Changelog

Version 0.5.6

  • Check if the column names of the alternative experiments match with the column names of the main experiment. This is the equivalent to the withDimnames parameter in the R implementation.

    • On getters of alternative experiments, if with_dim_names is True, column names of the alternative experiment are replaced with the column names of the main experiment.

    • On setters of alternative experiments, if with_dim_names is True, column names of the alternative experiment are checked with the column names of the main experiment and an Exception is raised if they do not match.

Version 0.5.1 - 0.5.5

  • Add wrapper class methods to combine experiments by rows or columns.

  • Expand function names for readability, still backwards compatible with the older function and method names.

  • Add getters and setters to replace a specific alternative experiment or reduced dimension.

  • Fixed an issue with numpy arrays as slice arguments. Code now uses Biocutils’s subset functions to perform these operations.

Version 0.5.0

  • chore: Remove Python 3.8 (EOL)

  • precommit: Replace docformatter with ruff’s formatter

Version 0.4.7

  • Fix package version issues to support Python<=3.9. Mostly related to how anndata dependencies are versioned in the MuData package discussed here.

  • The package now enforces the versions of mudata, anndata and numpy that are compatible with each other.

Version 0.4.2 - 0.4.6

  • Fix issue coercing SummarizedExperiments to AnnData objects and vice-versa.

  • Handling coercions when matrices are delayed arrays or backed (for AnnData).

  • Update sphinx configuration to run snippets in the documentation.

Version 0.4.0 to 0.4.1

This is a complete rewrite of the package, following the functional paradigm from our developer notes.

  • Migrates package to the newly udpated SE/RSE classes.

  • Implement combine generics on SCE.

  • Reduce dependency on a number of external packages.

  • Update docstrings, tests

Version 0.3.0

This release migrates the package to a more palatable Google’s Python style guide. A major modification to the package is with casing, all camelCase properties, methods, functions and parameters are now snake_case.

With respect to the classes,SingleCellExperiment now extends SummarizedExperiment. Typehints have been updated to reflect these changes.

In addition, docstrings and documentation has been updated to use sphinx’s features of linking objects to their types. Sphinx now also documents private and special dunder methods (e.g. __getitem__, __copy__ etc). Intersphinx has been updated to link to references from dependent packages.

Configuration for flake8, ruff and black has been added to pyproject.toml and setup.cfg to be less annoying.

Finally, pyscaffold has been updated to use “myst-parser” as the markdown compiler instead of recommonmark. As part of the pyscaffold setup, one may use pre-commits to run some of the routine tasks of linting and formatting before every commit. While this is sometimes annoying and can be ignored with --no-verify, it brings some consistency to the code base.

Version 0.1

  • Initial release of SCE class

  • Tests

  • Documentation