Developer Notes

This page will record implementation decisions and compatibility constraints that are important to future SNF2 contributors.

Design decisions

• make_affinity computes pairwise distances from sample-by-feature data and delegates the shared SNF kernel to affinity_matrix.
• affinity_matrix accepts precomputed distances rather than similarities, so callers remain responsible for choosing a scientifically appropriate similarity-to-distance transformation.

Compatibility notes

• Missing-value handling belongs in preprocessing or in the distance calculation. SNF2 does not define a generic nan_policy for SciPy metrics.

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