Your message dated Wed, 25 Jan 2023 12:22:31 +0000
with message-id <e1pkenp-003q6i...@fasolo.debian.org>
and subject line Bug#1029580: fixed in sepp 4.5.1+really4.5.1+dfsg-5
has caused the Debian Bug report #1029580,
regarding sepp fails with python3.11: "invalid mode rU"
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1029580: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1029580
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: sepp
Version: 4.5.1+really4.5.1+dfsg-4
Severity: grave
Tags: patch
Justification: renders package unusable
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu lunar ubuntu-patch
Dear maintainers,
sepp fails its autopkgtests with python3.11, revealing a bug in the
software, because it uses a mode flag to open() which has been deprecated
since python 3 and is now obsolete in python 3.11:
[...]
[06:42:37] checkpointing.py (line 68): INFO: Checkpoint Saved to:
/tmp/sepp/output.lmge6vob/checkpoints/dumpl7z66ff0 and linked in
/tmp/tmpae0xbm2t.
/usr/lib/python3/dist-packages/sepp/checkpointing.py:75: DeprecationWarning:
setDaemon() is deprecated, set the daemon attribute instead
checkpoint_manager.timer.setDaemon(True)
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/sepp/scheduler.py", line 321, in
call_back
join._tick(job_in)
File "/usr/lib/python3/dist-packages/sepp/scheduler.py", line 244, in _tick
self.perform()
File "/usr/lib/python3/dist-packages/sepp/exhaustive.py", line 196, in perform
fullExtendedAlignments = self.merge_subalignments()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/sepp/exhaustive.py", line 181, in
merge_subalignments
ap_alg = ap.read_extendend_alignment_and_relabel_columns(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/sepp/problem.py", line 253, in
read_extendend_alignment_and_relabel_columns
ap_alg.build_extended_alignment(
File "/usr/lib/python3/dist-packages/sepp/alignment.py", line 555, in
build_extended_alignment
self.read_filepath(base_alignment, "FASTA")
File "/usr/lib/python3/dist-packages/sepp/alignment.py", line 294, in
read_filepath
file_obj = open(filename, 'rU')
^^^^^^^^^^^^^^^^^^^^
ValueError: invalid mode: 'rU'
ERROR
[...]
(https://ci.debian.net/data/autopkgtest/unstable/amd64/s/sepp/30285435/log.gz)
This also impacts invocations of sepp in other autopkgtests
(q2-fragment-insertion; q2-sample-classifier) so I'm confident is reporting
this as 'grave'.
I've applied the attached straightforward patch in Ubuntu to fix the
regression there.
Thanks for considering,
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer https://www.debian.org/
slanga...@ubuntu.com vor...@debian.org
diff -Nru sepp-4.5.1+really4.5.1+dfsg/debian/patches/open-U-obsolete.patch
sepp-4.5.1+really4.5.1+dfsg/debian/patches/open-U-obsolete.patch
--- sepp-4.5.1+really4.5.1+dfsg/debian/patches/open-U-obsolete.patch
1969-12-31 16:00:00.000000000 -0800
+++ sepp-4.5.1+really4.5.1+dfsg/debian/patches/open-U-obsolete.patch
2023-01-24 12:07:06.000000000 -0800
@@ -0,0 +1,52 @@
+Description: Drop obsolete "U" mode passed to open()
+ The "U" mode has been deprecated in python since python3 and has had no
+ effect. In python 3.11, it is now disallowed. Drop this mode flag that
+ causes runtime failures.
+Author: Steve Langasek <steve.langa...@ubuntu.com>
+Last-Update: 2023-01-24
+Forwarded: no
+
+Index: sepp-4.5.1+really4.5.1+dfsg/sepp/alignment.py
+===================================================================
+--- sepp-4.5.1+really4.5.1+dfsg.orig/sepp/alignment.py
++++ sepp-4.5.1+really4.5.1+dfsg/sepp/alignment.py
+@@ -108,7 +108,7 @@
+ file_obj = None
+ if isinstance(src, str):
+ try:
+- file_obj = open(src, "rU")
++ file_obj = open(src, "r")
+ except IOError:
+ print(("The file `%s` does not exist, exiting gracefully" % src))
+ elif isinstance(src, filetypes):
+@@ -291,7 +291,7 @@
+ If duplicate sequence names are encountered then the old name will
+ be replaced.
+ """
+- file_obj = open(filename, 'rU')
++ file_obj = open(filename, 'r')
+ return self.read_file_object(file_obj, file_format=file_format)
+
+ def read_file_object(self, file_obj, file_format='FASTA'):
+@@ -582,7 +582,7 @@
+ columns. Labels insertion columns with special labels and labels the
+ rest of columns (i.e. original columns) sequentially.
+ """
+- handle = open(path, 'rU')
++ handle = open(path, 'r')
+ insertions = None
+ if aformat.lower() == "stockholm":
+ insertions = self._read_sto(handle)
+Index: sepp-4.5.1+really4.5.1+dfsg/sepp/tree.py
+===================================================================
+--- sepp-4.5.1+really4.5.1+dfsg.orig/sepp/tree.py
++++ sepp-4.5.1+really4.5.1+dfsg/sepp/tree.py
+@@ -314,7 +314,7 @@
+
+ def read_tree_from_file(self, treefile, file_format):
+ dataset = Dataset()
+- dataset.read(open(treefile, 'rU'), schema=file_format)
++ dataset.read(open(treefile, 'r'), schema=file_format)
+ dendropy_tree = dataset.trees_blocks[0][0]
+ self._tree = dendropy_tree
+ self.n_leaves = self.count_leaves()
diff -Nru sepp-4.5.1+really4.5.1+dfsg/debian/patches/series
sepp-4.5.1+really4.5.1+dfsg/debian/patches/series
--- sepp-4.5.1+really4.5.1+dfsg/debian/patches/series 2022-02-05
13:17:58.000000000 -0800
+++ sepp-4.5.1+really4.5.1+dfsg/debian/patches/series 2023-01-24
12:05:55.000000000 -0800
@@ -7,3 +7,4 @@
using_python3_interpreter.patch
hmmbuild_path_for_testUPP.patch
py310_collections_import.patch
+open-U-obsolete.patch
--- End Message ---
--- Begin Message ---
Source: sepp
Source-Version: 4.5.1+really4.5.1+dfsg-5
Done: Pierre Gruet <p...@debian.org>
We believe that the bug you reported is fixed in the latest version of
sepp, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1029...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Pierre Gruet <p...@debian.org> (supplier of updated sepp package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 25 Jan 2023 12:41:16 +0100
Source: sepp
Architecture: source
Version: 4.5.1+really4.5.1+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Pierre Gruet <p...@debian.org>
Closes: 1029580
Changes:
sepp (4.5.1+really4.5.1+dfsg-5) unstable; urgency=medium
.
* Dropping "U" mode from open() invocations, thanks to Steve Langasek!
(Closes: #1029580)
* Standards-Version: 4.6.2 (routine-update)
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Files:
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