SWE-bench: don't pass external environment variables into Apptainer containers

[ludwig-n]

With this PR, environment variables from the Nemo-Skills container are no longer passed through to the Apptainer containers. This was a security risk, as this gave the agent access to potentially sensitive info.

If an environment variable does need to be passed into the Apptainer containers, one can use the APPTAINERENV_ prefix. For example, setting an environment variable in the cluster config as APPTAINERENV_KEY=value will make it available inside of Apptainer as KEY=value. See the Apptainer docs for more info.

The Slurm SWE-bench tests pass.

Summary by CodeRabbit

• Bug Fixes
  • Improved container environment isolation during evaluation execution by ensuring a clean environment is maintained, preventing potential environment contamination issues.

_{✏️ Tip: You can customize this high-level summary in your review settings.}

[coderabbitai]

📝 Walkthrough

Walkthrough

The --cleanenv flag was added to Apptainer container execution commands in two locations within _execute_container_command to provide environment isolation inside containers, working alongside existing --writable-tmpfs and --no-mount options.

Changes

Cohort / File(s)	Change Summary
Container environment isolation nemo_skills/inference/eval/swebench.py	Added --cleanenv flag to Apptainer exec commands in two locations within _execute_container_command function

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.
Title check	✅ Passed	The title accurately describes the main change: adding the --cleanenv flag to prevent external environment variables from being passed into Apptainer containers, matching the core security improvement in the changeset.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch ludwig-n/swe-bench-clean-env

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