debian/changelog

+libmems (1.6.0+4725-5) unstable; urgency=medium
+
+  * Drop version number from package name
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+
+ -- Andreas Tille <tille@debian.org>  Wed, 18 Jul 2018 15:17:57 +0200
+
 libmems (1.6.0+4725-4) unstable; urgency=medium
 
   * Use fake watch file

debian/compat

-9
+11

debian/control

@@ -3,24 +3,23 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
-               dh-autoreconf,
+Build-Depends: debhelper (>= 11~),
                d-shlibs,
                pkg-config,
-               libgenome-1.3-dev,
+               libgenome-dev,
                libboost-filesystem-dev,
                libboost-iostreams-dev,
                libboost-program-options-dev,
-               libmuscle-3.7-dev
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libmems.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libmems.git
+               libmuscle-dev
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/libmems
+Vcs-Git: https://salsa.debian.org/med-team/libmems.git
 Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/
 
-Package: libmems-1.6-dev
+Package: libmems-dev
 Architecture: any
 Section: libdevel
-Depends: libmems-1.6-1v5 (= ${binary:Version}),
+Depends: libmems1 (= ${binary:Version}),
          ${misc:Depends},
          ${devlibs:Depends}
 Provides: libmems-1.6-dev
@@ -37,15 +36,19 @@ Description: development library to support DNA string matching and comparative
  This is the development package containing the statically linked
  library and the header files.
 
-Package: libmems-1.6-1v5
+Package: libmems1
 Architecture: any
 Multi-Arch: same
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Pre-Depends: ${misc:Pre-Depends}
-Conflicts: libmems-1.6-1
-Replaces: libmems-1.6-1
+Conflicts: libmems-1.6-1,
+           libmems-1.6-1v5
+Provides: libmems-1.6-1,
+          libmems-1.6-1v5
+Replaces: libmems-1.6-1,
+          libmems-1.6-1v5
 Description: library to support DNA string matching and comparative genomics
  libMems is a freely available software development library to support DNA
  string matching and comparative genomics. Among other things, libMems

debian/patches/drop-version-number.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 18 Jul 2018 15:15:58 +0200
+Description: Drop version number from library file name
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -8,7 +8,7 @@ projects/libMems.sln \
+ projects/libMems.vcproj
+ 
+ pkgconfigdir = $(libdir)/pkgconfig
+-pkgconfig_DATA = libMems-@GENERIC_API_VERSION@.pc
++pkgconfig_DATA = libMems.pc
+ 
+ SUBDIRS = libMems 
+ 
+--- /dev/null
++++ b/libMems.pc.in
+@@ -0,0 +1,12 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libMems 
++Description: c++ library supporting DNA sequence and genome alignment 
++Version: @VERSION@
++Requires: libGenome libMUSCLE
++Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ 
++Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ 
++
+--- a/libMems-1.6.pc.in
++++ /dev/null
+@@ -1,12 +0,0 @@
+-prefix=@prefix@
+-exec_prefix=@exec_prefix@
+-libdir=@libdir@
+-includedir=@includedir@
+-
+-Name: libMems 
+-Description: c++ library supporting DNA sequence and genome alignment 
+-Version: @VERSION@
+-Requires: libGenome-1.3 libMUSCLE-3.7
+-Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems-@GENERIC_API_VERSION@ @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ 
+-Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@-@GENERIC_API_VERSION@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ 
+-
+--- a/libMems/Makefile.am
++++ b/libMems/Makefile.am
+@@ -55,14 +55,14 @@ dmSML/util.c dmSML/sorting.c dmSML/dmsor
+ dmSML/timing.c dmSML/sml.c
+ 
+ 
+-libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)
++libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)
+ libmems_include_HEADERS = $(LIBMEMS_H) 
+ 
+ # build libraries with gcc (no suffix)
+-lib_LTLIBRARIES = libMems-1.6.la
+-libMems_1_6_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC)
+-libMems_1_6_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@  @BOOST_SYSTEM_LIBS@
+-libMems_1_6_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)  
++lib_LTLIBRARIES = libMems.la
++libMems_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC)
++libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@  @BOOST_SYSTEM_LIBS@
++libMems_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION)  
+ 
+ homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/HomologyHMM
+ homologyhmm_include_HEADERS = $(HOMOLOGYHMM_H)
+--- a/configure.ac
++++ b/configure.ac
+@@ -95,7 +95,7 @@ BOOST_PROGRAM_OPTIONS
+ BOOST_IOSTREAMS
+ 
+ dnl Get location of libGenome Headers
+-PKG_CHECK_MODULES(DEPS, libGenome-1.3 >= 1.3.1  libMUSCLE-3.7 >= 1.0.0)
++PKG_CHECK_MODULES(DEPS, libGenome >= 1.3.1  libMUSCLE >= 1.0.0)
+ AC_SUBST(DEPS_CFLAGS)
+ 
+ dnl Check for OpenMP
+@@ -133,5 +133,5 @@ AC_PROG_GCC_TRADITIONAL
+ dnl SAVE_LIBRARY_VERSION
+ AC_SUBST(LIBTOOL_VERSION_INFO)
+ 
+-AC_OUTPUT(Makefile libMems/Makefile libMems-1.6.pc )
++AC_OUTPUT(Makefile libMems/Makefile libMems.pc )
+ #doc/html/Makefile  doc/man/Makefile  doc/man/man3/Makefile)

debian/patches/series

@@ -6,3 +6,4 @@ pkg-config-directive.patch
 05_gcc-6.patch
 boost1.62.patch
 # automake_drop_version_info.patch
+drop-version-number.patch

debian/rules

@@ -3,22 +3,20 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
 
 %:
-	dh $@ --with autoreconf
+	dh $@
 
 override_dh_install:
 	dh_install
 	d-shlibmove --commit \
 	            --multiarch \
-	            --v5 \
 		    --devunversioned \
 		    --exclude-la \
+		    --override s/libGenome0-dev/libgenome-dev/ \
+		    --override s/libMUSCLE1-dev/libmuscle-dev/ \
 		    --movedev debian/tmp/usr/include usr \
 		    --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig \
 		    debian/tmp/usr/lib/*/*.so
 
-#override_dh_auto_test:
-#	echo 'Disable test since some header (gnDNXSource.h) seems to be missing.'
-
 get-orig-source:
 	. debian/get-orig-source