Update Trex

[ncborcherding]

Trex overhaul to be compatible with Seurat v5 and move away from reticulate. Similar to Ibex overhaul for the submission to Bioconductor.

Proposed Changes

• Integration of Ibex with immApex
• Move towards zenodo hosting of models
• Updated Seurat object to v5
• Dedicated basilisk environment
• Update support for SCE format for runTrex()
• Update CoNGAfy() to function with all versions of Seurat
• Update quietTCRgenes() to use VariableFeatures() call for SeuratV5 and backward compatibility.
• Update annotateDB() (per issue
  • Automate Library Pull
  • Add better support for HLA information/Add to meta data [see issue]
  • Expand matching system beyond edit distance

After these changes the plan will be to submit to bioconductor similar to the recently accepted Ibex.