Debug all tests

[siqizhu-uk]

Description

Debug all tests(slow and not slow).

• test_weighted_ensemble_explainer Failure
  • Issue: The test tests/plugins/ensemble/test_classifier.py::test_weighted_ensemble_explainer was failing due to a shape mismatch in the explain method's result from the KernelSHAPPlugin explainer for classification tasks.
  • Cause: In newer versions of shap (shap>=0.45.0), the shap_values implementation returns an ndarray with the shape (samples x features x output), which differs from the previous format (output x samples x features) for models with vector outputs.
  • Fix: Updated the output format of the explain method in src/autoprognosis/plugins/explainers/plugin_kernel_shap.py::KernelSHAPPlugin::explain to align with the new behavior for classification tasks.
• test_surv_app Failure
  • Issue: The test tests/apps/test_survival_app.py::test_surv_app was failing due to a missing required parameter.
  • Fix: Added the "extras_cbk" parameter to NewRiskEstimationAppProto, setting its default value to None.

@DrShushen changes:

• To fix pandas 1 --> 2 related AttributeError: 'DataFrame' object has no attribute 'append', in src/autoprognosis/plugins/explainers/plugin_risk_effect_size.py::RiskEffectSizePlugin._get_population_shifts a call to <dataframe>.append was replaced with pd.concat(), which should make this pandas 1 and 2 compatible.
• To fix tests/plugins/uncertainty/test_cohort_explainer.py::test_fit/test_predict_classifier failing due to not getting any important features from "risk_effect_size" explainer, effect_size: float parameter added to CohortExplainerPlugin and set to a value lower value in the test.
• Update actions/setup-python@v1 to v5 in GitHub workflows to avoid python setup errors.
• Remove PR triggers for test_R workflow, as this is relatively low priority.
• Add a score difference tolerance in test_surv_search test, to make the test more stable.

Affected Dependencies

• force shap to be >= 0.45.0 to avoid shap_values return shape mismatch as mentioned in Description.

How has this been tested?

• all tests in the tests directory

Checklist

• I have followed the Contribution Guidelines and Code of Conduct
• I have commented my code following the van der Schaar Lab Styleguide
• I have labelled this PR with the relevant Type labels
• My changes are covered by tests

[DrShushen]

@siqizhu-uk - I've triggered the default PR test suite, let us see if they all run successfully

[DrShushen]

@siqizhu-uk great work, thank you! Will aim to fix the issues causing current GH workflow failures in the next PR