fix: enable retrieving logs from terminated containers

[johanneskoester]

Summary by CodeRabbit

• Bug Fixes
  • Improved log retrieval for failed Kubernetes jobs by also fetching logs from the previous container instance after pod restarts.
  • Ensures logs remain available even if a pod has restarted, reducing missing or empty logs in failure reports.
  • Enhances reliability and consistency of failure diagnostics without altering user-facing workflows or configurations.

[coderabbitai]

📝 Walkthrough

Walkthrough

Adds previous=True to the Kubernetes read_namespaced_pod_log call used when fetching logs for failed jobs, enabling retrieval of logs from a pod’s previous container instance after restarts. No other logic, signatures, or control flow paths were changed.

Changes

Cohort / File(s)	Summary
Kubernetes log retrieval snakemake_executor_plugin_kubernetes/__init__.py	Modify log fetch for failed jobs to pass previous=True to read_namespaced_pod_log, allowing access to logs from the prior container instance on restart.

Sequence Diagram(s)

sequenceDiagram
  autonumber
  participant S as Snakemake Executor
  participant K as Kubernetes API
  participant P as Pod

  rect rgba(230,245,255,0.6)
    S->>K: read_namespaced_pod_log(pod, namespace) for running/success
    K-->>S: Current container logs
  end

  alt Pod failed / restarted
    note over S,K: Changed: request previous container logs
    S->>K: read_namespaced_pod_log(pod, namespace, previous=true)
    K-->>S: Previous container logs
  else Not failed
    S->>K: read_namespaced_pod_log(pod, namespace, previous=false/default)
    K-->>S: Current container logs
  end

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Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Pre-merge checks (2 passed, 1 warning)

❌ 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%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (2 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title Check	✅ Passed	The title “fix: enable retrieving logs from terminated containers” directly reflects the pull request’s core change of adding support for fetching logs from previously terminated container instances, doing so in a concise and focused manner without extraneous details.

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📜 Recent review details

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📥 Commits

Reviewing files that changed from the base of the PR and between 2cb2a7e and ff8a468.

📒 Files selected for processing (1)

• snakemake_executor_plugin_kubernetes/__init__.py (1 hunks)

🧰 Additional context used

📓 Path-based instructions (1)

**/*.py

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Files:

• snakemake_executor_plugin_kubernetes/__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

✨ Finishing Touches

• 📝 Generate Docstrings

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/get-previous-logs-from-term-containers

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