discussion and development of Emacs Snakemake mode
 help / color / mirror / code / Atom feed
From: Diane Trout <diane@ghic.org>
To: Kyle Meyer <kyle@kyleam.com>
Cc: snakemake-mode@inbox.kyleam.com
Subject: Re: snakemake mode test failures with emacs 28.2 on Debian
Date: Sat, 07 Jan 2023 20:10:19 -0800	[thread overview]
Message-ID: <336d19155aed2cffbbc289720b995f73bd5a33ce.camel@ghic.org> (raw)
In-Reply-To: <875ydhkhtc.fsf@kyleam.com>

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

$ 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
    class RateLimiter(object):
  File "/usr/lib/python3/dist-packages/ratelimiter.py", line 127, in
    __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"
  __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

    (check individual jobs above for details)
    missing output files:

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
  _warnings.warn(warn_message, ResourceWarning)

  reply	other threads:[~2023-01-08  4:10 UTC|newest]

Thread overview: 4+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2023-01-07 20:50 snakemake mode test failures with emacs 28.2 on Debian Diane Trout
2023-01-08  0:09 ` Kyle Meyer
2023-01-08  4:10   ` Diane Trout [this message]
2023-01-08  4:39     ` Kyle Meyer

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:

  List information: https://git.kyleam.com/snakemake-mode

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=336d19155aed2cffbbc289720b995f73bd5a33ce.camel@ghic.org \
    --to=diane@ghic.org \
    --cc=kyle@kyleam.com \
    --cc=snakemake-mode@inbox.kyleam.com \


* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
Code repositories for project(s) associated with this public inbox


This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).