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
