debian/changelog

+python-bx (0.8.4-2) unstable; urgency=medium
+
+  * Team upload.
+  * Breaks: python3-bx-tools
+    Closes: #933596
+  * debhelper-compat 12
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.4.0
+  * Testsuite: autopkgtest-pkg-python
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/copyright
+  * Fix license name
+  * hardening=+all
+
+ -- Andreas Tille <tille@debian.org>  Thu, 01 Aug 2019 09:55:20 +0200
+
 python-bx (0.8.4-1) unstable; urgency=medium
 
   * New upstream release. Removed Python2 binary packages; enabled the tests

debian/compat

-9

debian/control

 Source: python-bx
-Section: python
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller@debian.org>,
            Michael Crusoe <michael.crusoe@gmail.com>
-Build-Depends:
-	debhelper (>= 9),
-	dh-python,
-	zlib1g-dev,
-	python3-setuptools,
-	python3-all-dev,
-	python3-lzo,
-	python3-nose,
-	python3-numpy,
-	python3-six,
-	cython3
-Standards-Version: 4.2.1
-Homepage:  https://github.com/bxlab/bx-python
-Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
+Section: python
+Testsuite: autopkgtest-pkg-python
+Priority: optional
+Build-Depends: debhelper-compat (= 12),
+               dh-python,
+               zlib1g-dev,
+               python3-setuptools,
+               python3-all-dev,
+               python3-lzo,
+               python3-nose,
+               python3-numpy,
+               python3-six,
+               cython3
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/python-bx
+Vcs-Git: https://salsa.debian.org/med-team/python-bx.git
+Homepage: https://github.com/bxlab/bx-python
 
 Package: python3-bx
 Architecture: any
 Depends: python3-lzo,
-	 ${shlibs:Depends},
+         ${shlibs:Depends},
          ${misc:Depends},
-         ${python3:Depends},
-Replaces: python3-bx-tools
+         ${python3:Depends}
+Breaks: python3-bx-tools
 Provides: python3-bx-tools
+Replaces: python3-bx-tools
 Description: library to manage genomic data and its alignment
  The bx-python project is a python library and associated set of scripts to
  allow for rapid implementation of genome scale analyses. The library contains

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: bx-python
 Source:  https://github.com/bxlab/bx-python
-# Update the list of files to exclude by 
+# Update the list of files to exclude by
 # grep -rl "Generated by Cython"
-Files-Excluded: lib/bx/bbi/bbi_file.h lib/bx/_seqmapping.c lib/bx/bitset.c lib/bx/pwm/_position_weight_matrix.c lib/bx/motif/_pwm.c lib/bx/bbi/cirtree_file.c lib/bx/bbi/bbi_file.c lib/bx/bbi/bpt_file.c lib/bx/bbi/bigwig_file.c lib/bx/bbi/bigbed_file.c lib/bx/intseq/ngramcount.c lib/bx/seq/_twobit.c lib/bx/seq/_nib.c lib/bx/intervals/cluster.c lib/bx/intervals/intersection.c lib/bx/misc/_seekbzip2.c lib/bx/misc/bgzf.c lib/bx/arrays/wiggle.c lib/bx/arrays/bed.c lib/bx/arrays/array_tree.c lib/bx/align/_epo.c lib/bx/align/_core.c lib/bx/align/sitemask/_cpg.c 
+Files-Excluded: lib/bx/bbi/bbi_file.h lib/bx/_seqmapping.c lib/bx/bitset.c lib/bx/pwm/_position_weight_matrix.c lib/bx/motif/_pwm.c lib/bx/bbi/cirtree_file.c lib/bx/bbi/bbi_file.c lib/bx/bbi/bpt_file.c lib/bx/bbi/bigwig_file.c lib/bx/bbi/bigbed_file.c lib/bx/intseq/ngramcount.c lib/bx/seq/_twobit.c lib/bx/seq/_nib.c lib/bx/intervals/cluster.c lib/bx/intervals/intersection.c lib/bx/misc/_seekbzip2.c lib/bx/misc/bgzf.c lib/bx/arrays/wiggle.c lib/bx/arrays/bed.c lib/bx/arrays/array_tree.c lib/bx/align/_epo.c lib/bx/align/_core.c lib/bx/align/sitemask/_cpg.c
 
 Files: *
 Copyright: 2005-2015 The Pennsylvania State University
@@ -46,11 +46,11 @@ License: MIT
  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
  IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
- CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 
- TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
  SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-License: GPL-2.0
+License: GPL-2
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation version 2 of the License.

debian/rules

@@ -9,6 +9,8 @@ export NOSE_VERBOSE=2
 export PYBUILD_NAME=bx-python
 export PYBUILD_BEFORE_TEST=cp -r {dir}/test_data {build_dir}/
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@ --with python3 --buildsystem=pybuild