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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 {pr}53
Add the possibility to provide the current gene set when querying expected marker genes {pr}53
Add the possibility to filter expected marker genes to those presend in AnnData {pr}53
Add a new tutorial on spatial data annotation {pr}53
Added and improved tests for the new classes (e.g. ObsBeautifier, LLMBackend, etc) {pr}53
For each backend, add a small test_query method which can be used for diagnostics {pr}53

Changed

Moved the reorder_and_color utility into a new class: ObsBeautifier {pr}54
Improved class representations throughout the package {pr}53

Fixed

Fix the ObsBeautifier modifying cluster colors when only their order should be updated {pr}54

Version 0.1

0.1.5 (2025-07-24)

Changed

Update tutorials to use gpt-4.1 {pr}51

0.1.4 (2025-03-28)

Added

Use rapids_singlecell, cupy and cuml to accelerate cluster marker computation on GPUs {pr}37.
Add the possibility to softly enforce adherence to expected cell types {pr}42.

Changed

Run cluster label harmonization also for a single sample {pr}37.
Re-format prompts into a dataclass {pr}42.

Fixed

Fixed a bug with integer sample labels {pr}37.

0.1.3 (2025-02-07)

Added

Added tests for the single-sample case {pr}29.
Refer to issues and PRs with sphinx {pr}30.

Removed

Removed tenacity for query retries {pr}28.

Fixed

Fixed _get_annotation_summary_string for the single-sample case {pr}29.
Fixed the expected cell type marker test by adding additional marker genes {pr}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