Improved plotting, checkpointing and results collection

[gperdrizet]

No description provided.

[Copilot]

Pull request overview

This PR implements significant improvements to plotting, checkpointing, and results collection for the hill climbing optimizer, bumping the version from 1.0.1 to 1.0.2. The changes enhance user experience by automating progress visualization and checkpointing while introducing a more intuitive fractional perturbation parameter.

Key Changes

• Automated plotting and checkpointing: Replaced time-based intervals with batch-based triggers (after each exchange_interval steps), simplifying configuration by removing plot_progress and save_interval parameters in favor of show_progress boolean
• Improved step_spread parameter: Changed from absolute values to fractional (default 0.01 = 1% of data range) with automatic scaling based on input data bounds, making the parameter more intuitive and data-scale independent
• Enhanced plotting features: Added temperature exchange visualization, batch number display, initial data snapshots, and better layout with 2-row structure showing progress and data snapshots

Reviewed changes

Copilot reviewed 15 out of 16 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
pyproject.toml	Version bump to 1.0.2
hill_climber/init.py	Version bump to 1.0.2
docs/source/conf.py	Version bump to 1.0.2
CITATION.cff	Version bump to 1.0.2
tests/test_integration.py	Added show_progress=False to all test cases to disable plotting during automated tests
tests/test_hill_climber.py	Added show_progress=False to all test cases to disable plotting during automated tests
test_parallel.py	Removed obsolete test script (entire file deleted)
notebooks/05-feature_interactions.ipynb	Removed deprecated plot_progress parameter and reset execution count
notebooks/02-pearson_spearman.ipynb	Removed deprecated plot_progress parameter and reset execution count
hill_climber/optimizer_state.py	Added temperature_history tracking and record_temperature_change() method
hill_climber/optimizer.py	Major refactoring: replaced time-based checkpointing/plotting with batch-based, added verbose parameter, implemented fractional step_spread with backward compatibility, swapped temperature exchange logic, added reset_temperatures parameter to load_checkpoint()
hill_climber/plotting_functions.py	Enhanced plot_results() with exchange_interval parameter, added initial data snapshots, temperature exchange markers, and 2-row layout for progress and snapshots
docs/source/user_guide.rst	Updated documentation for new step_spread semantics, show_progress parameter, and batch-based checkpointing
docs/source/quickstart.rst	Updated examples to remove deprecated plot_progress parameter
docs/source/advanced.rst	Expanded checkpointing documentation with reset_temperatures feature and updated perturbation strategy examples

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[Copilot]

Multiple commented-out lines for tick parameters and locator params (lines 446-448, 459, 469-470, 530-532, 552-554). These should either be removed if they're not needed, or uncommented if they are. Leaving commented code in production reduces code maintainability.

Suggested change

	# ax.tick_params(axis='both', which='major', labelsize=7)
	# ax.locator_params(axis='x', nbins=4)
	# ax.locator_params(axis='y', nbins=4)

[Copilot]

Documentation inconsistency: The default value for exchange_interval is documented as 100 steps, but the actual default in the code (optimizer.py line 72) is 1000. Update the documentation to reflect the correct default value of 1000.

Suggested change

	The batch size is determined by ``exchange_interval`` (default: 100 steps).
	The batch size is determined by ``exchange_interval`` (default: 1000 steps).