#336 - Introduce Annotation class

[reckart]

What's in the PR

• Introduced Annotation class with default begin/end 0
• Update reference data accordingly
• Fixed several issues with sorting/ordering annotations

How to test manually

• No specific test procedure

Automatic testing

• PR includes unit tests

Documentation

• PR updates documentation

[Copilot]

Pull Request Overview

This PR introduces a concrete Annotation base class with default begin=0 and end=0 attributes to provide a stable typing foundation for annotation instances. This addresses sorting and serialization issues with runtime-generated annotation types.

• Introduced Annotation class that all annotation types inherit from
• Updated XMI test fixtures to include default begin="0" end="0" attributes for annotation-like types
• Refactored sorting logic to use stable key-based comparisons instead of comparator functions

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
cassis/typesystem.py	Added Annotation base class and updated type generation to inherit from it for annotation types
cassis/cas.py	Updated type hints to use Annotation instead of FeatureStructure where appropriate; improved duck-typing in _sort_func
cassis/xmi.py	Fixed offset conversion logic with defensive checks and improved comments
cassis/util.py	Replaced comparator-based sorting with stable key functions; refactored hash computation to return deterministic string representations
tests/test_files/xmi/*.xmi	Added begin="0" end="0" attributes to annotation instances in test fixtures
tests/test_ducktyping.py	New test file verifying runtime-generated annotations work correctly
tests/test_cas.py	Added tests for non-annotation feature structures and runtime-generated annotations

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[Copilot]

Pull Request Overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 6 comments.

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[Copilot]

Pull request overview

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

Comments suppressed due to low confidence (1)

cassis/cas.py:585

• select_all() is typed as List[Annotation], but the view index now contains arbitrary FeatureStructure instances (see add() adding any FS, and tests that add/select a non-annotation). The current return annotation is therefore incorrect and will mislead type-checkers/users; it also increases the risk that callers assume begin/end exist. Change the return type to List[FeatureStructure] (and adjust the docstring accordingly), or split into separate APIs for annotations vs all feature structures.

    def select_all(self) -> List[Annotation]:
        """Finds all feature structures in this Cas

        Returns:
            A list of all annotations in this Cas

        """
        return self._current_view.get_all_annotations()

[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

cassis/cas.py:585

• select_all() is annotated as returning List[Annotation], but it actually returns View.get_all_annotations(), which contains any FeatureStructure added to the view (including non-annotation FS). This makes the public API typing incorrect and also contradicts the docstring which still says it returns annotations. Update the return type to List[FeatureStructure] (and adjust the docstring wording accordingly).

    def select_all(self) -> List[Annotation]:
        """Finds all feature structures in this Cas

        Returns:
            A list of all annotations in this Cas

        """
        return self._current_view.get_all_annotations()

[Copilot]

Pull request overview

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Comments suppressed due to low confidence (1)

cassis/cas.py:585

• select_all() is documented as returning “all feature structures”, but the signature returns List[Annotation] and the docstring still says “A list of all annotations”. With non-annotation FS now being indexed/returned (see new test), this should be List[FeatureStructure] (or a new dedicated method for annotation-only selection) and the docstring should be updated to reflect the actual behavior.

    def select_all(self) -> List[Annotation]:
        """Finds all feature structures in this Cas

        Returns:
            A list of all annotations in this Cas

        """
        return self._current_view.get_all_annotations()

[Copilot]

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 3 comments.

[Copilot]

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.

[Copilot]

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.