2.1.2

[2.1.2] - 2025-08-16

Added

• Sopa is now also available on 🍏 nf-core (still in dev mode) - see this repo and the corresponding usage guide
• Added a sopa:latest-tangram Docker image for cell-type annotation
• Log a warning in case an annotation level group has multiple parents when running Tangram with multi-level.
• Docs clarifications, e.g., how to use dataset_id for Visium HD data, and others improvements.
• Store the cell to bins mapping in adata.obsm["bins_assignments"] during bins aggregation (#291)

Changed

• Minor Snakemake files simplification (e.g., no need to provide the gene column name anymore)

Fixed

• Preserve cell ids when converting to the explorer. Better interchangeability after filtering cells.
• sopa --version faster and returns no warning (prevent it from importing sopa)
• Preserve Xenium region_name and morphology_focus/mip files (via a symlink at the file level) when using sopa.io.explorer.write
• Remove warning in sopa.io.explorer.write when mode="+it" and used before running Sopa (typically, when running the Snakemake or Nextflow pipeline)