[Debian-med-packaging] Bug#1028175: snakemake rulename failes with asyncio has no attribute coroutine with python3.11

[Diane Trout]

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>

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