Merge Devel pre v4 to sc_spatial_wrapper

[ch99l]

Related Issue

Fixes # (issue number)

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (please specify if the change breaks existing functionality)
  • Non breaking change (the feature doesn't change existing functionality)
  • Breaking change (the feature that would cause existing functionality to not work as expected)
• Documentation update
• Performance optimization

Description

Please provide a summary and the motivation for the changes. Why is this change necessary? What problem does it solve?

Implementation Details

Briefly describe how the changes were implemented. Which specific code segments or logic paths within the primary functional arguments (e.g., demultiplexed, discovery, quant) are affected? Include relevant technical details for any algorithmic changes or data structure modifications specific to Bambu.

Impact of Changes

Briefly describe the impact of the implemented changes. For example:

• Results are identical to the previous version.
• Bug fix only (no changes to output).
• Adds one column to the SE object.
• Transcript quantification results show minimal differences.

Checklist

• My code follows the style guidelines of this project.
• I have performed a self-review of my own code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation (vignettes, man pages).
• I have tested the code on a full dataset, and any differences have been described in the Impact of Changes section.