debian/changelog

+emboss (6.6.0+dfsg-7) unstable; urgency=medium
+
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.5
+  * Drop unused lintian-overrides
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test
+  * Lintian override for script-with-language-extension
+  * More verbose package descriptions for all packages
+
+ -- Andreas Tille <tille@debian.org>  Fri, 03 Aug 2018 05:59:14 +0200
+
 emboss (6.6.0+dfsg-6) unstable; urgency=medium
 
   * debhelper 10

debian/compat

-10
+11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Charles Plessy <plessy@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
 #              javahelper,
                libx11-dev,
                x11proto-core-dev,
@@ -18,16 +18,14 @@ Build-Depends: debhelper (>= 10),
                libpq-dev,
                antiword,
                sharutils,
-               autotools-dev,
                tcsh | csh | c-shell,
-               dh-autoreconf,
 # Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031
                default-jdk,
                ant
-#Build-Depends-Indep: default-jdk
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/emboss.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/emboss.git
+# #Build-Depends-Indep: default-jdk
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/emboss
+Vcs-Git: https://salsa.debian.org/med-team/emboss.git
 Homepage: http://emboss.sourceforge.net
 
 Package: emboss
@@ -57,6 +55,16 @@ Package: emboss-data
 Architecture: all
 Depends: ${misc:Depends}
 Description: data files for the EMBOSS package
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
  This package includes data files needed by EMBOSS, the European Molecular
  Biology Open Software Suite.
 
@@ -66,6 +74,16 @@ Section: doc
 Depends: ${misc:Depends}
 Suggests: evince | pdf-viewer | postscript-viewer
 Description: documentation for EMBOSS
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
  This package includes non-essential user documentation for EMBOSS, the
  European Molecular Biology Open Software Suite.
 
@@ -76,6 +94,16 @@ Depends: ${misc:Depends}
 Recommends: tcsh | csh | c-shell
 Suggests: valgrind
 Description: test files for the EMBOSS package
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
  This package includes test files for EMBOSS, the European Molecular Biology
  Open Software Suite.
  .
@@ -121,5 +149,15 @@ Depends: ${shlibs:Depends},
          default-jre
 #         libgnujaf-java
 Description: graphical user interface to EMBOSS
+ EMBOSS is a free Open Source software analysis package specially developed for
+ the needs of the molecular biology (e.g. EMBnet) user community. The software
+ automatically copes with data in a variety of formats and even allows
+ transparent retrieval of sequence data from the web. Also, as extensive
+ libraries are provided with the package, it is a platform to allow other
+ scientists to develop and release software in true open source spirit. EMBOSS
+ also integrates a range of currently available packages and tools for sequence
+ analysis into a seamless whole. EMBOSS breaks the historical trend towards
+ commercial software packages.
+ .
  Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular
  Biology Open Software Suite. It is part of the EMBOSS distribution.

debian/emboss-doc.lintian-overrides

-# false positives:  These files are just carbon copies of the files in upstream tarball
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/adminguide.tar.gz
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/manuals/program.ps.gz
-emboss-doc: package-contains-timestamped-gzip usr/share/EMBOSS/doc/tutorials/emboss_tut.tar.gz
-

debian/jemboss.lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+jemboss: script-with-language-extension usr/bin/runJemboss.sh

debian/rules

@@ -10,7 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 #export CLASSPATH=/usr/share/java/activation.jar:
 
 %:
-	dh $@ --with autotools-dev,autoreconf
+	dh $@
 
 VERSION := $(shell dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1)
 RENAMED := cons pscan
@@ -37,7 +37,6 @@ DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS)
 #DEB_LDFLAGS += $(shell pg_config  | grep LIBS | cut -f2 -d=)
 
 override_dh_auto_configure:
-	dh_autotools-dev_updateconfig
 	dh_auto_configure -- $(CONFFLAGS)
 
 override_dh_auto_build:
@@ -47,7 +46,6 @@ override_dh_auto_build:
 	cd jemboss && jar uf lib/jemboss.jar resources/version resources/*.properties
 
 override_dh_clean:
-	dh_autotools-dev_restoreconfig
 	rm -rf debian/emboss_tmp
 	find jemboss/ -type f -name "*.class" -delete
 	[ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test )
@@ -107,6 +105,7 @@ override_dh_auto_install-indep:
 	find debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	$(RM) test-stamp
 	[ -d debian/testbackup ] || cp -a test debian/testbackup
 	sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc
@@ -115,6 +114,7 @@ override_dh_auto_test:
 	echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc
 	echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc
 	cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh
+endif
 
 override_dh_installchangelogs:
 	dh_installchangelogs -k ChangeLog