feat: Add support for third-party API models #164
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marcbal77
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This commit introduces a minimal framework for integrating third-party API models into biolearn, with Hurdle Bio's Inflammage model as the first implementation. Key changes: - Add HurdleAPIModel class to model.py for API-based predictions - Integrate HurdleAPIModel into ModelGallery for consistent usage - Implement privacy-first approach with explicit user consent - Add automatic imputation for missing CpG sites - Include comprehensive error handling with user-friendly messages Security & Privacy: - API keys managed via environment variables or direct input - Explicit consent required before sending data to external servers - Updated .gitignore to exclude credential files Documentation: - Add user guide in docs/hurdle_api_guide.md - Include working example in examples/hurdle_api_example.py - Placeholder for Hurdle CpG sites list Testing: - Add test suite for HurdleAPIModel functionality - Mock API calls to avoid requiring credentials in tests This implementation minimizes changes to the existing codebase while providing a robust foundation for future API model integrations.
- Add actual CpG sites to Hurdle_CpGs.csv.example file (first 100 sites) - Fix test_consent_denied decorator issue (missing mock_input parameter) - Skip HurdleAPIModel in main test_model.py suite (requires API credentials) - Update test data to include proper CpG site indices for Hurdle tests - Fix file path to use Hurdle_CpGs.csv.example instead of .csv
- Format biolearn/test/test_hurdle_model.py - Format biolearn/test/test_model.py
- Add real CpG sites to example file, improve error handling and validation - Simplify consent mechanism, reduce test redundancy, add type hints - Move documentation to doc/ folder, clean up examples
- Update HurdleAPIModel implementation to match latest codebase - Fix test imports and references after rebase - Maintain compatibility with existing model architecture
- Add self._consent_given flag to track consent state - Only ask for consent if not already given - Remove duplicate base_url initialization - Fixes failing test test_consent_only_asked_once
- Format base_url assignment as multi-line for consistency - Fixes CI formatting check failure
…ntation - Rename HurdleInflammage to HurdleInflammAge - Switch to production API (use_production=True) - Update registration URL to https://dashboard.hurdle.bio/register - Add non-commercial use disclaimer to documentation and docstring - Rename Hurdle_CpGs.csv.example to Hurdle_CpGs.csv - Document 0.5 imputation for missing CpG sites - Update example script with better error handling - Update all references in tests and documentation
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- Model now errors if any required CpG sites are missing - Provides informative error with count and examples of missing sites - Directs users to use ModelGallery imputation methods - Updated documentation to explain missing data handling - Added test for missing CpG error - All tests passing (143 passed, 4 skipped)
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Description
This PR introduces a minimal framework for integrating third-party API models into biolearn, with Hurdle Bio's Inflammage model as the first implementation.
Key Changes
Security & Privacy Features
Documentation
Testing
Usage Example