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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

Unreleased

[0.11.0]

Refactor

  • [breaking] Add Builder to build Ontology. This removes several methods from Ontology.
  • Remove aquamarine dependency, update docs

[0.10.1]

Refactor

  • Add some missing methods for Orpha diseases

[0.10.0]

Feature

  • Add Orphante diseases (OrphaDisease) to Ontology
  • Filter gene and disease annotations in subontology based on association with phenotypes
  • Add binary version 3
  • Add new example ontology

Documentation

  • Change orders of methods in Ontology to clean up the documentation.

Refactor

  • Improve the OBO parser with better error handling
  • [breaking] Add Disease trait that is needed to work with OmimDisease and OrphaDisease
  • Update example ontology
  • Update unit- and doctests to align with updated example ontology

[0.9.1] - 2024-03-30

Bugfix

  • Fix the name of the BMA SimilarityCombiner.

[0.9.0] - 2024-03-27

Feature

  • Genes 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

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