Your message dated Sun, 08 Jan 2023 07:16:04 +0000
with message-id <[email protected]>
and subject line Bug#1028175: fixed in python-ratelimiter 1.2.0.post0-4
has caused the Debian Bug report #1028175,
regarding snakemake rulename failes with asyncio has no attribute coroutine
with python3.11
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.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
1028175: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028175
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: snakemake
Version: 7.12.1-1
Severity: serious
Dear Maintainer,
I noticed that snakemake-modes tests were failing while I was trying to build
the package.
Eventually I found that running the snakemake executable was failing with
python 3.11, but worked with 3.10.
Using the test Snakefile from snakemake-mode for the tests I ran the command
with both python3.11 and python3.10. The results are below.
I should probably go try to package the throttle library and upload it to NEW.
Snakemake's upstream patched snakemake to use a different library throttle in
https://github.com/snakemake/snakemake/issues/1952
$ python3.11 /usr/bin/snakemake --dryrun aa.out
Building DAG of jobs...
Traceback (most recent call last):
File "/usr/lib/python3/dist-packages/snakemake/__init__.py", line 730, in
snakemake
success = workflow.execute(
^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/snakemake/workflow.py", line 942, in
execute
self.scheduler = JobScheduler(
^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/snakemake/scheduler.py", line 105, in
__init__
from ratelimiter import RateLimiter
File "/usr/lib/python3/dist-packages/ratelimiter.py", line 36, in <module>
class RateLimiter(object):
File "/usr/lib/python3/dist-packages/ratelimiter.py", line 127, in
RateLimiter
__aexit__ = asyncio.coroutine(__exit__)
^^^^^^^^^^^^^^^^^
AttributeError: module 'asyncio' has no attribute 'coroutine'
$ python3.10 -Wd /usr/bin/snakemake --dryrun aa.out
Building DAG of jobs...
/usr/lib/python3/dist-packages/ratelimiter.py:127: DeprecationWarning:
"@coroutine" decorator is deprecated since Python 3.8, use "async def" instead
__aexit__ = asyncio.coroutine(__exit__)
Job stats:
job count min threads max threads
----- ------- ------------- -------------
aa 1 1 1
total 1 1 1
[Sat Jan 7 19:56:59 2023]
rule aa:
output: aa.out
jobid: 0
reason: Missing output files: aa.out
resources: tmpdir=/tmp
Job stats:
job count min threads max threads
----- ------- ------------- -------------
aa 1 1 1
total 1 1 1
Reasons:
(check individual jobs above for details)
missing output files:
aa
This was a dry-run (flag -n). The order of jobs does not reflect the order of
execution.
/usr/lib/python3.10/tempfile.py:999: ResourceWarning: Implicitly cleaning up
<TemporaryDirectory '/home/diane/.cache/snakemake/snakemake/source-
cache/runtime-cache/tmplqpvu6li'>
_warnings.warn(warn_message, ResourceWarning)
-- System Information:
Debian Release: bookworm/sid
APT prefers testing-debug
APT policy: (500, 'testing-debug'), (500, 'stable-security'), (500,
'oldstable-debug'), (500, 'testing'), (500, 'stable'), (110, 'unstable'), (100,
'experimental')
merged-usr: no
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.0.0-6-amd64 (SMP w/4 CPU threads; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages snakemake depends on:
ii ca-certificates 20211016
ii libjs-bootstrap 3.4.1+dfsg-3
ii libjs-jquery 3.6.1+dfsg+~3.5.14-1
ii python3 3.10.6-3+b1
ii python3-appdirs 1.4.4-3
ii python3-configargparse 1.5.3-1
ii python3-connection-pool 0.0.3-2
ii python3-datrie 0.8.2-4
ii python3-docutils 0.17.1+dfsg-3
ii python3-git 3.1.27-1
ii python3-jinja2 3.0.3-2
ii python3-jsonschema 4.9.1-3
ii python3-nbformat 5.5.0-1
ii python3-pkg-resources 65.5.0-1.1
ii python3-psutil 5.9.4-1
ii python3-pulp 2.6.0+dfsg-1
ii python3-ratelimiter 1.2.0.post0-3
ii python3-requests 2.28.1+dfsg-1
ii python3-smart-open 5.2.1-5
ii python3-stopit 1.1.2-2
ii python3-tabulate 0.8.9-1
ii python3-toposort 1.7-1
ii python3-wrapt 1.14.1-2+b1
ii python3-yaml 6.0-3+b1
Versions of packages snakemake recommends:
ii cwltool 3.1.20221201130942-1
ii imagemagick 8:6.9.11.60+dfsg-1.3+b4
ii imagemagick-6.q16 [imagemagick] 8:6.9.11.60+dfsg-1.3+b4
ii python3-azure-storage 20221101+git-2
ii python3-biopython 1.80+dfsg-1
ii python3-boto3 1.26.27+dfsg-1
ii python3-botocore 1.29.27+repack-1
ii python3-dropbox 11.34.0-1
ii python3-flask 2.2.2-2
ii python3-ftputil 5.0.4-1
ii python3-irodsclient 0.8.1-3
ii python3-kubernetes 22.6.0-2
ii python3-pygments 2.13.0+dfsg-1
ii python3-tz 2022.7-1
ii python3-urllib3 1.26.12-1
ii python3-yappi 1.4.0-1
Versions of packages snakemake suggests:
pn snakemake-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: python-ratelimiter
Source-Version: 1.2.0.post0-4
Done: Diane Trout <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-ratelimiter, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Diane Trout <[email protected]> (supplier of updated python-ratelimiter 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sat, 07 Jan 2023 22:26:05 -0800
Source: python-ratelimiter
Architecture: source
Version: 1.2.0.post0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Python Team <[email protected]>
Changed-By: Diane Trout <[email protected]>
Closes: 1025119 1028175
Changes:
python-ratelimiter (1.2.0.post0-4) unstable; urgency=medium
.
* Add debian/patches/use-async-keyword.patch
- Makes package compatible with Python 3.11 Closes: #1025119
Closes: #1028175
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