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.

0.9.0#

Changed#

  • GitHub actions files to match an updated scverse cookiecutter template

  • Breaking! Rename wherever possible: patient_representation -> patpy

  • Breaking! Rename tl.basic.py to tl.sample_representation

0.8.0#

Added#

  • persistence_evaluation method in patient_representation.tl.evaluation

  • Persistent homology file src/patient_representation/tl/persistence.py

0.7.2#

Changed#

  • Fix typo: patient_representations -> sample_representation in correlation functions

0.7.1#

Changed#

  • Fixed typo in GloScope causing empty distance matrix

0.7.0#

Added#

  • GloScope sample representation method (interface to R package via rpy2)

  • conda environment for gloscope

Changed#

  • GloScope R script now accepts n_workers argument

0.6.1#

Changed#

  • Use layers instead of obsm to store layer data in _move_layer_to_X method

0.6.0#

Changed#

  • Use cell_group_key instead of cell_type_key in MOFA and _get_pseudobulk

  • Use sample_representation instead of patient_representation in MOFA

0.5.0#

Deleted#

  • Remove mandatory filtering of cell types in and small samples in prepare_anndata method of SampleRepresentationMethod descendants

Changed#

  • Rerun example notebook with updated API

  • Add minor comments to the example notebook

0.4.0 – Synthetic data generation#

Added#

  • Functions to generate synthetic data simulating disease severity in src/datasets/synthetic.py

  • Synthetic data generation example notebook: docs/notebooks/synthetic_data_generation.ipynb

  • plot_embedding method for sample representations now accepts custom axes

0.3.0#

Sample representation refactoring:#

  • “cell type” is renamed to “cell group” everywhere to be more general

  • Some representation methods are renamed accordingly:

    • CellTypesComposition -> CellGroupComposition

    • CellTypePseudobulk -> GroupedPseudobulk

    • TotalPseudobulk -> Pseudobulk

  • patient_representation argument is renamed to sample_representation

  • “Patient representation” is now renamed to “Sample representation” eveywhere

  • The base class is now called SampleRepresentationMethod instead of PatientRepresentationMethod. This is important only for developers, users shouldn’t use it anyway

Deleted#

  • Not used SCellBow class

  • Example notebook in the documentation

0.2.0#

Added#

  • Warning about ongoing development in README

  • Function correlate_composition to the tools

  • Function correlate_cell_type_expression to the tools

  • Function correlation_volcano to the plotting

  • Patients trajectory example notebook

Changed#

  • Rename patient_representation to patpy

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