fix: naming SLURM logs, SLURM logs not just "log files" #372
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WalkthroughSemantic updates to logging text in the SLURM executor plugin: three log-message string literals were changed to explicitly reference "SLURM". No control-flow, logic, API, or exported-symbol changes. Changes
Estimated code review effort🎯 1 (Trivial) | ⏱️ ~2 minutes
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✨ Finishing touches
🧪 Generate unit tests (beta)
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🧰 Additional context used🧠 Learnings (5)📓 Common learnings📚 Learning: 2024-12-11T14:17:08.749ZApplied to files:
📚 Learning: 2025-01-20T09:13:26.443ZApplied to files:
📚 Learning: 2025-06-03T17:10:51.292ZApplied to files:
📚 Learning: 2025-05-26T12:22:07.005ZApplied to files:
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🧹 Nitpick comments (1)
snakemake_executor_plugin_slurm/__init__.py (1)
243-243: Optional: Align existing logfile reference with SLURM log terminology.Line 243 still references "logfile" rather than "SLURM log file". While outside the scope of this PR, updating it would further reinforce the terminology distinction introduced by these changes.
- self.logger.error(f"Could not delete logfile {path}: {e}") + self.logger.error(f"Could not delete SLURM log file {path}: {e}")
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snakemake_executor_plugin_slurm/__init__.py(2 hunks)
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🧠 Learnings (4)
📓 Common learnings
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 193
File: .github/workflows/post_to_mastodon.yml:26-26
Timestamp: 2025-01-20T09:13:26.443Z
Learning: In the snakemake-executor-plugin-slurm repository, release PRs follow the naming pattern "chore(main): release X.Y.Z" where X.Y.Z is the version number.
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 178
File: snakemake_executor_plugin_slurm/__init__.py:0-0
Timestamp: 2024-12-11T14:17:08.749Z
Learning: In the `snakemake-executor-plugin-slurm` project, when handling exceptions in `snakemake_executor_plugin_slurm/__init__.py`, prefer concise error messages and avoid unnecessary verbosity or exception chaining when it's not necessary.
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 187
File: .github/workflows/post_to_mastodon.yml:0-0
Timestamp: 2025-01-17T17:27:32.446Z
Learning: In the mastodon publishing workflow for snakemake-executor-plugin-slurm, the PR_TITLE environment variable is required by the post_to_mastodon.sh script and should be preserved.
Learnt from: johanneskoester
Repo: snakemake/snakemake-executor-plugin-slurm PR: 173
File: docs/further.md:96-96
Timestamp: 2025-03-10T15:20:51.829Z
Learning: PR #173 in snakemake-executor-plugin-slurm implements GPU job support by adding resources: `gres` for generic resource specifications (e.g., 'gpu:1'), `gpu`/`gpus` for specifying GPU counts, and `gpu_model`/`gpu_manufacturer` for specifying GPU types, allowing users to request GPU resources directly rather than having to use slurm_extra.
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 0
File: :0-0
Timestamp: 2025-01-13T09:54:22.950Z
Learning: PR #173 (adding gres resource specification) depends on PR #28 in snakemake-executor-plugin-slurm-jobstep repository, as changes were required in the cpu-settings function of the jobstep-Executor module.
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 221
File: snakemake_executor_plugin_slurm/efficiency_report.py:0-0
Timestamp: 2025-06-16T08:54:07.957Z
Learning: In the context of SLURM executor plugin development, user cmeesters (experienced with SLURM) noted they are not aware of SLURM typically reporting memory values with decimals (like 1.5G), but accepted defensive programming to handle such cases anyway.
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 159
File: snakemake_executor_plugin_slurm/utils.py:43-53
Timestamp: 2025-01-07T18:48:09.845Z
Learning: In the SLURM executor plugin, when cleaning up working directories after job completion, all empty directories must be deleted recursively, including nested empty directories, as partial cleanup is not sufficient.
📚 Learning: 2024-12-11T14:17:08.749Z
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 178
File: snakemake_executor_plugin_slurm/__init__.py:0-0
Timestamp: 2024-12-11T14:17:08.749Z
Learning: In the `snakemake-executor-plugin-slurm` project, when handling exceptions in `snakemake_executor_plugin_slurm/__init__.py`, prefer concise error messages and avoid unnecessary verbosity or exception chaining when it's not necessary.
Applied to files:
snakemake_executor_plugin_slurm/__init__.py
📚 Learning: 2025-01-20T09:13:26.443Z
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 193
File: .github/workflows/post_to_mastodon.yml:26-26
Timestamp: 2025-01-20T09:13:26.443Z
Learning: In the snakemake-executor-plugin-slurm repository, release PRs follow the naming pattern "chore(main): release X.Y.Z" where X.Y.Z is the version number.
Applied to files:
snakemake_executor_plugin_slurm/__init__.py
📚 Learning: 2025-06-03T17:10:51.292Z
Learnt from: cmeesters
Repo: snakemake/snakemake-executor-plugin-slurm PR: 221
File: snakemake_executor_plugin_slurm/__init__.py:0-0
Timestamp: 2025-06-03T17:10:51.292Z
Learning: In the snakemake-executor-plugin-slurm repository, the create_efficiency_report method in snakemake_executor_plugin_slurm/__init__.py contains temporary testing/debugging code that logs directory contents using os.listdir() and directory paths. This code was inserted for testing purposes only and should be removed from the production implementation.
Applied to files:
snakemake_executor_plugin_slurm/__init__.py
⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (1)
- GitHub Check: testing
🔇 Additional comments (1)
snakemake_executor_plugin_slurm/__init__.py (1)
234-234: Text changes for SLURM log differentiation are good.The PR successfully clarifies log messages to distinguish SLURM logs from Snakemake logs. The updates at lines 234, 528, and 536 align with the PR objectives (once the spacing inconsistency at line 528 is fixed).
Also applies to: 528-528, 536-536
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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When a log message is directed to the terminal which refers to SLURM logfiles it should read "SLURM log<file" not "log" to differentiate between SLURM and Snakemake logs.
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