# Changelog
All notable changes to this project will be documented in this file.
## [0.9.0] - 2024-03-27
### Bugfix
- Fix the name of the `BMA` SimilarityCombiner.
## [0.9.0] - 2024-03-27
### Feature
- `Gene`s by default contain only direct `HpoTerm` associations, not transitive inherited ones.
- `Ontology::as_graohviz` method to generate graphviz data
## [0.8.3] - 2024-03-24
### Feature
- Add method to search for `OmimDisease`
### Bugfix
- Fix the JC similarity algorithm (see https://github.com/anergictcell/pyhpo/issues/20)
### Documentation
- Add a Changelog and a checklist for releases and patches
## [0.8.2] - 2024-03-09
### Data
- Update to HPO 2024-03-09
### Refactor
- Update dependencies
## [0.8.1] - 2023-06-25
### Feature
- Derive `Clone` for `Ontology`
## [0.8.0] - 2023-05-22
### Feature
- Add method to calculate hypergeometric enrichment of genes and diseases in HpoSets
- Add method to create dendogram clusters based on similarity
### Refactor
- Allow custom Similarity implementations to use Matrix
## [0.7.1] - 2023-04-27
### Refactor
- Derive `Debug` trait on more public structs
## [0.7.0] - 2023-04-22
### Feature
- New method to retrieve the shortest path between two HpoTerm
- Add modifier flag and categories of HpoTerm
### Refactor
- Use SmallVec for HpoGroup with default size 30
- Add more benchmarks
- Improve performance for adding, or-ing and comparing HpoGroups
## [0.6.3] - 2023-04-11
### Bugfix
- Fix issue parsing new HPO masterdata format
## [0.6.2] - 2023-04-05
### Bugfix
- Fix Subontology to not include all parents or children
### Refactor
- Add benchmark tests for Criterion
## [0.6.1] - 2023-03-30
### Documentation
- Add plenty of documentation
## [0.6.0] - 2023-03-18
### Feature
- Replace obsolete terms in an HpoSet
- allow different versions of binary masterdata
### Refactor
- add stricter clippy rules
- switch from `log` to `tracing`
## [0.5.0] - 2023-03-07
### Refactor
- clean up Similarity methods
- Simplify iterators across the full crate and add new ones
## [0.4.2] - 2023-02-11
### Feature
- new similarity method: Mutation
## [0.4.0] - 2023-02-04
### Feature
- Create a sub-ontology
- Calculate hypergeometric enrichment
### Bugfix
- Collecting into a HpoGroup will maintain order of the IDs internally