debian/changelog

-clustalo (1.2.4-3) UNRELEASED; urgency=medium
+clustalo (1.2.4-4) unstable; urgency=medium
 
+  [ Jelmer Vernooij ]
   * Use secure copyright file specification URI.
 
- -- Jelmer Vernooij <jelmer@debian.org>  Sat, 20 Oct 2018 13:51:21 +0000
+  [ Andreas Tille ]
+  * Do not replace autogenerated jquery.js
+    Closes: #946297
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Set field Upstream-Contact in debian/copyright.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata
+    (already present in machine-readable debian/copyright).
+
+ -- Andreas Tille <tille@debian.org>  Fri, 10 Jan 2020 11:44:03 +0100
 
 clustalo (1.2.4-2) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -4,13 +4,12 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
-               dh-linktree,
+Build-Depends: debhelper-compat (= 12),
                libargtable2-dev,
                doxygen,
                graphviz,
                sphinx-common
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/clustalo
 Vcs-Git: https://salsa.debian.org/med-team/clustalo.git
 Homepage: http://www.clustal.org/omega/

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: clustalo
 Source: http://www.clustal.org/omega/
+Upstream-Contact: Fabian Sievers (UCD Dublin, Ireland)
 
 Files: *
 Copyright: 2010 UCD Dublin <clustalw@ucd.ie>

debian/libclustalo-doc.linktrees

-replace usr/share/sphinx/themes/basic/static/jquery.js usr/share/doc/libclustalo-doc/api/html/jquery.js 

debian/rules

@@ -7,13 +7,15 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@ --with linktree
+	dh $@
 
 override_dh_auto_build-indep:
 	# nothing to do here
 
 override_dh_auto_test-indep:
-	# nothing to do here
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	echo "Do not run build time test"
+endif
 
 override_dh_auto_install-arch:
 	dh_auto_install -a

debian/upstream/metadata

-Contact: Fabian Sievers (UCD Dublin, Ireland)
-Name: Clustal Omega
 Reference:
 - Author: >
     Fabian Sievers and Andreas Wilm and David Dineen and Toby J Gibson and