Re: snakemake mode test failures with emacs 28.2 on Debian

[Diane Trout <diane@ghic.org>]

On Sat, 2023-01-07 at 19:09 -0500, Kyle Meyer wrote:
> Diane Trout writes:
> 
> > Hi,
> > 
> > I noticed there's 3 ert test failures running Emacs 28.2 on Debian
> > unstable.
> 
> Thanks for reporting.
> 
> With Emacs 28.2 and snakemake 7.7.0 from Guix, the tests pass on my
> end.
> It looks like Debian unstable currently has snakemake 7.12.1-1.  My
> guess is that these failures are triggered by a snakemake change.
> 
> I'll try to look into that within the next couple of days.

I discovered the snakemake ert tests run on my Debian testing system
but fail in the unstable package build environment.

I read through the snakemake.el code and figured out how it was calling
the snakemake executable. I found the problem, and it's not related to
snakemake-mode, it looks like snakemake executable has an
incompatibility with python3.11.

Upstream's solution is here and involves using a more recently updated
depedency.
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)