Merge ~ahasenack/ubuntu/+source/sepp:jammy-py310-collections-import into ubuntu/+source/sepp:ubuntu/devel

[Andreas Hasenack]

Another collections import fix. Submitted upstream[1] and to debian via BTS[2] and salsa[3].

I wondered about wrapping the import in a version check, but I went to old ubuntu releases, and in all current ones the import from collections.abc works. I'll leave it for upstream to check which python versions they support and decide if they want to do a version check or not.

PPA: https://launchpad.net/~ahasenack/+archive/ubuntu/py310-collections/+packages

1. https://github.com/smirarab/sepp/issues/117
2. https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1004968
3. https://salsa.debian.org/med-team/sepp/-/merge_requests/1

[Lucas Kanashiro (lucaskanashiro)]

LGTM, +1.

review: Approve

[Andreas Hasenack (ahasenack)]

Thanks, uploaded

[Andreas Hasenack (ahasenack)]

This migrated

diff --git a/debian/changelog b/debian/changelog
index fffa670..96941a6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+sepp (4.5.1+really4.5.1+dfsg-2ubuntu1) jammy; urgency=medium
+
+  * d/p/py310_collections_import.patch: fix collections import
+    under python 3.10+ (LP: #1959938)
+
+ -- Andreas Hasenack <[e-mail]>  Thu, 03 Feb 2022 21:21:56 +0000
+
 sepp (4.5.1+really4.5.1+dfsg-2) unstable; urgency=medium
 
   * Upload to unstable, tipp has now exited NEW
diff --git a/debian/control b/debian/control
index a6edc56..bc4a2e5 100644
--- a/debian/control
+++ b/debian/control
@@ -1,5 +1,6 @@
 Source: sepp
-Maintainer: Debian Med Packaging Team <[e-mail]>
+Maintainer: Ubuntu Developers <[e-mail]>
+XSBC-Original-Maintainer: Debian Med Packaging Team <[e-mail]>
 Uploaders: Andreas Tille <[e-mail]>,
            Pierre Gruet <[e-mail]>
 Section: science
diff --git a/debian/patches/py310_collections_import.patch b/debian/patches/py310_collections_import.patch
new file mode 100644
index 0000000..497f145
--- /dev/null
+++ b/debian/patches/py310_collections_import.patch
@@ -0,0 +1,25 @@
+Description: fix collections import
+ In 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.
+ .
+ 1. https://docs.python.org/3/whatsnew/3.10.html
+Author: Andreas Hasenack <[e-mail]>
+Bug: https://github.com/smirarab/sepp/issues/117
+Bug-Debian: https://bugs.debian.org/1004968
+Bub-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/sepp/+bug/1959938
+Last-Update: 2022-02-03
+diff --git a/sepp/alignment.py b/sepp/alignment.py
+index ada5de8..61e9adb 100644
+--- 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
diff --git a/debian/patches/series b/debian/patches/series
index 7d1d553..ea62f10 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ configuration_files_in_etc_and_per_user.patch
 deactivating_log_test.patch
 using_python3_interpreter.patch
 hmmbuild_path_for_testUPP.patch
+py310_collections_import.patch