT_CPPFLAGS@ extra_LDFLAGS += @EXPAT_LDFLAGS@ extra_LIBS += @EXPAT_LIBS@ endif ifdef USE_XERCES extra_CPPFLAGS += @XERCES_CPPFLAGS@ extra_LDFLAGS += @XERCES_LDFLAGS@ extra_LIBS += @XERCES_LIBS@ endif ifdef USE_LIBXML extra_CPPFLAGS += @LIBXML_CPPFLAGS@ extra_LDFLAGS += @LIBXML_LDFLAGS@ extra_LIBS += @LIBXML_LIBS@ endif # SBML package plug-ins ifdef USE_COMP SWIGFLAGS += -DUSE_COMP SWIGDOCDEFINES += --define USE_COMP endif # USE_COMP ifdef USE_FBC SWIGFLAGS += -DUSE_FBC SWIGDOCDEFINES += --define USE_FBC endif # USE_FBC ifdef USE_GROUPS SWIGFLAGS += -DUSE_GROUPS SWIGDOCDEFINES += --define USE_GROUPS endif # USE_GROUPS ifdef USE_LAYOUT SWIGFLAGS += -DUSE_LAYOUT SWIGDOCDEFINES += --define USE_LAYOUT endif # USE_LAYOUT ifdef USE_QUAL SWIGFLAGS += -DUSE_QUAL SWIGDOCDEFINES += --define USE_QUAL endif # USE_QUAL ifdef USE_MULTI SWIGFLAGS += -DUSE_MULTI SWIGDOCDEFINES += --define USE_MULTI endif # USE_MULTI ifdef USE_RENDER SWIGFLAGS += -DUSE_RENDER SWIGDOCDEFINES += --define USE_RENDER endif # USE_RENDER ifdef USE_L3V2EXTENDEDMATH SWIGFLAGS += -DUSE_L3V2EXTENDEDMATH SWIGDOCDEFINES += --define USE_L3V2EXTENDEDMATH endif # USE_L3V2EXTENDEDMATH # -fno-strict-aliasing option is added to CXXFLAGS when using GCC. As # written in the SWIG Manual (section 20.2.4), SWIG generated code could # cause crash problems when compiled by GCC with -fstrict-aliasing option # (automatically enabled when using -O2 or higher optimization in GCC 3 or # later) and the option should be disabled by adding -fno-strict-aliasing # option. # # Currently, we know that Java binding library causes crash when it is # compiled by GCC 4 with -O2 or higher optimization, and the problem can be # avoided by adding -fno-strict-aliasing option. ifeq (GCC,$(findstring GCC,$(shell $(CXX) -dumpversion | sed -e 's/^[34]\./GCC/' ))) CXXFLAGS += -fno-strict-aliasing endif # By default, the compliance level of eclipse JDT compiler (ecj) is Java # 1.4 which doesn't support covariant return types. To avoid the # incompatible issue, "-5" option which sets the compliance level to Java # 1.5 is added if ecj is detected. ifeq (1.5 compliance, $(findstring 1.5 compliance, $(shell ${JAVAC} -help 2>&1 | grep "1.5 compliance" ))) JAVAC_OPTION += -5 endif # We're building two libraries: the shared JNI library, and the Jar file. java_package = org.sbml.$(PACKAGE) jarfile = libsbmlj.jar jnifile = $(JNIBASENAME).$(JNIEXT) libraries = $(jarfile) $(jnifile) # We generate the $(jnifile) (C++ library for System.loadLibrary) with an # object file in this directory (libsbml_wrap.o) and other object files in # sub directories in 'src' directory (src/sbml, src/common, ... ) instead # of linking a shared library of libSBML (libsbml.$(SHAREDLIBEXT)). # All directories that contain *.{c,cpp} (implementation) files of libSBML # need to be listed in the following 'otherdirs' variable. otherdirs = ../../sbml/common ../../sbml/util ../../sbml/xml \ ../../sbml/math ../../sbml/validator ../../sbml/validator/constraints \ ../../sbml/units ../../sbml/annotation ../../sbml/compress \ ../../sbml/ ../../sbml/extension ../../sbml/conversion ifdef USE_COMP otherdirs += ../../sbml/packages/comp/common \ ../../sbml/packages/comp/extension \ ../../sbml/packages/comp/sbml \ ../../sbml/packages/comp/util \ ../../sbml/packages/comp/validator \ ../../sbml/packages/comp/validator/constraints endif ifdef USE_FBC otherdirs += ../../sbml/packages/fbc/common \ ../../sbml/packages/fbc/extension \ ../../sbml/packages/fbc/sbml \ ../../sbml/packages/fbc/util \ ../../sbml/packages/fbc/validator \ ../../sbml/packages/fbc/validator/constraints endif ifdef USE_GROUPS otherdirs += ../../sbml/packages/groups/common \ ../../sbml/packages/groups/extension \ ../../sbml/packages/groups/sbml \ ../../sbml/packages/groups/validator \ ../../sbml/packages/groups/validator/constraints endif ifdef USE_LAYOUT otherdirs += ../../sbml/packages/layout/common \ ../../sbml/packages/layout/extension \ ../../sbml/packages/layout/sbml \ ../../sbml/packages/layout/util \ ../../sbml/packages/layout/validator \ ../../sbml/packages/layout/validator/constraints endif ifdef USE_QUAL otherdirs += ../../sbml/packages/qual/common \ ../../sbml/packages/qual/extension \ ../../sbml/packages/qual/sbml \ ../../sbml/packages/qual/validator \ ../../sbml/packages/qual/validator/constraints endif ifdef USE_MULTI otherdirs += ../../sbml/packages/multi/common \ ../../sbml/packages/multi/extension \ ../../sbml/packages/multi/sbml \ ../../sbml/packages/multi/validator \ ../../sbml/packages/multi/validator/constraints endif ifdef USE_L3V2EXTENDEDMATH otherdirs += ../../sbml/packages/l3v2extendedmath/common \ ../../sbml/packages/l3v2extendedmath/extension \ ../../sbml/packages/l3v2extendedmath/validator \ ../../sbml/packages/l3v2extendedmath/validator/constraints endif objfiles = libsbml_wrap.lo $(wildcard $(addsuffix /*.lo,$(otherdirs))) # The next set of variable definitions are special to this file and not # hooks into `makefile-common-actions.mk'. The values depend in part on # Java conventions and the output of SWIG. outdir = java-files pkg_path = $(subst .,/,$(java_package)) outpath = $(outdir)/$(pkg_path) java_files = $(wildcard $(outpath)/*.java) class_files = $(java_files:.java=.class) # The libSBML Java API library on MacOS X has to be built as a "bundle" # rather than a .dylib library. This is different from the default rules # used elsewhere in libSBML and requires the following special value for # `platform_link_flags'. The rest of the default rules for .so's will # behave properly once this is set. ifeq "$(HOST_TYPE)" "darwin" platform_link_flags = -bundle endif # Files for test system. test_dir = test test_src_path = test/org/sbml/libsbml/test check_sources = AutoTestRunner.java $(wildcard $(test_src_path)/**/Test*.java) # `distfiles' determines the files and directories included in a # distribution. The strategy here is that we include the output of SWIG # (both libsbml_wrap.cpp and the java files) but not the compiled class # files. distfiles = Makefile.in \ Manifest.txt.in \ CMakeLists.txt \ compile-native-files.cmake \ swig-binding.cmake.in \ TestPrintVersion.java \ $(check_sources) \ $(extra_sources) \ $(java_files) \ $(sources) # `extra_clean' and `extra_distclean' determine the files and directories # removed during "make clean" and "make distclean". extra_clean = $(class_files) $(check_sources:.java=.class) test_copy1.xml \ test_write.xml TestFilenameFilter.class $(wildcard test.xml.*) out.xml extra_distclean = Manifest.txt local-downcast-extension.i \ local-downcast-namespaces.i local-packages.i javadoc.i # For Linux/Unix, LD_LIBRARY_PATH *may* need to contain one or more library # paths to libsbml.so, libxerces-c.so and/or libexpat.so and/or the # libsbml.so _libsbml.so generated by this Makfile. (For BSD/MacOS X # replace LD_LIBRARY_PATH with DYLD_LIBRARY_PATH.) # ----------------------------------------------------------------------------- # Primary build actions # ----------------------------------------------------------------------------- # This whole setup is more or less custom and mostly doesn't use the common # build directives of `makefile-common-actions.mk'. .SUFFIXES: .SUFFIXES: .i .cpp .h .java .class .jar .o .obj .so .dylib .lo .la # The default action is to remake everything. ifdef USE_JAVA all: Makefile libsbml_wrap.cpp $(outpath)/libsbml.class $(libraries) else all: @echo @echo "Reconfigure libSBML using --with-java to enable Java support."; @echo @exit 1 endif # Rummage through ../swig/libsbml.i to figure out the core libSBML files that # are our dependencies. main_sources = \ $(shell grep '%include sbml' ../swig/libsbml.i | grep -v 'libsbml-version.h' \ | cut -f2- -d'/' | sed -e 's,^,../../sbml/,g') # Recreate SWIG files when one of the following conditions is true: # # (1) libsbml_wrap.cpp does not exist # (2) libsbml_wrap.cpp exists, but the file is not consistent with the # current USE_LAYOUT, USE_COMP, etc., values. # # If the last run was made with a package flag like --enable-layout, and this # run isn't, or vice-versa, the swig wrap files will be wrong for this run. # However, you can't tell just by looking at file mod times, so you can't use # normal make dependencies. So we do this grungy trick of looking inside # libsbml_wrap.cpp to see what's inside. # # The check_foo macros works as follows. They return a non-empty string # "do_reswig" if re-swig'ing is called for, and this string is a phony make # target declared below. When check_layout is used as a dependency of # libsbml_wrap.cpp via a call like this, # # libsbml_wrap.cpp: $(shell $(call check_layout)) ...other dependencies... # ...ACTIONS... # # what will happen is either check_layout will return nothing, in which # case the dependency is satisfied and no swig'ing needs to be done, or # it will return "do_reswig", a phony target that is never satisfied, # in which case the ...ACTIONS... will be executed. .PHONY: do_reswig ifdef USE_COMP define check_comp if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep getListOfSubmodels libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_comp if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep getListOfSubmodels libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_FBC define check_fbc if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep ListOfFluxBounds libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_fbc if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep ListOfFluxBounds libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_GROUPS define check_groups if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep ListOfGroups libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_groups if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep ListOfGroups libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_LAYOUT define check_layout if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep getListOfLayouts libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_layout if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep getListOfLayouts libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_QUAL define check_qual if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep ListOfQualitativeSpecies libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_qual if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep ListOfQualitativeSpecies libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_MULTI define check_multi if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep ListOfSpeciesFeatures libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_multi if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep ListOfSpeciesFeatures libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_RENDER define check_render if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -z "`grep ListOfGlobalRenderInformation libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef else define check_render if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; \ if test -n "`grep ListOfGlobalRenderInformation libsbml_wrap.cpp`"; then echo "do_reswig"; fi; endef endif ifdef USE_L3V2EXTENDEDMATH define check_l3v2extendedmath if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; endef else define check_l3v2extendedmath if test ! -f libsbml_wrap.cpp; then echo "do_reswig"; exit; fi; endef endif # Generate the documentation files. # # javadoc-extras.i contain manually-written javadoc additions that are appended # to the javadoc.i file created by our swigdoc.py. It contains things that are # Java-specific (thus, don't belong in libsbml.i) and don't need to be # processed by swigdoc.py. javadoc.i: $(main_sources) $(swig_sources) ../swig/swigdoc.py $(wildcard ../swig/*.i) touch ../../../docs/src/libsbml-converters.txt && ../swig/swigdoc.py --language java --top ../../.. $(SWIGDOCDEFINES) \ --extra ../../../docs/src/libsbml-converters.txt \ --master ../swig/libsbml.i --output javadoc.i # libsbml_wrap.cpp is a stand-in for the .java files. Its creation results # in the creation of the .java files too -- both are made by running swig. libsbml_wrap.cpp $(outpath): javadoc.i $(swig_sources) $(main_sources) \ $(shell $(call check_comp)) $(shell $(call check_fbc)) \ $(shell $(call check_layout)) $(shell $(call check_qual)) \ $(shell $(call check_groups)) $(shell $(call check_multi)) @top_srcdir@/config/chk_swig_version.sh || exit ifneq "$(MAKEFLAGS)" "" $(MAKE) -$(MAKEFLAGS) clean-swigfiles else $(MAKE) clean-swigfiles endif test -d $(outpath) || mkdir -p $(outpath) "$(SWIG)" $(SWIGFLAGS) $(sort $(default_includes) $(INCLUDES)) \ -c++ -java -package $(java_package) \ -outdir $(outpath) -o libsbml_wrap.cpp libsbml.i # We use a trick involving marking methods as deprecated with the Javadoc # @deprecated comment directive, but unfortunately javac seems to pay # attention to that and thinks we're trying to use deprecated methods. We # used to use a "grep -v" to filter them out, but in Java 9 each warning # prints multiple lines and the simple grep filter doesn't work. Resorting # to the use of -nowarn even though this is dangerous and could mask # a problem. compile_command = "$(JAVAC)" $(JAVAC_OPTION) -d $(outdir) $(outpath)/*.java $(outpath)/libsbml.class: libsbml_wrap.cpp $(outpath) @echo $(compile_command) $(compile_command) -nowarn $(jarfile): $(outpath)/libsbml.class $(CD) $(outdir) && "$(JAR)" -cvfm ../$(jarfile) ../Manifest.txt $(pkg_path)/*.class # Force removal of the java-files directory. clean-swigfiles: clean-generic clean-libtool clean-extras -rm -rf $(outdir) libsbml_wrap.cpp # ----------------------------------------------------------------------------- # Checking. # ----------------------------------------------------------------------------- check_classes = $(check_sources:.java=.class) ifeq "$(HOST_TYPE)" "cygwin" classpath = $(shell cygpath -wp $(jarfile):$(TOP_BUILDDIR)/src:$(test_dir):.) CPPFLAGS += -DNOMINMAX else classpath = $(jarfile):$(TOP_BUILDDIR)/src:$(test_dir):. endif # See the note above regarding the Javadoc @deprecated comment and the # reason for the following contortion. check_compile_command = "$(JAVAC)" $(JAVAC_OPTION) -g -classpath "$(classpath)" $(check_sources) $(check_classes): Makefile $(libraries) $(check_sources) @echo $(check_compile_command) $(shell $(check_compile_command) 2>&1 | grep -v deprecat) ifeq "$(HOST_TYPE)" "darwin" define runjavatest env DYLD_LIBRARY_PATH="$(RUN_LDPATH):$(DYLD_LIBRARY_PATH):." "$(JAVA)" -classpath "$(classpath)" AutoTestRunner endef else define runjavatest env LD_LIBRARY_PATH="$(RUN_LDPATH):$(LD_LIBRARY_PATH):." "$(JAVA)" -Djava.library.path=. -classpath "$(classpath)" AutoTestRunner endef endif # 2010-07-05 For some reason, I can't get runjavatest # or the previous version of it to work in my environment anymore. I'm # switching to a straight invocation of java. check: $(check_classes) $(shell $(call check_layout)) \ $(shell $(call check_comp)) $(shell $(call check_fbc)) \ $(shell $(call check_qual)) $(shell $(call check_groups)) \ $(shell $(call check_multi)) $(shell $(call check_render)) \ $(shell $(call check_l3v2extendedmath)) @echo @echo @echo Running Tests in $(thisdir) @echo ----------------------------------------------------------------- $(runjavatest) @echo ----------------------------------------------------------------- @echo # # 'make test-files' will reconstruct the test files. This is not made part # of 'make check' (yet). # test-files: $(call test_translator,j,xml math annotation sbml,test/org/sbml/libsbml/test) # ----------------------------------------------------------------------------- # Tags. # ----------------------------------------------------------------------------- tags: etags ctags # ----------------------------------------------------------------------------- # Installation. # ----------------------------------------------------------------------------- JNI_INSTPATH=$(DESTDIR)$(LIBDIR)/$(jnifile) JAR_INSTPATH=$(DESTDIR)$(DATADIR)/java/$(jarfile) install: $(libraries) $(shell $(call check_layout)) \ $(shell $(call check_comp)) $(shell $(call check_fbc)) \ $(shell $(call check_qual)) $(shell $(call check_groups)) $(INSTALL_SH) $(jnifile) $(JNI_INSTPATH) $(INSTALL_SH) $(jarfile) $(JAR_INSTPATH) uninstall: @list='$(JNI_INSTPATH) $(JAR_INSTPATH)'; for lib in $$list; do \ if test -f "$$lib"; then \ echo rm "$$lib"; \ rm $$lib; \ fi; \ done; installcheck: # ----------------------------------------------------------------------------- # Creating distribution (for libSBML maintainers only) # ----------------------------------------------------------------------------- dist: libsbml_wrap.cpp $(outdir) dist-normal distcheck: distcheck-normal # ----------------------------------------------------------------------------- # Miscellaneous # ----------------------------------------------------------------------------- include @top_srcdir@/config/makefile-common-actions.mk # ----------------------------------------------------------------------------- # End. # -----------------------------------------------------------------------------