PartSeg chore: Drop python 3.8

Python 3.8 reached EOL so it is time to drop it.

Summary by Sourcery

Drop support for Python 3.8 across the codebase and CI configuration. Update type annotations to use modern Python syntax and refactor code for improved readability and consistency.

Enhancements:

Update type annotations to use Python 3.9+ syntax, replacing typing.List and typing.Dict with list and dict.
Refactor test cases to use updated type annotations and improve readability.
Refactor code to use context managers with parentheses for better readability and consistency.

CI:

Remove Python 3.8 from the CI configuration as it has reached end-of-life.

Summary by CodeRabbit

New Features
- Updated Python version support for testing workflows to include versions 3.9 to 3.12.
- Enhanced type hinting across various components for improved code clarity and modern practices.
Bug Fixes
- Corrected inconsistencies in method signatures and type annotations throughout the codebase.
Documentation
- Improved docstring formatting for consistency and clarity.
Refactor
- Refactored methods and classes to utilize built-in types over typing module constructs for better readability.

Oct 09 '24 12:10 Czaki

Reviewer's Guide by Sourcery

This pull request drops support for Python 3.8 and updates the codebase to use more modern Python syntax, particularly with type annotations. The changes primarily involve updating type hints to use the new syntax introduced in Python 3.9+, such as using list[int] instead of List[int]. Additionally, some minor code style improvements and syntax updates have been made throughout the project.

Class diagram for updated type annotations

classDiagram
    class ComponentsInfo {
        np.ndarray roi_components
        np.ndarray mask_components
        dict[int, list[int]] components_translation
        bool has_components()
    }

    class MeasurementResult {
        ComponentsInfo components_info
        OrderedDict _data_dict
        dict[str, str] _units_dict
        dict[str, tuple[PerComponent, AreaType]] _type_dict
        void set_filename(str path_fo_file)
        tuple[bool, bool] get_component_info(bool all_components)
        list[str] get_labels(bool expand, bool all_components)
        list[str] get_units(bool all_components)
        list[list[MeasurementValueType]] get_separated(bool all_components)
    }

    class MaskProjectTuple {
        Union[Image, str, None] image
        Optional[np.ndarray] mask
        ROIInfo roi_info
        dict[str, AdditionalLayerDescription] additional_layers
        list[int] selected_components
        dict[int, Optional[ROIExtractionProfile]] roi_extraction_parameters
        list[HistoryElement] history
        str errors
        Optional[list[float]] spacing
        Optional[np.ndarray] points
        int frame_thickness
    }

    class ImageInfo {
        Image image
        list[NapariImage] layers
        list[tuple[NoiseFilterType, float]] filter_info
        Optional[Labels] mask
        Optional[np.ndarray] mask_array
        Optional[Labels] roi
        int roi_count
        Optional[Labels] highlight
        bool coords_in(Union[list[int], np.ndarray] coords)
        np.ndarray translated_coords(Union[list[int], np.ndarray] coords)
    }

File-Level Changes

Change	Details	Files
Drop support for Python 3.8	Remove Python 3.8 from CI/CD workflows Update minimum Python version in configuration files	`.github/workflows/tests.yml` `azure-pipelines.yml` `.pre-commit-config.yaml`
Update type annotations to use Python 3.9+ syntax	Replace `List`, `Dict`, `Tuple`, and `Set` with their lowercase equivalents Update `typing.Union` to use the `	`operator where applicable</li><li>Remove explicit`typing` imports where possible
Update syntax for context managers	Use parenthesized context managers for multiple context managers	`package/tests/test_PartSeg/test_channel_control.py` `package/PartSegImage/image_reader.py` `package/PartSeg/_launcher/check_version.py`

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Oct 09 '24 12:10 sourcery-ai[bot]

Walkthrough

This pull request includes modifications to the workflow files for testing napari widgets, updating Python version compatibility, and adjusting type annotations in several files. The workflows now exclude Python 3.8, focusing on versions 3.9 to 3.12. The napari versions tested have also been updated. Additionally, type annotations have been modernized across various classes and functions, reflecting a shift from the typing module to built-in types. The overall structure of the workflows and modules remains intact while implementing these changes.

Changes

File Path	Change Summary
`.github/workflows/test_napari_widgets.yml`	Updated `napari` versions in `test-latest-release` and `test-pyqt5` jobs, modified trigger branches for the workflow.
`.github/workflows/tests.yml`	Excluded Python 3.8 from `base-test`, `base-test-main`, and updated Python versions for other jobs.
`package/PartSeg/plugins/napari_widgets/lables_control.py`	Updated parameter type from `List` to `list` in constructors of `NapariLabelShow` and `NapariLabelChoose`.
`package/PartSegCore/register.py`	Updated `register` function's `target` parameter type from `Type[AlgorithmDescribeBase]` to `type[AlgorithmDescribeBase]`.
Various files in `package/PartSeg` and `package/PartSegCore`	Updated type hints to use built-in types instead of `typing` across multiple classes and functions.

Possibly related PRs

#1148: The changes in this PR involve updates to the napari version in the workflow configuration for testing, which directly relates to the updates made in the main PR regarding the napari parameter in the .github/workflows/test_napari_widgets.yml file.
#1192: This PR includes modifications to the napari_image_view.py file that enhance compatibility with different versions of napari, which aligns with the main PR's focus on updating napari versions in the testing workflows.
#1203: The changes in this PR to the .github/workflows/tests.yml file include enhancements to the testing framework, which may relate to the overall structure and configuration updates seen in the main PR's workflow files.

Suggested labels

skip check PR title

🐇 In the fields of code we play,
Python's new versions lead the way.
Dependencies fresh, we hop along,
Modernizing our project, making it strong!
With every change, our code takes flight,
A brighter future, oh what a sight! 🌟

📜 Recent review details

Configuration used: CodeRabbit UI Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 4e7e31fb4378aedef382cfc3b49643663289b983 and c06e15d0190e31a797fef0bc8f02dc5e2684f56c.

📒 Files selected for processing (4)

.github/workflows/test_napari_widgets.yml (2 hunks)
.github/workflows/tests.yml (4 hunks)
package/PartSeg/plugins/napari_widgets/lables_control.py (4 hunks)
package/PartSegCore/register.py (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (4)

.github/workflows/test_napari_widgets.yml
.github/workflows/tests.yml
package/PartSeg/plugins/napari_widgets/lables_control.py
package/PartSegCore/register.py

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Oct 09 '24 12:10 coderabbitai[bot]

Codecov Report

Attention: Patch coverage is 99.70674% with 1 line in your changes missing coverage. Please review.

Project coverage is 93.12%. Comparing base (24978a5) to head (c06e15d). Report is 24 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/PartSegCore/algorithm_describe_base.py	92.85%	1 Missing :warning:

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1206      +/-   ##
===========================================
- Coverage    93.13%   93.12%   -0.01%     
===========================================
  Files          210      210              
  Lines        33149    33149              
===========================================
- Hits         30873    30870       -3     
- Misses        2276     2279       +3

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.