debian/changelog

+python-biotools (1.2.12-5) unstable; urgency=medium
+
+  * Really drop Python2 support
+    Closes: #937607
+  * Standards-Version: 4.4.1
+  * Set upstream metadata fields: Bug-Database.
+
+ -- Andreas Tille <tille@debian.org>  Fri, 13 Dec 2019 12:13:05 +0100
+
 python-biotools (1.2.12-4) unstable; urgency=medium
 
   * Drop Python2 support

debian/control

@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper-compat (= 12),
                dh-python,
                python3-all
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-biotools
 Vcs-Git: https://salsa.debian.org/med-team/python-biotools.git
 Homepage: https://github.com/sonwell/biotools

debian/patches/fix_python_interpreter.patch

+Description: Really drop Python2 support
+Bug-Debian: https://bugs.debian.org/937607
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 13 Dec 2019 12:11:10 +0100
+
+--- a/grepseq
++++ b/grepseq
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ from optparse import OptionParser
+ import biotools.IO as io
+--- a/prok-geneseek
++++ b/prok-geneseek
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # 1. predict
+ # 2. cluster
+--- a/setup.py
++++ b/setup.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ from distutils.core import setup
+ 
+--- a/src/BLAST.py
++++ b/src/BLAST.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ '''
+ A module to manage BLAST databases and interface with the BLAST+ standalone
+@@ -144,7 +144,7 @@ class Result(object):
+     start and stop positions for both sequences. This class should be used in
+     a for loop like so:
+ 
+-    ```python
++    ```python3
+         for res in Result(file_or_data):
+             pass
+     ```
+--- a/src/IO/manager.py
++++ b/src/IO/manager.py
+@@ -11,7 +11,7 @@ class IOManager(object):
+     methods for the different file types. Additional file types can be added 
+     to the manager by using 
+ 
+-    ```python
++    ```python3
+     manager[format] = methods
+     ```
+ 
+--- a/src/align.py
++++ b/src/align.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ '''
+ This module is used to align sequences. Currently, there is only a single
+--- a/src/analysis/cluster.py
++++ b/src/analysis/cluster.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import biotools.sequence as sequ
+ import biotools.IO as io
+ import biotools.translate as tran
+--- a/src/analysis/loaddata.py
++++ b/src/analysis/loaddata.py
+@@ -5,7 +5,7 @@ dumped the the string representation of
+ 
+ The real difference is that you must specify a variable name, e.g.:
+ 
+-```python
++```python3
+ my_stuff = { ... }
+ ```
+ 
+@@ -13,7 +13,7 @@ These variable names don't need to be on
+ should be able to omit any and all whitespace. The result of a successful 
+ parse is a dictionary:
+ 
+-```python
++```python3
+ {'my_stuff': { ... }}
+ ```
+ 
+--- a/src/analysis/predict.py
++++ b/src/analysis/predict.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import biotools.IO as io
+ import biotools.BLAST as BLAST
+ import biotools.analysis.options as options
+--- a/src/analysis/run.py
++++ b/src/analysis/run.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import biotools.analysis.predict as genepredict
+ import biotools.analysis.options as options
+--- a/src/analysis/variance.py
++++ b/src/analysis/variance.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import biotools.IO as io
+ import biotools.analysis.options as options
+--- a/src/annotation.py
++++ b/src/annotation.py
+@@ -19,7 +19,7 @@ class Annotation(object):
+         (version 3) file and the name_token and gff_token parameters are the
+         defaults for a gff version 3 file from phytozome. Just write (e.g.)
+ 
+-        ```python
++        ```python3
+         Annotation(*line.split('\\t'))  #(splitting on tabs)
+         ```
+ 
+--- a/src/clustal.py
++++ b/src/clustal.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import biotools.IO as io
+ import subprocess
+ from os import remove
+--- a/src/complement.py
++++ b/src/complement.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ from biotools.sequence import isprot
+ 
+ _ref = {

debian/patches/series

 2to3.patch
 add_missing_grepseq.patch
 2to3_grepseq.patch
+fix_python_interpreter.patch

debian/upstream/metadata

@@ -18,3 +18,4 @@ Reference:
   DOI: 10.1073/pnas.1208003109
   PMID: 22699502
   URL: http://www.pnas.org/content/109/28/E1972
+Bug-Database: https://github.com/sonwell/biotools/issues