Add CiLISI as new metric component

[JGarnica22]

Describe your changes

Add metrics/cilisi new metric component.

CiLISI measures batch mixing in a cell type-aware manner by computing iLISI within each cell type and normalizing the scores between 0 and 1. Unlike iLISI, ciLISI preserves sensitivity to biological variance and avoids favoring overcorrected datasets with removed cell type signals.
We propose adding this metric to substitute iLISI.

More information at:

• Describing publication: Andreatta et al., 2024
• Implementation in R package: scIntegrationMetrics
• Independent benchmarking using CiLISI: Rautenstrauch & Ohler. bioRxiv (2025)

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!

[mumichae]

Looking great! Just some minor comments on documentation and removing boilerplate code.

[JGarnica22]

Thanks!! Requested changes addressed and resolved.

[rcannood]

@mumichae Do you have any additional feedback or can this be merged?

[JGarnica22]

Hi,

Check test failed despite running successfully locally. The issue is the same as commented in #58 (comment) . However, in this case I didn't have to turn off dependencies by the github installing.

Could be the problem given by the container when installing R dependencies?

thanks,

[JGarnica22]

Hi, thanks for your help. The changes have been applied and merged to upstream/main

[mumichae]

Looking great! Will merge