debian/changelog

+jellyfish (2.2.10-2) unstable; urgency=medium
+
+  * debian/control: removed unused valgrind dependency
+  * Standards-Version: 4.3.0
+  * Improve reproducibilty, drop /usr/share/doc/jellyfish-
+    examples/examples/swig*
+  * Remove dependency_libs field in libjellyfish-2.0.la.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 24 Dec 2018 06:46:27 -0800
+
 jellyfish (2.2.10-1) unstable; urgency=medium
 
   * New upstream version

debian/control

@@ -12,14 +12,13 @@ Build-Depends: debhelper (>= 11~),
                bc,
                time,
                procps,
-               valgrind,
                swig,
                python3-all-dev,
                python-all-dev,
                dh-python,
                perl,
                chrpath
-Standards-Version: 4.1.4
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish
 Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git
 Homepage: http://www.cbcb.umd.edu/software/jellyfish/

debian/patches/reproducible.patch

@@ -4,9 +4,9 @@ Bug-Debian: https://bugs.debian.org/863015
 Description: Enable reproducible build by avoiding the current
  date with time zone in json output
 
---- a/include/jellyfish/generic_file_header.hpp
-+++ b/include/jellyfish/generic_file_header.hpp
-@@ -180,6 +180,8 @@ public:
+--- jellyfish.orig/include/jellyfish/generic_file_header.hpp
++++ jellyfish/include/jellyfish/generic_file_header.hpp
+@@ -180,6 +180,8 @@
  
  protected:
    std::string get_hostname() const {
@@ -15,7 +15,7 @@ Description: Enable reproducible build by avoiding the current
      struct utsname buf;
      if(uname(&buf) == -1)
        return "";
-@@ -187,6 +189,8 @@ protected:
+@@ -187,6 +189,8 @@
    }
  
    std::string get_pwd() const {
@@ -24,7 +24,7 @@ Description: Enable reproducible build by avoiding the current
  #ifdef PATH_MAX
      size_t len = PATH_MAX;
  #else
-@@ -202,6 +206,16 @@ protected:
+@@ -202,6 +206,16 @@
    std::string get_localtime() const {
      time_t t = time(0);
      std::string res(ctime(&t));

debian/rules

@@ -13,12 +13,20 @@ export PKG_CONFIG_SYSROOT_DIR=${CURDIR}/debian/tmp/
 export PERL_MM_OPT=INSTALLDIRS=vendor
 export PYBUILD_BUILD_ARGS=build_ext --rpath "${CURDIR}/debian/tmp/usr/lib/${DEB_HOST_MULTIARCH}"
 
+export DEB_LDFLAGS_MAINT_APPEND = -lpthread
+
 %:
 	dh $@ # --with python3
 
 override_dh_auto_install:
 	dh_auto_install -- install-data
 
+override_dh_installexamples:
+	dh_installexamples
+	sed '/SRCDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+	sed '/BUILDDIR=/d' debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/compat.sh*
+	rm -f debian/jellyfish-examples/usr/share/doc/jellyfish-examples/examples/swig*
+
 override_dh_install:
 	# dh_install -X*.a -X*.la -Xpkgconfig
 #	dh_install -ppython3-dna-jellyfish
@@ -40,6 +48,7 @@ override_dh_install:
 		    --movedev "debian/tmp/usr/include/$(DEB_SOURCE)*/$(DEB_SOURCE)/*.hpp" usr/include/$(DEB_SOURCE) \
 		    --movedev "debian/tmp/usr/include/$(DEB_SOURCE)*/$(DEB_SOURCE)/*.h" usr/include/$(DEB_SOURCE) \
 			debian/tmp/usr/lib/*/lib$(DEB_SOURCE)-*.so
+	sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/${DEB_HOST_MULTIARCH}/*.la
 
 override_dh_auto_configure:
 	dh_auto_configure -- --enable-swig --enable-perl-binding # --enable-python-binding