#1944 Add pre-computed neighbors to PCA h5ad files Pull request opened by nictru Summary • Adds pre-computed neighbor graphs (

sc.pp.neighbors(adata, use_rep='X_pca')

, default parameters) to

pbmc/SRR28679759_filtered_pca.h5ad

and

pbmc/combined_filtered_pca.h5ad

• These files already contained pre-computed PCA embeddings; this extends them with the neighbor graph (

obsp/connectivities

,

obsp/distances

,

uns/neighbors

) so downstream module tests no longer need to run

SCANPY_NEIGHBORS

in their setup blocks Context These files are used by the

scdownstream

pipeline module tests. Adding pre-computed neighbors allows removing the

SCANPY_NEIGHBORS

step from test setup blocks, reducing test complexity and eliminating a source of numerical non-determinism across platforms. nf-core/test-datasets