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.

[0.2.7] 2025-11-04

Added automatic inference of the chemistry version from simpleaf quantification metadata.
Removed the default chemistry assumption — QCatch now requires either:
1. a successfully inferred chemistry from simpleaf’s metadata,
2. an explicitly specified chemistry via --chemistry (-c), or
3. a custom number of partitions provided via --n_partitions (-n).
If none of these are supplied, QCatch will stop and prompt the user to specify one.

Updated QCatch documentation and included an interactive demo page
Add tutorial scripts in the README.
Transitioned to uv for building and package management and relaxed dependencies for compatibility.

Adopted Cookiecutter-style structure based on the Scanpy project template.
Added a new flag to export summary metrics as a CSV file.
The HTML report now also includes a warning for low mapping rate.
Added unit tests and scripts to download test data
Updated the EmptyDrops step by removing the limitation on the number of candidate barcodes and making the FDR threshold dynamically adjustable based on the chemistry version.
Added source code snippets to the help text section of clustering plots