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.

Release notes for v0.7.1 and earlier are available on the Releases page.

[Unreleased]#

Added#

  • spatialdata_io ships a py.typed marker, so downstream type checkers use its annotations.

  • xenium reads pre-1.3.0 (XOA < 1.3.0) and CSV-only bundles: when the parquet files and cells.zarr.zip are absent, the table, boundaries, and transcripts are read from the cells.csv, cell_boundaries.csv, nucleus_boundaries.csv and transcripts.csv outputs (.gz or plain), and the raster cell/nucleus labels are reconstructed by rasterizing the boundary polygons. The cell feature matrix falls back to a cell_feature_matrix/ MatrixMarket directory or cell_feature_matrix.tar.gz when cell_feature_matrix.h5 is missing.

Changed#

  • Adopted the current cookiecutter-scverse template: hatch-managed test environments, uv-based CI and documentation builds, mypy type checking of src and tests, biome/pyproject-fmt/zizmor pre-commit hooks, and Dependabot updates.

Removed#

  • Support for Python 3.11.