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…alidation Expanded mutation testing coverage to critical modules and implemented a comprehensive suite of robustness tests to address identified logic gaps. Key changes: Mutation Testing: Established cosmic-ray configurations and sessions for losses.py , splitting.py , dataset.py , and pathways.py . Bug Fix (Augmentation): Corrected operation mapping in apply_dihedral_to_tensor where vertical flips (op 5) were incorrectly handled as horizontal flips (op 4). Refactor (Normalization): Rewrote normalize_coordinates to use explicit grid-step detection (np.diff), ensuring robust coordinate scaling across different spatial transcriptomics datasets and environments. Robustness Suite: Added 12 new test cases across four modules: tests/test_dataset_logic.py : Validates spatial normalization and dihedral symmetry. tests/test_splitting_robust.py : Verifies strict patient isolation and CLI parameter integrity. tests/test_losses_robust.py : Confirms gradient flow for ZINB loss and numerical stability under extreme count values. tests/test_pathways_robust.py : Ensures integrity of gene-to-pathway adjacency matrix construction. Data Loading Fixes: Resolved a dimension permute error in HEST_Dataset and refined dataset validation logic.
- Improve test_dataset_logic.py with comprehensive verification for all 8 dihedral transformations and boundary conditions for coordinate normalization. - Implement test_dataset_mocks.py to verify HEST_Dataset and HEST_FeatureDataset integration logic (augmentations, neighborhood dropout, log1p) using mocks. - Fix RuntimeError in ZINBLoss.forward caused by incorrect mask expansion dimensions when using spatial padding.
…uests for all branches ("**").
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