fix: initializing self.slurm_logdir

[cmeesters]

setting self.slurm_logdir in post_init, else starts without something… to do, will encounter uninitialized `self.slurm_logdir attribute

This PR ought to fix #198

Summary by CodeRabbit

• Improvements
  • Enhanced SLURM log directory management
  • Added flexibility for custom log directory configuration
  • Simplified log directory initialization process

[coderabbitai]

Walkthrough

The pull request modifies the initialization of the slurm_logdir attribute in the SLURM executor plugin. The changes enhance log directory management by introducing a more flexible approach to setting the log directory. Instead of directly assigning None, the code now checks the workflow.executor_settings for a custom log directory. If no custom directory is specified, it defaults to a resolved path of ".snakemake/slurm_logs". This modification addresses potential issues with log file handling and provides more configurability for users.

Changes

File	Change Summary
snakemake_executor_plugin_slurm/__init__.py	Improved slurm_logdir initialization in __post_init__ method, adding logic to set log directory from workflow settings or use a default path

Assessment against linked issues

Objective	Addressed	Explanation
Fix AttributeError during job file cleaning	✅
Ensure slurm_logdir is initialized correctly	✅

Possibly related PRs

• feat: in job stability #137: Modifications to job context management methods
• fix: logfile quoting and scancel error handling #140: Changes in run_job method related to log handling
• feat: custom log file behaviour #159: Enhancements to log management in Executor class

Suggested reviewers

• johanneskoester
• fgvieira

Poem

🐰 A Rabbit's Log Tale 🐰

In SLURM's domain, where jobs take flight,
A log directory, now set just right
No more None to cause a fright
Default path gleaming, oh so bright
Code dancing with elegant might!

✨ Finishing Touches

• 📝 Generate Docstrings (Beta)

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[coderabbitai]

Actionable comments posted: 0

🧹 Nitpick comments (1)

snakemake_executor_plugin_slurm/__init__.py (1)

125-129: Consider adding docstring and type hints.

While the implementation is solid, consider these improvements for better maintainability:

1. Add a docstring to document the log directory initialization behavior
2. Add type hints for the slurm_logdir attribute

 class Executor(RemoteExecutor):
+    slurm_logdir: Path
     def __post_init__(self):
+        """Initialize the executor.
+        
+        Sets up the SLURM log directory using the following precedence:
+        1. Custom directory from executor settings if provided
+        2. Default directory at '.snakemake/slurm_logs' if no custom directory
+        """
         # run check whether we are running in a SLURM job context
         self.warn_on_jobcontext()

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📥 Commits

Reviewing files that changed from the base of the PR and between 6dd0105 and fc4863d.

📒 Files selected for processing (1)

• snakemake_executor_plugin_slurm/__init__.py (1 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (1)

• GitHub Check: testing

🔇 Additional comments (1)

snakemake_executor_plugin_slurm/__init__.py (1)

125-129: LGTM! The initialization of self.slurm_logdir looks good.

The implementation properly handles the log directory initialization by:

1. Checking for a custom log directory in the executor settings
2. Providing a sensible default path
3. Using proper path handling with Path and resolve()