Add multi label capabilities for regression and add hyperparameter search

[ysims]

Some bug fixes for categorical data also included.
Multi label for classification also included.
Long files broken up.

[Copilot]

Pull request overview

This pull request adds significant functionality to EcoNetToolkit by introducing multi-label/multi-output prediction capabilities for both classification and regression tasks, along with a comprehensive hyperparameter tuning framework. The changes also include a major refactoring of the evaluation module and bug fixes for categorical data handling.

Key Changes

• Multi-output support: Models can now predict multiple target variables simultaneously, with automatic wrapping for models that don't natively support multi-output
• Hyperparameter tuning: New hyperopt.py module with GridSearchCV/RandomizedSearchCV support, grouped cross-validation, and proper train/val/test splits
• Evaluation refactoring: Split monolithic eval.py into modular components (metrics.py, plotting.py, feature_importance.py, reporting.py)

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
tests/test_models.py	Adds tests for multi-output model wrapping behavior
tests/test_integration.py	Integration tests for multi-output classification and regression pipelines
tests/test_hyperopt.py	Comprehensive test suite for hyperparameter tuning functionality
tests/test_eval.py	Tests for multi-output metrics computation and evaluation
tests/test_data.py	Tests for multi-label data loading and splitting
run.py	Main script updated to support tuning mode, CV mode, and regular mode
ecosci/trainer.py	Adds run_cv() and run_with_tuning() methods for new training modes
ecosci/models.py	Implements wrap_for_multioutput() for automatic multi-output wrapping
ecosci/hyperopt.py	New module providing hyperparameter tuning for all model types
ecosci/evaluation/*.py	Refactored evaluation code into modular structure
ecosci/data.py	Multi-label support, grouped splits, and CV fold preparation
ecosci/init.py	Updated imports to use new evaluation module
configs/*.yaml	Example configurations for multi-label prediction
README.md	Documentation updates for new features

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[Copilot]

Pull request overview

Copilot reviewed 27 out of 27 changed files in this pull request and generated 5 comments.

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[Copilot]

Pull request overview

Copilot reviewed 28 out of 28 changed files in this pull request and generated 3 comments.

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