Clarify API documentation

[tovrstra]

These are some collected minor clarifications to the API documentation (docstrings and type hints).

[Copilot]

Pull request overview

This PR improves API documentation clarity by updating docstrings and type hints across the codebase. The changes focus on replacing plain text references with Sphinx cross-references (:class:, :func:), improving type annotations, and expanding documentation for better user understanding.

• Enhanced cross-references using Sphinx notation for better documentation navigation
• Added return type annotations to functions in cost.py
• Expanded documentation in estimate.py with detailed property descriptions
• Updated Sphinx configuration to include __call__ methods in generated documentation

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/stacie/utils.py	Reformatted example text and converted plain text references to Sphinx cross-references
src/stacie/spectrum.py	Updated docstring to use Sphinx cross-references and clarified return value usage
src/stacie/model.py	Converted NotImplementedError reference to Sphinx cross-reference
src/stacie/estimate.py	Significantly expanded documentation with detailed property lists and Sphinx cross-references
src/stacie/cutoff.py	Added type hint NDArray[float] to dictionary parameter and updated method reference
src/stacie/cost.py	Added return type annotations list[NDArray[float]] to three functions
docs/source/conf.py	Added __call__ to special-members in autodoc configuration
docs/clean.sh	Added jupyter_execute directory to cleanup script

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[gozdetoraman]

@tovrstra looks good to me, just some minor suggestions to docstrings.

[tovrstra]

@gozdetoraman Thanks for checking. To avoid repetition, I've mentioned elsewhere which are statistical estimates. I'll merge soon but further adjustments remain welcome.