Add SLURM_CONF to kept environment variables

[gmanthey]

Hi all,

first of all, thanks a lot for this great tool, I've been enjoying using snakemake a lot recently! I've only just now, when dealing with a different issue (#46 (comment)), updated to the latest version of this plugin, only to find out that nothing related to slurm submission works anymore. It seems that on my cluster we are using a non-default path to the slurm configuration, which is passed to slurm in the environment variable SLURM_CONF. However this variable is now being removed from the environment, causing various issues.

I've raised this first in a comment on the PR causing the issue, but have now decided to just put in a PR given how simple the fix is.

Cheers!
Georg

Summary by CodeRabbit

• Bug Fixes
  • Preserves SLURM_CONF when launching nested job steps, helping srun inherit the expected Slurm configuration in step-based executions.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: 093b7003-636d-4a39-ad3d-ce7b70a5fb8f

📥 Commits

Reviewing files that changed from the base of the PR and between c09349d and f3ecb8f.

📒 Files selected for processing (1)

• snakemake_executor_plugin_slurm_jobstep/__init__.py

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📝 Walkthrough

Walkthrough

The environment-variable allowlist used to sanitize the environment for nested srun/sbatch calls in Executor.run_job was extended to include SLURM_CONF, preventing it from being stripped from popen_env during job step execution.

Changes

Environment variable allowlist update

Layer / File(s)	Summary
Add SLURM_CONF to keep_slurm allowlist snakemake_executor_plugin_slurm_jobstep/__init__.py	The keep_slurm allowlist in Executor.run_job now includes SLURM_CONF, preserving it in the sanitized environment for nested srun/sbatch calls.

Estimated code review effort: 1 (Trivial) | ~2 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately and concisely describes the main change: preserving SLURM_CONF in the kept environment variables.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

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