Feat/thermo#7
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- Removed the nnparams.go file, which contained deprecated functions. - Introduced a new thermo scoring model with enhanced functionality. - Updated relevant tests to reflect changes in the scoring model. - Adjusted conditions handling to utilize the new model. - Ensured backward compatibility with legacy scoring where applicable.
- Introduces NNStructureV1 for secondary-structure competition scoring. - Removes the previously exported function related to the old model. - Updates scoring logic to include hairpin, self-dimer, and cross-dimer penalties. - Enhances API to support new thermodynamic details in outputs.
…ding - Add new `imperfect` package for condition-aware duplex calculations. - Implement `ImperfectDuplex` function to compute mismatches and penalties. - Enhance `ThermoEndpoint` structure with additional mismatch metrics. - Update API to include new mismatch-related fields in responses. - Add tests for the new duplex model to ensure accuracy and reliability.
- Add terminal mismatch penalties and adjustments for primer-template duplexes. - Introduce dangling end contributions to improve scoring accuracy. - Update API to include new fields for terminal and dangling end metrics. - Enhance tests to validate new terminal and dangling end functionalities.
- Added new structure evaluation functions for V2 models. - Updated thermodynamic calculations to support new parameters. - Removed deprecated exported functions related to V1 models. - Adjusted tests to validate new V2 functionality. - Enhanced API to include additional thermodynamic details.
- Introduced IUPAC thermodynamic policies: strict, worst, best, mean, enumerate. - Added IUPAC expansion count and capped flag to thermodynamic details. - Updated scoring logic to handle IUPAC primer variants. - Modified API to include new IUPAC fields in product details. - Enhanced tests to validate IUPAC policy behavior and expansions.
- Introduced ProbeThermoDetails for internal probe annotations. - Enhanced scoring model to include probe thermodynamics. - Updated API to return probe-related thermodynamic data. - Modified CLI options to configure probe scoring behavior. - Added tests for probe thermodynamics integration and validation.
…tion - Introduced comprehensive documentation for `ipcr-thermo` thermodynamic models. - Added a detailed release checklist to ensure compliance with thermodynamic claims. - Updated README and architecture documentation to reflect new thermodynamic features. - Created tests to validate the presence of key thermodynamic concepts in documentation.
- Introduced comprehensive golden tests for various thermodynamic scenarios. - Added functions to read and parse TSV files for test data. - Enhanced test coverage for duplex and structure scoring models. - Updated documentation for thermodynamic models and scoring profiles.
- Added a new mismatch parameter registry for curated pairs. - Updated mismatch handling to utilize curated pair-family data. - Removed the exported function for direct triplet lookup. - Enhanced tests to validate curated pair-family behavior. - Updated API to include curated pair count in results.
- Introduced ensemble fields in ThermoStructure for partitioning results. - Added new partitioning functions for hairpin, self-dimer, and cross-dimer structures. - Updated StructureOptions to include PartitionMaxCandidates. - Enhanced JSON API representation to include new ensemble metadata. - Updated tests to validate partitioning behavior and metadata.
…ld tables - Added support for triplet-level mismatch scoring in the ImperfectDuplex function. - Introduced new constants for triplet mismatch policies. - Removed the exported function that previously handled mismatch scoring. - Updated tests to validate new triplet scoring behavior. - Added new golden test data for triplet mismatch scenarios.
- Add mismatch sources, parameter sets, citations, and notes to API. - Update internal structures to track mismatch contributions. - Modify output formats to include new mismatch metadata. - Enhance tests to validate mismatch provenance in outputs. - Update documentation to reflect changes in mismatch handling.
- Introduced new `DanglingEndParameter` and `DanglingEndKey` types. - Added functions for looking up dangling-end parameters based on strand orientation. - Implemented tests for dangling-end contributions and their effects on duplex stability. - Updated documentation to reflect new dangling-end modeling capabilities.
- Introduced terminal mismatch scoring parameters in the API. - Updated `ProbeThermoDetails` and `ThermoEndpoint` structures. - Enhanced mismatch contribution handling in `ImperfectDuplex`. - Added tests for terminal mismatch provenance in outputs. - Created new file for terminal mismatch parameters.
- Removed redundant terminalPenalty function. - Streamlined mismatch policy selection with clearer conditions. - Improved code readability and maintainability.
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