--- a +++ b/docs/release_notes/index.md @@ -0,0 +1,49 @@ +# Release notes + +All notable changes to this project will be documented in this file. The format +is based on [keep a changelog], and this project adheres to +[Semantic Versioning]. Full commit history is available in the [commit logs]. + +### 0.2.3 (17.02.2025) + +- Added numpy<2 dependency as version upgrade of NumPy to major version 2 breaks required scanpy version. +[@sebastianbirk] + +### 0.2.2 (09.01.2025) + +- Synced repository with Zenodo to mint DOI for publication. +[@sebastianbirk] + +### 0.2.1 (15.10.2024) + +- Added a user guide to the package documentation. +[@sebastianbirk] + +### 0.2.0 (22.08.2024) + +- Fixed a bug in the configuration of random seeds. +- Fixed a bug in the definition of MEBOCOST prior gene programs. +- Raised the default quality filter threshold for the retrieval of OmniPath gene programs. +- Modified the GP filtering logic to combine GPs with the same source genes and drop GPs that do not have source genes if they have a specified overlap in target genes with other GPs. +- Changed the default hyperparameters for model training based on ablation experiments. +[@sebastianbirk] + +### 0.1.2 (13.02.2024) + +- The version was incremented due to package upload requirements. +[@sebastianbirk] + +### 0.1.1 (13.02.2024) + +- The version was incremented due to package upload requirements. +[@sebastianbirk] + +### 0.1.0 (13.02.2024) + +- First NicheCompass version. +[@sebastianbirk] + +[keep a changelog]: https://keepachangelog.com/en/1.0.0/ +[Semantic Versioning]: https://semver.org/spec/v2.0.0.html +[commit logs]: https://github.com/Lotfollahi-lab/nichecompass/commits +[@sebastianbirk]: https://github.com/sebastianbirk