Fix output formatting for PEER evaluation callback#152
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July 18, 2025 22:16
- Convert NumPy scalars to Python types for clean YAML formatting - Use clean enum values (e.g., 'bindingdb') instead of 'PEERTask.BINDINGDB' - Move convert_numpy_to_python utility to _peer_utils.py for reusability - Ensure consistent markdown formatting with other evaluation callbacks This makes PEER evaluation results display cleanly in evaluation reports, matching the format of CALM and MoleculeACE callbacks.
- Fix cache key assertions to use task.value instead of str(task) - Fix probe storage assertions to use task.value instead of str(task) - Ensure all tests pass with updated PEER callback implementation
ncfrey
approved these changes
Jul 21, 2025
src/lobster/callbacks/_peer_utils.py
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| def convert_numpy_to_python(obj): | ||
| """Recursively convert NumPy scalars to Python types for clean YAML formatting.""" | ||
| if isinstance(obj, dict): |
- Updated test splits to use only most important split per task: * humanppi/yeastppi: only 'test' (removed cross_species_test) * bindingdb: only 'holdout_test' (removed random_test) * fold: only 'test_superfamily_holdout' for remote homology detection * secondarystructure: only 'cb513' benchmark - Removed categories section and task averaging logic since each task now has single split - Added descriptive comments to fold and secondarystructure task constants - Updated convert_numpy_to_python to use modern match-case syntax - Updated tests to match simplified evaluation behavior - Kept global mean aggregation across all tasks
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This makes PEER evaluation results display cleanly in evaluation reports, matching the format of CALM and MoleculeACE callbacks.
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Testing
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