debian/changelog

@@ -2,6 +2,11 @@ mapdamage (2.0.9+dfsg-2) UNRELEASED; urgency=medium
 
   * Use 2to3 to port to Python3
     Closes: #936989
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Trim trailing whitespace.
+  * buildsystem=pybuild
+  * python3-pysam <!nocheck>
 
  -- Andreas Tille <tille@debian.org>  Tue, 03 Sep 2019 11:02:34 +0200
 

debian/compat

-11

debian/control

@@ -3,18 +3,19 @@ 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),
                python3-all,
                dh-python,
-               python3-setuptools
-Standards-Version: 4.2.1
+               python3-setuptools,
+               python3-pysam <!nocheck>
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/mapdamage
 Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git
 Homepage: https://ginolhac.github.io/mapDamage/
 
 Package: mapdamage
 Architecture: all
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
          ${misc:Depends},
          r-base-core,
          r-cran-gam,

debian/patches/2to3.patch

@@ -310,12 +310,18 @@ Last-Update: Tue, 03 Sep 2019 11:02:34 +0200
          # No missing libraries
 --- a/mapdamage/seq.py
 +++ b/mapdamage/seq.py
-@@ -1,4 +1,4 @@
+@@ -1,9 +1,9 @@
 -#!/usr/bin/env python
 +#!/usr/bin/python3
  import sys
  import string
  
+ # from Martin Kircher, to complement DNA
+-TABLE = string.maketrans('TGCAMRWSYKVHDBtgcamrwsykvhdb', \
++TABLE = str.maketrans('TGCAMRWSYKVHDBtgcamrwsykvhdb', \
+     'ACGTKYWSRMBDHVacgtkywsrmbdhv')
+ 
+ LETTERS = ("A", "C", "G", "T")
 --- a/mapdamage/tables.py
 +++ b/mapdamage/tables.py
 @@ -1,4 +1,4 @@

debian/rules

@@ -6,7 +6,7 @@ include /usr/share/dpkg/default.mk
 TESTDIR        := debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/tests
 
 %:
-	dh $@ --with python3
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_fixperms:
 	dh_fixperms
@@ -18,3 +18,5 @@ override_dh_install:
 	mv `find debian -name rescale_test.py` $(TESTDIR)
 	sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py
 
+override_dh_python3:
+	dh_python3 --no-ext-rename