[Debian-med-packaging] Bug#1004968: sepp: py3.10 direct import of Mapping from collections does not work

[Andreas Hasenack]

Package: sepp
Version: 4.5.1+really4.5.1+dfsg-2
Severity: normal

Dear Maintainer,

Starting with python 3.10, directly importing Mapping from collections
does not work.

python 3.10[1] deprecated aliases to Collections Abstract Base Classes from
 the collections module have been removed. These imports must be done from
 collections.abc.

sepp does such an import in sepp/alignment.py, and I suggest the
following simple patch:
--- a/sepp/alignment.py
+++ b/sepp/alignment.py
@@ -26,7 +26,8 @@ import re

 from sepp.filemgr import open_with_intermediates

-from collections import Mapping
+
+from collections.abc import Mapping
 import copy
 from sepp import get_logger
 import io

I also filed an upstream bug at [2].

Cheers!


1. https://docs.python.org/3/whatsnew/3.10.html
2. https://github.com/smirarab/sepp/issues/117