Changelog

Changelog#

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.

Version 0.2#

Unreleased#

0.2.0 (2025-07-26)#

Added#

  • Added a generic LLM backend that supports OpenAI, Claude and Gemini models #53

  • Add the possibility to provide the current gene set when querying expected marker genes #53

  • Add the possibility to filter expected marker genes to those presend in AnnData #53

  • Add a new tutorial on spatial data annotation #53

  • Added and improved tests for the new classes (e.g. ObsBeautifier, LLMBackend, etc) #53

  • For each backend, add a small test_query method which can be used for diagnostics #53

Changed#

  • Moved the reorder_and_color utility into a new class: ObsBeautifier #54

  • Improved class representations throughout the package #53

Fixed#

  • Fix the ObsBeautifier modifying cluster colors when only their order should be updated #54

Version 0.1#

0.1.5 (2025-07-24)#

Changed#

  • Update tutorials to use gpt-4.1 #51

0.1.4 (2025-03-28)#

Added#

  • Use rapids_singlecell, cupy and cuml to accelerate cluster marker computation on GPUs #37.

  • Add the possibility to softly enforce adherence to expected cell types #42.

Changed#

  • Run cluster label harmonization also for a single sample #37.

  • Re-format prompts into a dataclass #42.

Fixed#

  • Fixed a bug with integer sample labels #37.

0.1.3 (2025-02-07)#

Added#

  • Added tests for the single-sample case #29.

  • Refer to issues and PRs with sphinx #30.

Removed#

  • Removed tenacity for query retries #28.

Fixed#

  • Fixed _get_annotation_summary_string for the single-sample case #29.

  • Fixed the expected cell type marker test by adding additional marker genes #28.

0.1.2 (2025-01-29)#

Added#

  • Update the documentation, in particular the installation instructions.

0.1.1 (2025-01-29)#

Added#

  • Initial push to PyPI

0.1.0 (2025-01-29)#

Initial package release

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