* snakemake mode test failures with emacs 28.2 on Debian @ 2023-01-07 20:50 Diane Trout 2023-01-08 0:09 ` Kyle Meyer 0 siblings, 1 reply; 4+ messages in thread From: Diane Trout @ 2023-01-07 20:50 UTC (permalink / raw) To: snakemake-mode Hi, I noticed there's 3 ert test failures running Emacs 28.2 on Debian unstable. My knowledge of elisp is pretty poor so I'm not entirely sure what's broken, but to start the debugging process here's the errors reported from running M-x ert RET t RET after having run this command emacs -Q -l package --eval "(add-to-list 'package-directory-list \"/usr/share/emacs/site-lisp/elpa\")" --eval "(add-to-list 'package- directory-list \"/usr/share/emacs/site-lisp/elpa-src\")" -f package- initialize -L . -l snakemake-test.el --eval \(ert-run-tests-batch-and- exit\) F snakemake-test-check-target (ert-test-failed ((should (snakemake-with-temp-dir (snakemake-check-target "aa.out"))) :form (let* ((vnew #'...) (old (symbol-function ...))) (unwind-protect (progn (fset ... vnew) (let* ... ...)) (fset 'message old))) :value nil)) F snakemake-test-file-targets-at-point (ert-test-failed ((should (equal '("aa.out") (snakemake-with-temp-dir (with-temp-buffer ... ... ...)))) :form (equal ("aa.out") nil) :value nil :explanation (different-types ("aa.out") nil))) F snakemake-test-rule-at-point (ert-test-failed ((should (equal '("aa") (snakemake-with-temp-dir (with-temp-buffer ... ... ... ...)))) :form (equal ("aa") nil) :value nil :explanation (different-types ("aa") nil))) Thanks for any advice you can offer. Diane ^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: snakemake mode test failures with emacs 28.2 on Debian 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 0 siblings, 1 reply; 4+ messages in thread From: Kyle Meyer @ 2023-01-08 0:09 UTC (permalink / raw) To: Diane Trout; +Cc: snakemake-mode 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. ^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: snakemake mode test failures with emacs 28.2 on Debian 2023-01-08 0:09 ` Kyle Meyer @ 2023-01-08 4:10 ` Diane Trout 2023-01-08 4:39 ` Kyle Meyer 0 siblings, 1 reply; 4+ messages in thread From: Diane Trout @ 2023-01-08 4:10 UTC (permalink / raw) To: Kyle Meyer; +Cc: snakemake-mode 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) ^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: snakemake mode test failures with emacs 28.2 on Debian 2023-01-08 4:10 ` Diane Trout @ 2023-01-08 4:39 ` Kyle Meyer 0 siblings, 0 replies; 4+ messages in thread From: Kyle Meyer @ 2023-01-08 4:39 UTC (permalink / raw) To: Diane Trout; +Cc: snakemake-mode Diane Trout writes: > 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. I see. Thanks for investigating. > Upstream's solution is here and involves using a more recently updated > depedency. > https://github.com/snakemake/snakemake/issues/1952 It looks like the associated fix came in with 50b8f160 (fix: Change ratelimiter dependency to throttler (#1958), 2022-11-10), which was part of the v7.18.2 release. So, the issue should be resolved whenever unstable gets bumped to the latest Snakemake. ^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2023-01-08 4:39 UTC | newest] Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed) -- links below jump to the message on this page -- 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 2023-01-08 4:39 ` Kyle Meyer
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