debian/changelog

+libmuscle (3.7+4565-3) UNRELEASED; urgency=medium
+
+  * Drop version number from package name
+  * Fake watch file
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+
+ -- Andreas Tille <tille@debian.org>  Tue, 10 Jul 2018 15:33:34 +0200
+
 libmuscle (3.7+4565-2) unstable; urgency=medium
 
   * Take over patches from parsnp to avoid internal copy there

debian/compat

-9
+11

debian/control

@@ -3,21 +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
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libmuscle.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libmuscle.git
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/libmuscle
+Vcs-Git: https://salsa.debian.org/med-team/libmuscle.git
 Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/muscle/trunk/
 
-Package: libmuscle-3.7-dev
+Package: libmuscle-dev
 Architecture: any
 Section: libdevel
-Depends: libmuscle-3.7-1 (= ${binary:Version}),
+Depends: libmuscle1 (= ${binary:Version}),
          ${misc:Depends},
          ${devlibs:Depends}
+Conflicts: libmuscle-3.7-dev
+Provides: libmuscle-3.7-dev
+Replaces: libmuscle-3.7-dev
 Description: multiple alignment development library for protein sequences
  MUSCLE is a multiple alignment program for protein sequences. MUSCLE
  stands for multiple sequence comparison by log-expectation. In the
@@ -30,11 +32,14 @@ Description: multiple alignment development library for protein sequences
  .
  This package contains the static library and header files.
 
-Package: libmuscle-3.7-1
+Package: libmuscle1
 Architecture: any
 Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Conflicts: libmuscle-3.7-1
+Provides: libmuscle-3.7-1
+Replaces: libmuscle-3.7-1
 Description: multiple alignment library for protein sequences
  MUSCLE is a multiple alignment program for protein sequences. MUSCLE
  stands for multiple sequence comparison by log-expectation. In the

debian/patches/drop_version_from_library_name.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 10 Jul 2018 15:33:34 +0200
+Description: Drop version number from library name
+
+--- a/libMUSCLE/Makefile.am
++++ b/libMUSCLE/Makefile.am
+@@ -22,20 +22,20 @@ intmath.cpp local.cpp makerootmsab.cpp m
+ msa2.cpp msa.cpp msadistkimura.cpp msf.cpp muscle.cpp muscleout.cpp nucmx.cpp nwdasimple2.cpp nwdasimple.cpp nwdasmall.cpp nwrec.cpp nwsmall.cpp objscore2.cpp objscore.cpp objscoreda.cpp onexception.cpp options.cpp outweights.cpp pam200mafft.cpp params.cpp phy2.cpp phy3.cpp phy4.cpp phy.cpp phyfromclust.cpp phyfromfile.cpp physeq.cpp phytofile.cpp posgap.cpp ppscore.cpp profdb.cpp profile.cpp profilefrommsa.cpp progalign.cpp progress.cpp progressivealign.cpp pwpath.cpp readmx.cpp realigndiffs.cpp realigndiffse.cpp refine.cpp refinehoriz.cpp refinesubfams.cpp refinetree.cpp refinetreee.cpp refinevert.cpp refinew.cpp savebest.cpp scoregaps.cpp scorehistory.cpp scorepp.cpp seq.cpp seqvect.cpp setblosumweights.cpp setgscweights.cpp setnewhandler.cpp spfast.cpp sptest.cpp stabilize.cpp subfam.cpp subfams.cpp sw.cpp termgaps.cpp textfile.cpp threewaywt.cpp traceback.cpp tracebackopt.cpp tracebacksw.cpp treefrommsa.cpp typetostr.cpp upgma2.cpp usage.cpp validateids.cpp vtml2.cpp writescorefile.cpp \
+ blosum62.cpp globalsother.cpp maketree.cpp scoredist.cpp tomhydro.cpp
+ 
+-library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)
++library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)
+ library_include_HEADERS = $(LIBMUSCLE_H)
+ 
+ INCLUDES = -I$(top_srcdir)
+ 
+-lib_LTLIBRARIES = libMUSCLE-3.7.la
+-libMUSCLE_3_7_la_SOURCES = $(LIBMUSCLE_SRC)
+-libMUSCLE_3_7_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) 
+-libMUSCLE_3_7_la_CXXFLAGS= -D_LIB $(AM_CXXFLAGS)
++lib_LTLIBRARIES = libMUSCLE.la
++libMUSCLE_la_SOURCES = $(LIBMUSCLE_SRC)
++libMUSCLE_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) 
++libMUSCLE_la_CXXFLAGS= -D_LIB $(AM_CXXFLAGS)
+ 
+ bin_PROGRAMS = muscle 
+ 
+ 
+ muscle_SOURCES = main.cpp
+-muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la
++muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE.la
+ 
+ 
+--- /dev/null
++++ b/libMUSCLE.pc.in
+@@ -0,0 +1,11 @@
++prefix=@prefix@
++exec_prefix=@exec_prefix@
++libdir=@libdir@
++includedir=@includedir@
++
++Name: libMUSCLE 
++Description: The MUSCLE multiple sequence alignment code turned into a library 
++Version: @VERSION@
++Libs: -L${libdir} -lMUSCLE @OPENMP_CXXFLAGS@
++Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @OPENMP_CXXFLAGS@ 
++
+--- a/libMUSCLE-3.7.pc.in
++++ /dev/null
+@@ -1,11 +0,0 @@
+-prefix=@prefix@
+-exec_prefix=@exec_prefix@
+-libdir=@libdir@
+-includedir=@includedir@
+-
+-Name: libMUSCLE 
+-Description: The MUSCLE multiple sequence alignment code turned into a library 
+-Version: @VERSION@
+-Libs: -L${libdir} -lMUSCLE-@GENERIC_API_VERSION@ @OPENMP_CXXFLAGS@
+-Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@-@GENERIC_API_VERSION@ @OPENMP_CXXFLAGS@ 
+-
+--- a/configure.ac
++++ b/configure.ac
+@@ -108,4 +108,4 @@ AC_PROG_GCC_TRADITIONAL
+ dnl SAVE_LIBRARY_VERSION
+ AC_SUBST(LIBTOOL_VERSION_INFO)
+ 
+-AC_OUTPUT(Makefile libMUSCLE/Makefile libMUSCLE-3.7.pc )
++AC_OUTPUT(Makefile libMUSCLE/Makefile libMUSCLE.pc )
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -9,7 +9,7 @@ projects/libmuscle.doxygen
+ 
+ 
+ pkgconfigdir = $(libdir)/pkgconfig
+-pkgconfig_DATA = libMUSCLE-@GENERIC_API_VERSION@.pc
++pkgconfig_DATA = libMUSCLE.pc
+ 
+ SUBDIRS = libMUSCLE  
+ 

debian/patches/series

 parsnp_changes.patch
+drop_version_from_library_name.patch

debian/rules

@@ -3,7 +3,10 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@ --with autoreconf
+	dh $@
+
+override_dh_auto_build:
+	dh_auto_build --no-parallel
 
 override_dh_install:
 	dh_install

debian/watch

-# There is no tarball download location, libMuscle is only available in SVN
+version=4
+
+opts=dversionmangle=s/.*/0.No-Release/ \
+ https://people.debian.org/~eriberto/ FakeWatchNoUpstreamReleaseForThisPackage-(\d\S+)\.gz