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.

0.1.6#

Fixed#

  • deprecated_arg now indents the version-deprecated directive correctly for parameters without a description (previously it was rendered as a separate parameter).

0.1.5#

Added#

  • An arg_alias decorator that simplifies handling of function arguments taking on one of a fixed set of values, where each value may have multiple aliases (e.g. the axis argument of many scverse functions).

0.1.4#

Added#

  • The datasets module can now download files from fallback URLs if a download from the primary URL fails.

0.1.3#

Fixed#

  • The sphinx extension now handles module aliases correctly.

0.1.2#

Added#

  • The sphinx extension ships templates for sphinx.ext.autosummary that were previously part of cookiecutter-scverse.

0.1.1#

Fixed#

  • The sphinx extension no longer adds parameter types to override and reset docstrings if the users have sphinx-autodoc-typehints enabled or autodoc_typehints = 'description' | 'both' set.

0.1.0#

Fixed#

  • Allow additional methods on Settings subclasses.

  • Allow the Sphinx extension to go anywhere in the conf.py extension list.

  • anndata isn’t a core dependency anymore again.

0.0.9#

Added#

  • A Sphinx extension to take care of documentation. This moves docstring processing from import time to documentation building time.

  • A reusable datasets subpackage (behind the datasets extra): typed DatasetEntry/ FileEntry + parse_registry (YAML), a thin pooch-based fetch (SHA-256 verification, retries, archive processors), and a pluggable type -> loader registry (register_loader) so packages can share dataset-download infrastructure. Ships built-in anndata and spatialdata loaders (the latter behind the spatialdata extra); other types are consumer-registered.

  • anndata is now a core dependency.

Changed#

  • Docstrings are no longer generated or modified at import time.

Fixed#

  • Marking a setting as Field(deprecated=...) will show a deprecation notice in the documentaiton.

0.0.8#

Fixed#

  • The Settings class can now handle .env files containing unrelated environment variables.

0.0.7#

Added#

  • A reset method for Settings to reset settings to their default values.

0.0.6#

Added#

  • A deprecated_arg decorator to deprecate function arguments.

0.0.5#

Added#

  • The docstring_style used by scanpy, "scverse", which looks like "numpy" but with no parameter types in the docstring.

Changed#

  • The Settings class and the make_register_namespace_decorator function now require passing a docstring_style argument.

Fixed#

  • The Settings docstrings longer have :value: PydanticUndefined for fields with no defaults.

  • Remove the “default” text from override parameters so we don’t imply that override resets all settings the user isn’t overriding.

0.0.4#

Added#

  • A Settings base class that packages can inherit from for their settings. This is based on Pydantic Settings and provides validation for settings values as well as loading settings from environment variables and .env files.

0.0.3#

Added#

  • A deprecated decorator wrapping warnings.deprecated that additionally modifies the docstring to include a deprecation notice.

0.0.2#

Removed#

  • The Pandas utility functions

0.0.1#

  • Initial release