Briefly describe the purpose of this pull request.
Select all that apply.
- Documentation update
- Bug fix
- New analysis feature
- Workflow or notebook update
- Dependency/environment update
- Figure/table/output update
- Repository maintenance
- Other
Describe the main files, functions, notebooks, settings, or documentation sections changed in this pull request.
Explain the reason for the change.
Does this pull request affect any of the following?
- Input data
- Data preprocessing
- Analysis settings
- Metric definitions
- Output files
- Figures or tables
- Dependency versions
- Release or DOI documentation
- No reproducibility impact
If any item is checked, briefly explain the impact.
For notebook changes, complete the relevant checks below:
- Notebook JSON opens correctly and is not corrupted.
- All edited cells run without syntax or indentation errors.
- Step 1 Scotch Tape reference validation still passes.
- Step 2 file upload/manual-path workflow displays correctly.
- Step 3 mapping confirmation still works.
- Step 4 manuscript-baseline profile can still be activated.
- Step 5 analysis can run on the reference/example dataset.
- No manuscript-baseline parameters were changed unless intentionally documented.
- No metric definitions were changed unless intentionally documented.
- No generated output folders, temporary files, or large raw datasets were accidentally committed.
Additional notes:
For manuscript-linked repositories, state whether this change affects submitted, published, or archived results.
- Affects manuscript/public-release results
- Does not affect manuscript/public-release results
- Not applicable
Explanation:
- The change is focused and described clearly.
- README or documentation was updated if needed.
- CHANGELOG was updated if appropriate.
- Dependency files were updated if needed.
- Generated or temporary files were not accidentally committed.
- Large or sensitive data were not committed without approval.