✅ Code Quality and Best Practices

Excellent:

• Changes are minimal and focused on a single concern
• Consistent updates across all relevant locations (config defaults, code, schema, docs)
• Good use of fallback values in the code: config.export_plots_timeout if hasattr(config, "export_plots_timeout") else 60
• Proper regeneration of JSON schema from the Python schema definition

Documentation:

• The new documentation section in running_multiqc.md is clear and helpful
• Explains both the "why" (Kaleido can hang) and the "how" (config file and env var)
• Good choice linking to Kaleido's GitHub for users who want more context

🔧 Issues Found

Formatting Issues (CI Failures):
The pre-commit checks are failing due to formatting issues that can be easily fixed:

1. Prettier modified docs/markdown/getting_started/running_multiqc.md:

   • Line 206 needs the comment moved: export_plots_timeout: 60 # seconds (no double space)

2. Ruff modified multiqc/utils/config_schema.py:

   • One file needs reformatting (likely whitespace)

3. Config schema JSON was modified by prettier (indentation changes)

To fix: Run pre-commit run --all-files locally and commit the formatting changes.

🎯 Potential Improvements

Schema Description (multiqc/utils/config_schema.py:128):
The updated description is good, but could be slightly more concise:

# Current:
description="Timeout in seconds for exporting each plot to a static image (default: 60)"

# Suggestion:
description="Timeout in seconds for exporting each plot to a static image. Kaleido can occasionally hang; if timeout is exceeded, plot export is skipped and report generation continues. Default: 60"

This would match the detailed explanation in the documentation and provide context for why the timeout exists.

⚡ Performance Considerations

Positive Impact:

• Doubling the timeout from 30s to 60s should significantly reduce the number of plots that timeout with Kaleido
• The timeout is per-plot, so this doesn't add unnecessary wait time for successful exports
• The graceful degradation (skipping failed plots) ensures reports still complete

No Concerns:

• The timeout is already implemented efficiently using process joins
• No performance regressions expected

🔒 Security Considerations

No Issues:

• Changes are configuration-only, no security implications
• Timeout values are validated by the schema as integers
• No user input is directly executed

🧪 Test Coverage

Observations:

• No tests were added or modified
• The existing test suite should cover this change adequately since it's just a default value change

Recommendation (Optional):
Consider adding a test to verify:

1. The config value is correctly read from config_defaults.yaml
2. The fallback value of 60 is used when the config is not set
3. Environment variable MULTIQC_EXPORT_PLOTS_TIMEOUT works correctly

However, this is not critical for this PR since it's a straightforward config change.

📝 Other Notes

Changes Summary:

• config_defaults.yaml: ✅ Timeout changed from 30 to 60
• plot.py: ✅ Two locations updated with new default (lines 1434, 1508)
• config_schema.py: ✅ Schema description enhanced
• config_schema.json: ✅ Auto-regenerated (large diff is just formatting)
• running_multiqc.md: ✅ New documentation section added

Commit Message:
The PR description is clear and matches the commit. Good practice!

🎬 Action Items

1. Required: Run pre-commit run --all-files and commit the formatting fixes
2. Optional: Consider enhancing the schema description with more context
3. Optional: Add basic test coverage for the timeout config