Fix show overlay

[zoccoler]

This pull request introduces several updates to the biaplotter library, including a version bump, bug fixes, and enhancements to the toolbar functionality. The most significant changes involve the addition of a new show_overlay_button to the toolbar and improvements to the overlay visibility logic.

Version Update

• Updated the library version from 0.2.0 to 0.3.0 in src/biaplotter/__init__.py.

Bug Fixes

• Fixed a bug in color_indices_to_rgba where the method incorrectly used self._color_indices instead of the indices parameter.
• Updated the overlay_visible method to ensure the overlay is properly reset when toggled off by using a zeroed array for _color_indices.

Toolbar Enhancements

• Added a new show_overlay_button to the toolbar in CanvasWidget, allowing users to toggle the visibility of the plot overlay. This includes:
  • Adding the show_overlay_signal to emit visibility changes. [1] [2]
  • Modifying the _initialize_toolbar and _build_selection_toolbar_layout methods to include the new button. [1] [2] [3]
  • Replacing the old hide_color_overlay method with show_color_overlay to align with the new button functionality.

Code Refinements

• Updated imports in src/biaplotter/plotter.py to include CustomToolButton for the new toolbar button.

[codecov]

Codecov Report

Attention: Patch coverage is 87.50000% with 9 lines in your changes missing coverage. Please review.

Project coverage is 90.47%. Comparing base (233336f) to head (bb777c0).
Report is 20 commits behind head on main.

Files with missing lines	Patch %	Lines
src/biaplotter/artists.py	78.26%	5 Missing ⚠️
src/biaplotter/plotter.py	86.20%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #49      +/-   ##
==========================================
- Coverage   90.95%   90.47%   -0.49%     
==========================================
  Files           9        9              
  Lines         951      976      +25     
==========================================
+ Hits          865      883      +18     
- Misses         86       93       +7     

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[Copilot]

Pull Request Overview

This pull request fixes issues in the overlay visibility logic, adds a new toolbar button for toggling the plot overlay, and updates tests and documentation to reflect these changes. Key updates include:

• Adding a new signal and property (show_color_overlay) with corresponding toolbar button functionality.
• Correcting the bug in color_indices_to_rgba by using the passed indices parameter.
• Updating tests and docs to use the new overlay API and deprecating the old hide_color_overlay method.

Reviewed Changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
src/biaplotter/plotter.py	Added new toolbar button and associated signal/property updates.
src/biaplotter/artists_base.py	Minor formatting updates and import reordering.
src/biaplotter/artists.py	Fixed bug in color_indices_to_rgba and improved overlay logic.
src/biaplotter/_tests/test_widget.py	Updated tests to reflect overlay property usage.
src/biaplotter/_tests/test_artists.py	Adjusted tests to match updated API and formatting.
src/biaplotter/init.py	Bumped version from 0.2.0 to 0.3.0.
docs/plotter_api.md	Updated API documentation to include the new overlay properties.