debian/changelog

+transdecoder (5.0.1-3) unstable; urgency=medium
+
+  * Use 2to3 to port from Python2 to Python3
+    Closes: #945719
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 10 Jan 2020 12:04:54 +0100
+
 transdecoder (5.0.1-2) unstable; urgency=medium
 
   * Point Vcs fields to salsa.debian.org

debian/compat

-11

debian/control

@@ -4,9 +4,9 @@ Uploaders: Michael R. Crusoe <michael.crusoe@gmail.com>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                liburi-perl
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/transdecoder
 Vcs-Git: https://salsa.debian.org/med-team/transdecoder.git
 Homepage: https://transdecoder.github.io/
@@ -17,7 +17,7 @@ Depends: ${misc:Depends},
          ${perl:Depends},
          liburi-perl,
          r-base-core,
-         python
+         python3
 Description: find coding regions within RNA transcript sequences
  TransDecoder identifies candidate coding regions within transcript sequences,
  such as those generated by de novo RNA-Seq transcript assembly using Trinity,

debian/patches/2to3.patch

+Description: Use 2to3 to port from Python2 to Python3
+Bug-Debian: https://bugs.debian.org/945719
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 10 Jan 2020 12:00:47 +0100
+
+--- a/util/misc/get_FP_FN_scores.py
++++ b/util/misc/get_FP_FN_scores.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os, sys, re
+ 
+--- a/util/misc/plot_indiv_seq_likelihood_profile.py
++++ b/util/misc/plot_indiv_seq_likelihood_profile.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import os,sys
+ import re
+@@ -39,9 +39,9 @@ def main():
+         score_vec.sort()
+ 
+     if args.cumsum:
+-        plt.plot(range(1,len(score_vec)+1), np.cumsum(score_vec), marker ='o')
++        plt.plot(list(range(1,len(score_vec)+1)), np.cumsum(score_vec), marker ='o')
+     else:
+-        plt.plot(range(1,len(score_vec)+1), score_vec, marker ='+')
++        plt.plot(list(range(1,len(score_vec)+1)), score_vec, marker ='+')
+     
+     
+     plt.show()
+--- a/util/misc/select_TD_orfs.py
++++ b/util/misc/select_TD_orfs.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import sys, os, re
+ import collections

debian/patches/series

 fix-whatis
 reproducible-sample_data.patch
+2to3.patch

debian/upstream/metadata

@@ -7,3 +7,7 @@ Registry:
   Entry: NA
 - Name: conda:bioconda
   Entry: transdecoder
+Bug-Database: https://github.com/TransDecoder/Transdecoder/issues
+Bug-Submit: https://github.com/TransDecoder/Transdecoder/issues/new
+Repository: https://github.com/TransDecoder/Transdecoder.git
+Repository-Browse: https://github.com/TransDecoder/Transdecoder