What problem does it solve? In topological data analysis (TDA) pipelines, errors in how embeddings (PCA/UMAP/scaler fits, GMM labels, recoding) are frozen or applied silently corrupt every downstream persistent homology claim. The signature bug is a null operation that permutes already-embedded rows, leaving the persistence diagram invariant to the very operation the null is meant to test. ## Core Features & Use Cases - Freeze Verification: Confirms loadings, scalers, GMMs, and recoding are frozen before any null draw or cross-group comparison, and fit on reference data with transform-only application elsewhere. - Null Placement Audit: Checks that label/cohort/order shuffles act on raw inputs before embedding, so the persistence diagram actually changes under the null. - Path Separation: Ensures frozen and provisional embeddings write to distinct output paths and provisional embeddings are never consumed as the frozen reference. - Use Case: When reviewing a TDL task that compares persistent homology across cohorts or surrogates, run this audit to get a PASS/FAIL report per checklist item with code locations and an assessment of whether failures invalidate downstream topological results. ## Quick Start Audit this TDA experiment code to verify the embedding is frozen before null shuffles and that shuffles operate on pre-embedding inputs.
