[Debian-med-packaging] Bug#934882: rambo-k: Please switch to python3

[Steve Langasek]

Package: rambo-k
Version: 1.21+dfsg-2
Severity: normal
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu eoan ubuntu-patch

Hi Andreas,

The rambo-k package appears to support python3 upstream, so requires only a
small patch to switch it over to python3.  Please consider applying the
attached patch.

-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
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diff -Nru rambo-k-1.21+dfsg/debian/control rambo-k-1.21+dfsg/debian/control
--- rambo-k-1.21+dfsg/debian/control	2018-07-19 00:38:27.000000000 -0700
+++ rambo-k-1.21+dfsg/debian/control	2019-08-16 00:35:46.000000000 -0700
@@ -7,7 +7,7 @@
                javahelper,
                default-jdk,
                dh-python,
-               python-all,
+               python3-all,
                libcommons-cli-java,
                liblog4j1.2-java
 Standards-Version: 4.1.5
@@ -18,9 +18,9 @@
 Package: rambo-k
 Architecture: all
 Depends: ${java:Depends},
-         ${python:Depends},
+         ${python3:Depends},
          ${misc:Depends},
-         python-sklearn
+         python3-sklearn
 Description: Read Assignment Method Based On K-mers
  RAMBO-K is a tool for rapid and sensitive removal of background sequences
  from Next Generation Sequencing data.
diff -Nru rambo-k-1.21+dfsg/debian/patches/python3.patch rambo-k-1.21+dfsg/debian/patches/python3.patch
--- rambo-k-1.21+dfsg/debian/patches/python3.patch	1969-12-31 16:00:00.000000000 -0800
+++ rambo-k-1.21+dfsg/debian/patches/python3.patch	2019-08-16 00:35:46.000000000 -0700
@@ -0,0 +1,10 @@
+Index: rambo-k-1.21+dfsg/RAMBOK.py
+===================================================================
+--- rambo-k-1.21+dfsg.orig/RAMBOK.py
++++ rambo-k-1.21+dfsg/RAMBOK.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ import os
+ import argparse
+ import simulate_reads
diff -Nru rambo-k-1.21+dfsg/debian/patches/series rambo-k-1.21+dfsg/debian/patches/series
--- rambo-k-1.21+dfsg/debian/patches/series	1969-12-31 16:00:00.000000000 -0800
+++ rambo-k-1.21+dfsg/debian/patches/series	2019-08-16 00:35:46.000000000 -0700
@@ -0,0 +1 @@
+python3.patch
diff -Nru rambo-k-1.21+dfsg/debian/rules rambo-k-1.21+dfsg/debian/rules
--- rambo-k-1.21+dfsg/debian/rules	2018-07-19 00:38:27.000000000 -0700
+++ rambo-k-1.21+dfsg/debian/rules	2019-08-16 00:35:46.000000000 -0700
@@ -5,7 +5,7 @@
 include /usr/share/dpkg/default.mk
 
 %:
-	dh $@ --with javahelper --with python2
+	dh $@ --with javahelper --with python3
 
 override_dh_auto_build:
 	CLASSPATH=/usr/share/java/commons-cli.jar:ReadTrainer_eclipse/src/org/rki/readtrainer/:ReadClassifier_eclipse/src/ jh_build classifier.jar ReadClassifier_eclipse