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.

0.3.2 (04.11.2025)

  • Remove fixed versioning of package dependencies for uv installation with jax CUDA 12.4 support. @sebastianbirk

0.3.1 (04.11.2025)

  • Fixed issue in retrieval of omnipath gene programs due to omnipath db version update. @sebastianbirk

0.3.0 (07.08.2025)

  • Fixed dependency issues in optional dependencies and updated decoupler to version 2.0.0. @sebastianbirk

0.2.4 (02.08.2025)

  • Fixed issue in pyproject.toml that prevented “pip install nichecompass[all]” from installing optional dependencies. @sebastianbirk

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)

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)