fix: skip account setting upon user request #224
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WalkthroughThis pull request modifies error handling in a Mastodon posting shell script, updates documentation regarding SLURM account configuration in Snakemake, and enhances the SLURM executor functionality. Specifically, error messages in the workflow script are now sent to standard error, the docs explain nuances around multiple SLURM accounts and the Changes
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Cherry picking the commit and putting it on top of main worked for me. |
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good. I will add some docs, tomorrow. |
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🧹 Nitpick comments (1)
docs/further.md (1)
21-22: Typos in the new documentationThe explanation of the SLURM account configuration is helpful, but there are a couple of typos in the text:
- "attept" should be "attempt"
- "behauvior" should be "behavior"
-Some clusters, however, have a pre-defined default per user and _do not_ allow users to set their account. The plugin will attept to always set an account. To override this behauvior, the `--slurm-no-account` flag can be used. +Some clusters, however, have a pre-defined default per user and _do not_ allow users to set their account. The plugin will attempt to always set an account. To override this behavior, the `--slurm-no-account` flag can be used.
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🔇 Additional comments (3)
.github/workflows/post_to_mastodon.sh (1)
4-5: Improved error handling by redirecting to stderrThe change properly redirects error messages to standard error (stderr) using
>&2instead of printing them to standard output. This follows shell scripting best practices for error reporting.snakemake_executor_plugin_slurm/__init__.py (2)
88-96: Well-defined new no_account settingThe new
no_accountfield inExecutorSettingsis properly structured with appropriate defaults and clear help documentation. This addition aligns with the PR objective of allowing users to skip account settings when required.
225-227: Clean implementation of conditional account settingThe conditional addition of the account argument based on the
no_accountsetting is well implemented. This change directly addresses the PR objective by providing a way to skip account settings upon user request.
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@DrYak there is now rudimentary documentation. Please review. More detailed documentation changes are upcoming. |
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🧹 Nitpick comments (1)
snakemake_executor_plugin_slurm/__init__.py (1)
644-686: Improve exception chaining in the error handling.The account validation logic has been improved to first try
sshareand then fall back tosacctmgr, with appropriate warning when both return empty results. However, there's a minor issue with the exception handling.According to best practices for Python exception handling, you should use explicit exception chaining with
raise ... from e:raise WorkflowError( f"The 'sshare' reported: '{sshare_report}' " f"and likewise 'sacctmgr' reported: '{sacctmgr_report}'." - ) + ) from eThis helps distinguish between errors in the original operation and errors in exception handling.
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671-674: Within an
exceptclause, raise exceptions withraise ... from errorraise ... from Noneto distinguish them from errors in exception handling(B904)
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snakemake_executor_plugin_slurm/__init__.py(3 hunks)
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snakemake_executor_plugin_slurm/__init__.py
671-674: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
(B904)
🔇 Additional comments (2)
snakemake_executor_plugin_slurm/__init__.py (2)
88-96: LGTM: Clean implementation of the no_account setting.The new boolean field follows the established pattern for boolean settings in the ExecutorSettings class, with appropriate default value and helpful documentation.
225-227: LGTM: Core functionality implemented correctly.The conditional check for the no_account setting works as intended, allowing users to skip account settings upon request, which aligns with the PR objectives.
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@DrYak now, the order of account tests with @coderabbitai please, update the PR summary accordingly. |
🧩 Analysis chainI'll need to gather more information about issue #233 and check the code changes to properly update the PR summary. 🏁 Script executed: Length of output: 3973 @cmeesters I'll update the PR summary to include the information about the new order of account tests and how this PR also addresses issue #233. The PR now accomplishes two main things:
✅ Actions performedSummary regeneration triggered. |
Summary by CodeRabbit
Bug Fixes
Documentation
New Features