Merge pull request #73 from Lotfollahi-lab/revision

Update package version and release notes

docs/release_notes/index.md

@@ -4,17 +4,29 @@ 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].
 
+### 0.2.0 (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]
+-   First NicheCompass version.
+[@sebastianbirk]
 
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [Semantic Versioning]: https://semver.org/spec/v2.0.0.html

pyproject.toml

@@ -4,7 +4,7 @@ requires = ["hatchling"]
 
 [project]
 name = "nichecompass"
-version = "0.1.3"
+version = "0.2.0"
 description = "End-to-end analysis of spatial multi-omics data"
 readme = "README.md"
 requires-python = ">=3.9"