Your message dated Sun, 08 Jan 2023 07:16:04 +0000 with message-id <e1pepuw-004gmm...@fasolo.debian.org> 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 message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1028175: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1028175 Debian Bug Tracking System Contact ow...@bugs.debian.org 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
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--- Begin Message ---Source: python-ratelimiter Source-Version: 1.2.0.post0-4 Done: Diane Trout <di...@ghic.org> 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 1028...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Diane Trout <di...@ghic.org> (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 ftpmas...@ftp-master.debian.org) -----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 <team+pyt...@tracker.debian.org> Changed-By: Diane Trout <di...@ghic.org> 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 Checksums-Sha1: ec0025feab03bf8fa5f7f7e1e0539a1c52f697ac 2162 python-ratelimiter_1.2.0.post0-4.dsc fe57af82a377f27b6d0111c2a7e505e3b3bf85c0 3704 python-ratelimiter_1.2.0.post0-4.debian.tar.xz f1610e08d399c518898d76ec1bd1c66c575da7f3 6838 python-ratelimiter_1.2.0.post0-4_amd64.buildinfo Checksums-Sha256: 804915fcb2872a8f1715f1942c469f90f8027c1bbcd138cc763652867ca97ef4 2162 python-ratelimiter_1.2.0.post0-4.dsc 110b977168b544855b03844c93d5933b0889abed78a3d954063b9ee0c6ce84d4 3704 python-ratelimiter_1.2.0.post0-4.debian.tar.xz 895563f47dbea1a5fe6944391ee044c99ccdd551aa97f3b9b6d2fc8f80efd670 6838 python-ratelimiter_1.2.0.post0-4_amd64.buildinfo Files: 700a2e243a8d5733cdf13467a0d3b246 2162 python optional python-ratelimiter_1.2.0.post0-4.dsc a731391cd7aaed83c9299f8bf7323ec1 3704 python optional python-ratelimiter_1.2.0.post0-4.debian.tar.xz b46c4132ffa4a9945d7dd4daac8866a0 6838 python optional python-ratelimiter_1.2.0.post0-4_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQVcMeSBIEX5AQ11mQ04NnM013AFAmO6YzgACgkQmQ04NnM0 13AUBg//ZzsCPQ24cE6xG+QdLBJ0zWF+k52gseivKyKhdqFr8xEFgP22/XcAr5av oH+2MDBN/PZWJ5HDYc1AoVormL0luQk3pfUmlaiCEDYtI7L7cOrHxtfzc/PMAqWS f1/Z32CEzU34id6+vXlk6AEHtB0RjJCWP1fcf/KhsF0ggouBszw8hbGHUvS8ozky 4EGP4uHUBTqf6yM6j4Qw0koXGsw96B71MZs7HaBPcRThh9dx+AenW0TY4I1nSE7d t5QIvG2Z94JIW0La9RwL9J/zmdrOBXs/xcu3OT6vqQXGN3Ciw5apoxAF7c5BAbsG xrYPJTgrxBUfx9a4zCVkW862rLSYIbvn6nYjuqemZm9M6sl8ckqqnZet39oz66vD I/3tlMynhhHybxStZE18dwdmDMF65jo9MX6AwynV9jgeKEeto5W5Bh6BBcgUWb2Z O5LOZeq5ZqwzkpYNBPhm67eKjRUURzu0JTdqGXT7mfAY5ZTgWlVokEys6WND2rpE gCXEdn57iq2/bip4trMYI1oDe8/Asr1WAJR33QYl2oYeSjtklseiso9QV1g75reT fiHcsykpjbo7MEHDt2VT/O0VVDRKntSfRCFXvZWJHVCuLVSI5A4ESxaE2IuMeZ8s z5sLv6fGsG4MqqIxFWdWjA/V3ADWoWNgYi7o5nozatGhpaMT1T4= =9G/9 -----END PGP SIGNATURE-----
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