fix: fix string resource definition in CLI and profile #2627
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@johanneskoester does this make sense? Any progress on this side? |
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🤖 I have created a release *beep* *boop* --- ## [8.4.3](v8.4.2...v8.4.3) (2024-02-02) ### Bug Fixes * Do not scheduler execution message if no jobs are ready ([b1c4f47](b1c4f47)) * fix string resource definition in CLI and profile ([#2627](#2627)) ([bbd76ae](bbd76ae)) * if report files are within storage, retrieve them from storage before loading into report ([60041bd](60041bd)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Thank you for the fix! Alas, case no. 1 is not covered, yet - as it seems. |
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Description
The PR is related to the issue described for the slurm submit executor plugin to not correctly hand over arguments.
The test folder is named
test_slurm_resource_propagation meestersand may not be complete, as it covers multiple related scenarios to provoke the error.Note, that the tests were carried out when using a cluster:
$ snakemake --executor slurm -j2 --workflow-profile ./profiles/ --default-resources slurm_account=<account>yields
``Error:
WorkflowError:
Failed to evaluate default resources value '<function eval_resource_expression..callable at 0x7f5c19ed0e00>'.```
when the patition is defined at the rule level in a profile. (see the directory of the test case)
likewise
$ snakemake --executor slurm -j2 --workflow-profile ./profiles/ --default-resources slurm_account=<account> --set-resources slurm_extra="--nice=150"yields
ValueError: Invalid resource definition: entries have to be defined as RULE:RESOURCE=VALUE, with VALUE being a positive integer a quoted string, or a Python expression (e.g. min(max(2*input.size_mb, 1000), 8000)).These errors can both be triggered on the command line and in the config file, of course.
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).