debian/NEWS.Debian.hyphy-mpi

+hyphy (2.5.1+dfsg-1) unstable; urgency=medium
+
+  Since version 2.5.1 the upstream names for the binaries have changed.
+  In Debian we do not derive from upstream names any more.  The executable
+  MPI executable is now
+          /usr/bin/HYPHYMPI
+
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 13:30:30 +0100

debian/NEWS.Debian.hyphy-pt

+hyphy (2.5.1+dfsg-1) unstable; urgency=medium
+
+  Since version 2.5.1 the upstream names for the binaries have changed.
+  In Debian we do not derive from upstream names any more.  The executable
+  is now
+          /usr/bin/hyphy
+
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 13:30:30 +0100

debian/changelog

-hyphy (2.5.1+dfsg-1) UNRELEASED; urgency=medium
+hyphy (2.5.1+dfsg-1) unstable; urgency=medium
 
   [ Helmut Grohne ]
   * Add pkg-config to Build-Depends as FindMPI.cmake will need it for cross
@@ -14,9 +14,13 @@ hyphy (2.5.1+dfsg-1) UNRELEASED; urgency=medium
   * Use secure URI in Homepage field.
   * Remove patches msse_option_only_if_available.patch that are missing
     from debian/patches/series.
-  TODO: Fix build failure
+  * Skip GTEST target for the moment since this is currently in flux
+    see https://github.com/veg/hyphy/issues/1058
+  * No need to rename executables any more since upstream is doing this now
+  * Autopkgtest exists since last release - so close bug
+    Closes: #909707
 
- -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 13:30:30 +0100
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 22:47:47 +0100
 
 hyphy (2.3.14+dfsg-2) unstable; urgency=medium
 

debian/hyphy-mpi.install

-usr/bin/*mpi
+usr/bin/HYPHYMPI

debian/hyphy-pt.install

-usr/bin/*mp
+usr/bin/hyphy

debian/rules

@@ -21,19 +21,20 @@ override_dh_auto_configure:
 
 override_dh_auto_build:
 	# no idea about the purpose of the dynamic library - executables are not simply linked against it
-	dh_auto_build -- MP MPI GTEST # LIB
+	dh_auto_build -- MP MPI
+	# GTEST
+	echo "Skip GTEST target for the moment - see https://github.com/veg/hyphy/issues/1058"
+	# LIB
 
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	find obj-* -name HYPHYGTEST -exec \{\} \;
 endif
 
-override_dh_install:
-	# smallcaps for executables
-	for bindir in `find . -type d -name bin` ; do \
-	    for bin in $${bindir}/* ; do \
-	        # ln -s `basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
-	        mv $${bindir}/`basename $${bin}` $${bindir}/`basename $${bin} | tr [A-Z] [a-z]` ; \
-	    done ; \
+override_dh_installdocs:
+	dh_installdocs
+	for news in debian/NEWS.Debian.* ; do \
+	    pkg=`echo $${news} | sed 's/.*NEWS.Debian.//'` ; \
+	    cp -a $${news} debian/$${pkg}/usr/share/doc/$${pkg}/NEWS.Debian ; \
 	done
-	dh_install
+

debian/tests/run-unit-tests

@@ -28,7 +28,7 @@ rm -f MolecularClockHKY85.bf MolecularClockF81.bf RelativeRatePBS.bf ParametricB
 
 for i in *.bf; do
     [ -f "$i" ] || break
-    hyphymp "$i"
+    hyphy "$i"
 done
 
 # Clean up