Add method: CellMapper

[Marius1311]

Describe your changes

This PR includes CellMapper for modality prediction, see the CellMapper docs for more infos: https://cellmapper.readthedocs.io/en/latest/

It includes two variants that differ in how the shared latent space is computed between train and test datasets in modality 1:

• Variant 1: use simple fallback representations, PCA or CCA
• Variant 2: use modality-specific scvi-tools models, e.g. scVI for GEX data, PeakVI for ATAC data

The rest happens in CellMapper and is modality-agnostic. We construct a k-NN graph given some kernel function and map expression in modality 2 from train to test data.

Currently, running viash test src/methods/cellmapper_scvi/config.vsh.yaml fails because my utils.py file isn't detected, that's because I don't know how to provide the resources_dir path in meta. Currently, I do:

meta = {
  'name': 'cellmapper_scvi',
  'resources_dir': 'target/executable/methods/cellmapper_scvi',
}

but that doesn't work locally. I've also looked around a bit what other methods do and tried different variants but could not get it to work. I would appreciate some input here how I could fix this. Thanks in advance!

Running the scripts for both variants and different parameter combinations as simple Python scripts works locally.

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!

[lazappi]

@rcannood Anything else you want to check?

[rcannood]

No, LGTM! :)

[Marius1311]

Amazing, thank you! I forgot to add myself as a contributer, I'll do this next time when I need to fix/update something.