- chore: Remove Python 3.8 (EOL)
- precommit: Replace docformatter with ruff's formatter
- 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.
- Fix issue coercing
SummarizedExperimentstoAnnDataobjects and vice-versa. - Handling coercions when matrices are delayed arrays or backed (for
AnnData). - Update sphinx configuration to run snippets in the documentation.
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
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.
- Initial release of SCE class
- Tests
- Documentation