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

 Reference:
- - Author: >
+- Author: >
     Rebecca Bart and Megan Cohn and Andrew Kassen and Emily J. McCallum
     and Mikel Shybut and Annalise Petriello and Ksenia Krasileva and
     Douglas Dahlbeck and Cesar Medina and Titus Alicai and Lava Kumar
@@ -7,14 +7,15 @@ Reference:
     and María Angélica Santana and Nuttima Kositcharoenkul and Hervé
     Vanderschuren and Wilhelm Gruissem and Adriana Bernal and Brian
     J. Staskawicz
-   Title: >
+  Title: >
     High-throughput genomic sequencing of cassava bacterial blight strains
     identifies conserved effectors to target for durable resistance
-   Journal: PNAS
-   Year: 2012
-   Volume: 109
-   Number: 28
-   Pages: E1972-9
-   DOI: 10.1073/pnas.1208003109
-   PMID: 22699502
-   URL: http://www.pnas.org/content/109/28/E1972
+  Journal: PNAS
+  Year: 2012
+  Volume: 109
+  Number: 28
+  Pages: E1972-9
+  DOI: 10.1073/pnas.1208003109
+  PMID: 22699502
+  URL: http://www.pnas.org/content/109/28/E1972
+Bug-Database: https://github.com/sonwell/biotools/issues