debian/changelog

+seqan (1.4.2+dfsg-4) UNRELEASED; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #943260
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/copyright
+  * Set upstream metadata fields: Bug-Database.
+  * Remove obsolete fields Contact, Name from debian/upstream/metadata.
+  * Rely on pre-initialized dpkg-architecture variables.
+
+ -- Andreas Tille <tille@debian.org>  Mon, 16 Dec 2019 17:19:24 +0100
+
 seqan (1.4.2+dfsg-3) unstable; urgency=medium
 
   * debhelper 11
@@ -17,7 +32,7 @@ seqan (1.4.2+dfsg-2) unstable; urgency=medium
 
 seqan (1.4.2+dfsg-1) unstable; urgency=medium
 
-  [Andreas Tille] 
+  [Andreas Tille]
   * New upstream version
     Closes: #766741
   * Moved packaging to Git
@@ -33,9 +48,9 @@ seqan (1.4.2+dfsg-1) unstable; urgency=medium
     Closes: #816988, #809058
   * Install cmake files
     Closes: #818088
- 
+
   [Gert Wollny]
-  * d/rules: Add -DNDEBUG to CXXFLAGS, Closes: #811841 
+  * d/rules: Add -DNDEBUG to CXXFLAGS, Closes: #811841
   * d/rules: enable parallel build
 
  -- Andreas Tille <tille@debian.org>  Tue, 02 Aug 2016 15:58:06 +0200

debian/compat

-11

debian/control

@@ -5,7 +5,7 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Kevin Murray <spam@kdmurray.id.au>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                cmake,
                zlib1g-dev,
                libbam-dev,
@@ -13,7 +13,7 @@ Build-Depends: debhelper (>= 11~),
                dh-exec,
                help2man,
                python
-Standards-Version: 4.1.5
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/seqan
 Vcs-Git: https://salsa.debian.org/med-team/seqan.git
 Homepage: http://www.seqan.de/

debian/copyright

@@ -144,7 +144,7 @@ License: LGPL-3+
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 3 of the License, or (at your option) any later version.
- . 
+ .
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU

debian/patches/series

 skip_extras_and_apps.patch
 skip_doc_creation.patch
+2to3.patch

debian/rules

@@ -8,9 +8,8 @@ export DH_VERBOSE=1
 export DEB_BUILD_MAINT_OPTIONS = hardening=-stackprotector
 # alternatively: export DEB_CXXFLAGS_STRIP='-fstack-protector'
 
-DEB_HOST_ARCH       ?= $(shell dpkg-architecture -qDEB_HOST_ARCH)
+include /usr/share/dpkg/architecture.mk
 
-DEB_BUILD_ARCH          ?= $(shell dpkg-architecture -qDEB_BUILD_ARCH)
 ifneq (,$(filter $(DEB_BUILD_ARCH),mips mipsel))
     export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS | sed 's/-O[1-9]//') -O0 -mxgot
 endif
@@ -41,12 +40,14 @@ override_dh_auto_clean:
 	rm -rf orig
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 # Run test suite only on powerfull architectures (amd64) at build time
 ifneq (,$(filter $(DEB_HOST_ARCH),amd64 kfreebsd-amd64))
 	dh_auto_test
 else
 	echo "Do not run test suite when building on architecture $(DEB_HOST_ARCH)"
 endif
+endif
 
 override_dh_fixperms:
 	dh_fixperms

debian/upstream/metadata

-Contact: SeqAn Team (http://www.seqan.de/contact-us.html)
 Donation: http://www.seqan.de/
-Name: SeqAn
 Reference:
- Author: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
- Title: SeqAn An efficient, generic C++ library for sequence analysis
- Journal: BMC Bioinformatics
- Volume: 9
- Year: 2008
- Number: 1
- Pages: 11
- DOI: 10.1186/1471-2105-9-11
- PMID: 18184432
- URL: http://www.biomedcentral.com/1471-2105/9/11
- ePrint: http://www.biomedcentral.com/content/pdf/1471-2105-9-11.pdf
- ISSN: 1471-2105
+  Author: Doring, Andreas and Weese, David and Rausch, Tobias and Reinert, Knut
+  Title: SeqAn An efficient, generic C++ library for sequence analysis
+  Journal: BMC Bioinformatics
+  Volume: 9
+  Year: 2008
+  Number: 1
+  Pages: 11
+  DOI: 10.1186/1471-2105-9-11
+  PMID: 18184432
+  URL: http://www.biomedcentral.com/1471-2105/9/11
+  ePrint: http://www.biomedcentral.com/content/pdf/1471-2105-9-11.pdf
+  ISSN: 1471-2105
 Registry:
- - Name: OMICtools
-   Entry: OMICS_14825
- - Name: SciCrunch
-   Entry: NA
- - Name: conda:bioconda
-   Entry: NA
- - Name: bio.tools
-   Entry: seqan
+- Name: OMICtools
+  Entry: OMICS_14825
+- Name: SciCrunch
+  Entry: NA
+- Name: conda:bioconda
+  Entry: NA
+- Name: bio.tools
+  Entry: seqan
+Bug-Database: https://github.com/seqan/seqan/issues