debian/README.source

-Please use the 'get-orig-source' rules target to get the source. It needs to be repacked for dfsg reasons.

debian/changelog

 aegean (0.16.0+dfsg-2) UNRELEASED; urgency=medium
 
-  * Team upload
-
   [ Jelmer Vernooij ]
   * Move source package lintian overrides to debian/source.
 
   [ Andreas Tille ]
-  * Standards-Version: 4.2.1
+  * Standards-Version: 4.4.0
   * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
   * Do not parse d/changelog
-
- -- Andreas Tille <tille@debian.org>  Fri, 26 Oct 2018 20:11:46 +0200
+  * Use 2to3 to convert from Python2 to Python3
+    Closes: #936109
+  * Drop git from Build-Depends
+  * Drop redundant debian/README.source
+  * debhelper-compat 12
+  * Use secure URI in Homepage field.
+  * Set fields Upstream-Contact in debian/copyright.
+  * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Andreas Tille <tille@debian.org>  Sun, 01 Sep 2019 00:02:16 +0200
 
 aegean (0.16.0+dfsg-1) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Sascha Steinbiss <satta@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11),
+Build-Depends: debhelper-compat (= 12),
                libcairo2-dev,
                libgenometools0-dev,
-               python,
-               git
-Standards-Version: 4.2.1
+               python3
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/aegean
 Vcs-Git: https://salsa.debian.org/med-team/aegean.git
-Homepage: http://standage.github.io/AEGeAn
+Homepage: https://standage.github.io/AEGeAn
 
 Package: aegean
 Architecture: amd64 arm64 armel armhf i386 mipsel powerpc ppc64el s390x hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64 x32

debian/copyright

@@ -2,6 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: aegean
 Source: http://aegean.readthedocs.org/en/v0.10.2/license.html
 Files-Excluded: data/share/vendor/jquery.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.js data/share/vendor/jquery.dataTables.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/jquery.dataTables.js data/share/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-core-1.3.2-full-nocompat-yc.js data/share/vendor/mootools-more-1.3.2.1.js data/misc/amel-ogs-vs-ncbi-parseval-html/vendor/mootools-more-1.3.2.1.js
+Upstream-Contact: Daniel Standage <daniel.standage@gmail.com>
 
 Files:
  *

debian/patches/2to3.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Sun, 01 Sep 2019 00:01:00 +0200
+Bug-Debian: https://bugs.debian.org/936109
+Description: Use 2to3 to convert from Python2 to Python3
+
+--- a/data/scripts/align-convert.py
++++ b/data/scripts/align-convert.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import re
+ import sys
+ 
+@@ -24,14 +24,14 @@ class Peeker:
+     def __iter__(self):
+         return self
+ 
+-    def next(self):
++    def __next__(self):
+         if self.buffer:
+             return self.buffer.pop(0)
+         else:
+             return next(self.iter)
+ 
+     def __next__(self):
+-        return self.next()
++        return next(self)
+ 
+     def peek(self, n=0):
+         """Return an item n entries ahead in the iteration."""
+--- a/data/scripts/check-gff3.py
++++ b/data/scripts/check-gff3.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -8,7 +8,7 @@
+ #
+ # Usage: check-gff3.py < annot.gff3
+ 
+-from __future__ import print_function
++
+ import re
+ import sys
+ 
+@@ -50,7 +50,7 @@ for line in sys.stdin:
+         topleveltypes[values[2]] += 1
+ 
+ print('\n===== Types =====')
+-featuretypes = counts.keys()
++featuretypes = list(counts.keys())
+ featuretypes.sort()
+ for featuretype in featuretypes:
+     count = counts[featuretype]
+@@ -60,7 +60,7 @@ for featuretype in featuretypes:
+     print('%s (%lu total, %lu top-level)' % (featuretype, count, topcount))
+ 
+ print('\n===== Relationships (child --> parent) =====')
+-childtypes = relationships.keys()
++childtypes = list(relationships.keys())
+ childtypes.sort()
+ for childtype in childtypes:
+     parenttypes = list(relationships[childtype].keys())
+--- a/data/scripts/lpdriver.py
++++ b/data/scripts/lpdriver.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import argparse
+ import os
+ import re
+--- a/data/scripts/miloci.py
++++ b/data/scripts/miloci.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import re
+ import sys
+ 
+--- a/data/scripts/seq-reg.py
++++ b/data/scripts/seq-reg.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2015, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import argparse
+ import os
+ import re
+--- a/data/scripts/uloci.py
++++ b/data/scripts/uloci.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import argparse
+ import re
+ import sys
+--- a/data/scripts/version.py
++++ b/data/scripts/version.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Copyright (c) 2010-2016, Daniel S. Standage and CONTRIBUTORS
+ #
+@@ -6,7 +6,7 @@
+ # the 'LICENSE' file in the AEGeAn source code distribution or
+ # online at https://github.com/standage/AEGeAn/blob/master/LICENSE.
+ 
+-from __future__ import print_function
++
+ import re
+ import subprocess
+ import sys

debian/patches/includepaths

@@ -3,7 +3,7 @@ Description: Adjust include paths
 Author: Sascha Steinbiss <sascha@steinbiss.name>
 --- a/Makefile
 +++ b/Makefile
-@@ -62,6 +62,7 @@
+@@ -62,6 +62,7 @@ endif
  INCS=$(shell pkg-config --silence-errors --cflags-only-I cairo) \
       -I inc/core \
       -I /usr/local/include/genometools \

debian/patches/series

@@ -4,3 +4,4 @@ remove_license
 adjust_datapath
 follow_links
 includepaths
+2to3.patch

debian/tests/control

 Tests: functional-tests
-Depends: @, python
+Depends: @, python3

debian/tests/functional-tests

@@ -24,4 +24,3 @@ for f in *.sh; do
 done
 
 echo "run: OK"
-

debian/upstream/metadata

-Name: AEGeAn 
 Bug-Database: https://github.com/standage/AEGeAn/issues
 Bug-Submit: https://github.com/standage/AEGeAn/issues/new
-Contact: Daniel Standage <daniel.standage@gmail.com>
 Reference:
   Author: Standage, Daniel S and Brendel, Volker P
   Title: >