From cb546b7f36f1044deea1c4686cfe8406fe13f9ef Mon Sep 17 00:00:00 2001 From: LTLA Date: Sun, 15 Dec 2024 12:57:31 -0800 Subject: [PATCH] Updated CHANGELOG and README. --- CHANGELOG.md | 13 +++++++------ README.md | 4 ++-- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90322e9..0746432 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,14 +1,15 @@ # Changelog -## Version 0.5.0 +## Version 0.4.0 - Switch to using **pybind11** for the Python/C++ interface. - Update to the latest **singlepp** C++ library. - -## Version 0.4.0 - -- chore: Remove Python 3.8 (EOL). -- precommit: Replace docformatter with ruff's formatter. +- Store marker lists as lists of `StringList` objects in the metadata of the `BiocFrame` objects. +- Automatically remove `None` labels in the reference. +- Automatically remove duplicated feature names in the reference. +- Remove the `ref_names=` option in `train_integrated()` for simplicity. +- Remove support for auto-loading of references based on their names; users should extract references from **celldex** instead. +- Deprecate options to extract features/labels from a `SummarizedExperiment` based on the column name; users should explicitly pass the column contents to each function. ## Version 0.3.0 diff --git a/README.md b/README.md index 4cb5e6a..01b651a 100644 --- a/README.md +++ b/README.md @@ -11,13 +11,13 @@ [![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/) [![PyPI-Server](https://img.shields.io/pypi/v/singler.svg)](https://pypi.org/project/singler/) [![Monthly Downloads](https://static.pepy.tech/badge/singler/month)](https://pepy.tech/project/singler) -![Unit tests](https://github.com/BiocPy/singler/actions/workflows/pypi-test.yml/badge.svg) +![Unit tests](https://github.com/SingleR-inc/singler-py/actions/workflows/pypi-test.yml/badge.svg) # Tinder for single-cell data ## Overview -This package provides Python bindings to the [C++ implementation](https://github.com/SingleR-inc/singlepp) of the [SingleR algorithm](https://github.com/SingleR-inc/SingleR), +This package provides Python bindings to the [C++ implementation](https://github.com/SingleR-inc/singlepp) of the [SingleR method](https://github.com/SingleR-inc/SingleR), originally developed by [Aran et al. (2019)](https://www.nature.com/articles/s41590-018-0276-y). It is designed to annotate cell types by matching cells to known references based on their expression profiles. So kind of like Tinder, but for cells.