debian/README.source

@@ -11,25 +11,7 @@ also needs to link against the NCSA native library (via JNI) at runtime.
 
 So, trying to package sis-jhdf5:
 
-The 'source' distribution' linked on the web page only have the Java source.
-The real source you need is in SVN:
-
-svn co http://svncisd.ethz.ch/repos/cisd/jhdf5/trunk/
-
-For compilation to succeed, we also need sis-base, not to be confused
-with the entirely separate project at sis.apache.org!
-
-http://svncisd.ethz.ch/repos/cisd/base/trunk/
-See the libsis-base-java package for this.
-
-The code also depends on their own args4j library, but only for the CLI
-under ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java which we can
-simply leave out just now.  I delete it from jsrc/ before compiling and
-also leave out the h5ar.sh script which invokes it.  Once args4j is packaged
-this can be reinstated and the h5ar command can be added to /usr/bin
-( http://bs-svn01.ethz.ch/repos/cisd/libraries/trunk/cisd-args4j/ )
-
-So - can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
+Can we exclude the ncsa.hdf.hdf5lib.* classes from sis-jhdf5 and
 compile it against the existing classes in /usr/share/java/jhdf5.jar?
 My conclusion is not, because...
 

debian/control

@@ -14,6 +14,7 @@ Build-Depends: debhelper (>= 11~),
                libcommons-io-java,
                libsis-base-java (>= 18.08.0~),
                libhdf5-dev (>> 1.8.13),
+               libargs4j-java,
                junit4,
                testng,
                libjmock2-java
@@ -27,7 +28,8 @@ Architecture: all
 Depends: ${misc:Depends},
          ${java:Depends},
          libsis-jhdf5-jni (>= ${binary:Version}),
-         libsis-jhdf5-jni (<< ${source:Version}.1~)
+         libsis-jhdf5-jni (<< ${source:Version}.1~),
+         libargs4j-java
 Description: easy-to-use HDF library for Java
  JHDF5 is a Java binding to the HDF Group library for HDF5 focusing on
  ease-of-use, which was developed by CISD and is now maintained by ETH SIS.
@@ -39,4 +41,9 @@ Architecture: any
 Depends: ${misc:Depends},
          ${shlibs:Depends}
 Description: native libs used by libsis-jhdf5-java package
- This package is only useful with libsis-jhdf5-java.
+ This package is only useful with libsis-jhdf5-java which is a
+ Java binding to the HDF Group library for HDF5 focusing on
+ ease-of-use, which was developed by CISD and is now maintained
+ by ETH SIS.
+ .
+ This package provides a native interface for the library.

debian/patches/fix_build_dir.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 13 Aug 2018 14:30:28 +0200
-Description: Do not make wrong assumptions about directory name
-
---- a/javaproject.gradle
-+++ b/javaproject.gradle
-@@ -50,13 +50,9 @@ sourceSets {
- buildDir = 'targets/gradle'
- 
- buildscript {
--    apply from: '../jhdf5/repository.gradle'
-+    apply from: 'repository.gradle'
-     
-     repositories repositoryConfig
--    
--    dependencies {
--        classpath 'cisd:cisd-ant-tasks:+'
--    }
- }
- 
- repositories repositoryConfig

debian/patches/series

 # fix_dodgy_cast.patch
 # remove_ch_rinn_imports.patch
 # load_native_debian.patch
-fix_build_dir.patch

debian/rules

@@ -10,10 +10,9 @@ DPKG_EXPORT_BUILDFLAGS = 1
 include /usr/share/dpkg/buildflags.mk
 include /usr/share/java/java_defaults.mk
 
-CPPFLAGS += ${jvm_includes}
+CPPFLAGS += ${jvm_includes} -Ijni
 
 TESTIGNORE = sourceTest/java/ch/systemsx/cisd/hdf5/HDF5RoundtripTest.java \
-             sourceTest/java/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverTest.java \
              sourceTest/java/ch/systemsx/cisd/hdf5/io/HDF5DataSetRandomAccessFileTest.java
 
 %:
@@ -37,13 +36,10 @@ override_dh_auto_build:
 		$(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
-	# Java build - see README.source about the file being removed
-	mkdir jsrc ; cp -r source/java/ch source/java/ncsa jsrc
-	rm jsrc/ch/systemsx/cisd/hdf5/h5ar/HDF5ArchiverMain.java
-	# This line is still needed on Ubuntu 14.04
-	jh_build sis-jhdf5.jar jsrc
+	jh_build sis-jhdf5.jar src
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# FIXME
 	# Due to bug #842815 several tests are failing
 	# To get at least some installable package these tests are ignored here
@@ -72,3 +68,9 @@ override_dh_auto_test:
 	# FIXME: Second part of hacking around bug #842815
 	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