Clean up rules and document current issue with private header of hdf5 lib H5private.h

             sourceTest/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFileTest.java

%:

	dh $@ --with javahelper --buildsystem=gradle

	dh $@ --with javahelper

override_jh_installlibs:

	mv targets/gradle/libs/sis-jhdf5-1.jar targets/gradle/libs/sis-jhdf5.jar

	jh_installlibs --version-strip='[~pre1]*[+]git[.0-9a-f]*[+]dfsg[.0-9]*'

_override_dh_auto_clean:

	rm -rf build *.jar

	rm -rf source/c/*.log

	rm -rf source/c/*.so

	# Stuff generated during testing

	find sourceTest/java -name '*.class' -delete

	cd sourceTest/java && rm -f *.hdf *.h5

	rm -f sourceTest/java/sourceTest/java/test/hdf5lib/h5ex_g_iterate.hdf

	rm -rf test-output targets

	#Things that we'd probably exclude from the orig.tar.gz anyway

	rm -rf jsrc lib ./sourceTest/java/jni

_override_dh_auto_build:

	# C build

override_dh_auto_build:

	dh_auto_build

	# Create JNI manually since this is not part of the build system

	# Upsteam seems to `cd source/c` and call a script which in turn calls compile_hdf5_gcc.sh

	# In this script hdf5 source is unpacked, possibly patched, build and used for the JNI build

	# Most problematic issue is that private header H5private.h is used

	cd source/c && \

		$(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS)  -shared -fPIC -Wl,--exclude-libs,ALL \

		-I/usr/lib/jvm/default-java/include/ -I/usr/include/hdf5/serial \

		*.c jni/*.c -o libsis-jhdf5.so -lz -lhdf5_serial

	jh_build sis-jhdf5.jar src

override_jh_installlibs:

	mv targets/gradle/libs/sis-jhdf5-1.jar targets/gradle/libs/sis-jhdf5.jar

	jh_installlibs --version-strip='[~pre1]*[+]git[.0-9a-f]*[+]dfsg[.0-9]*'

_override_dh_auto_test:

ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))

	mv debian/tmptestignore/* sourceTest/java/test/hdf5lib

	rmdir debian/tmptestignore

endif

_override_dh_install:

	dh_install

	mkdir -p debian/libsis-jhdf5-java/usr/bin

	cp -a dist/bin/h5ar.sh debian/libsis-jhdf5-java/usr/bin