debian/NEWS.Debian

+parsnp (1.2+dfsg-6) unstable; urgency=medium
+
+  Parsnp was converted to Python3 by the Debian Med team since
+  Python2 will be removed from Debian 11.
+  If you notice any issues that might be connected to this conversion
+  please do
+
+     reportbug parsnp
+
+  to let us know.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Sep 2019 12:08:17 +0200
+
+

debian/changelog

+parsnp (1.2+dfsg-6) unstable; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #937242
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Use secure URI in Homepage field.
+  * buildsystem=pybuild
+  * Inform users about Python3 migration in NEWS.Debian
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Sep 2019 13:07:43 +0200
+
 parsnp (1.2+dfsg-5) unstable; urgency=medium
 
   * Build-Depends: dh-python

debian/compat

-11

debian/control

@@ -3,27 +3,27 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all-dev,
-               python-setuptools,
-               cython,
+               python3-all-dev,
+               python3-setuptools,
+               cython3,
                libmuscle-dev
-Standards-Version: 4.1.5
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/parsnp
 Vcs-Git: https://salsa.debian.org/med-team/parsnp.git
-Homepage: http://harvest.readthedocs.org/en/latest/content/parsnp.html
+Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html
 
 Package: parsnp
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python:Depends},
-         python-numpy,
+         ${python3:Depends},
+         python3-numpy,
          fasttree,
          mummer,
          phipack
-Recommends: python-dendropy
+Recommends: python3-dendropy
 Description: rapid core genome multi-alignment
  Parsnp was designed to align the core genome of hundreds to thousands of
  bacterial genomes within a few minutes to few hours. Input can be both

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: ParSNP
 Upstream-Contact: Todd J Treangen <treangen@gmail.com>
 Source: https://github.com/marbl/parsnp/releases

debian/docs

+debian/NEWS.Debian

debian/patches/series

@@ -8,3 +8,4 @@ proper_calls_to_tools.patch
 drop_m64.patch
 fix_build_with_as-needed.patch
 non-versioned-libs.patch
+2to3_new.patch

debian/rules

@@ -7,14 +7,17 @@ include /usr/share/dpkg/default.mk
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3
+
+override_dh_auto_clean:
+	dh_auto_clean -O--buildsystem=pybuild
 
 override_dh_auto_configure:
 	dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7
 
 override_dh_auto_install:
 	dh_auto_install
-	# The actual user interface is the Python script so move the binary to /usr/lib
+	# The actual user interface is the Python3 script so move the binary to /usr/lib
 	mkdir -p debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)
 	mv debian/$(DEB_SOURCE)/usr/bin/$(DEB_SOURCE) debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)