diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 09a1fa2..63b9d6c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -14,7 +14,7 @@ jobs: strategy: matrix: - python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] + python-version: ["3.11", "3.12", "3.13", "3.14"] fail-fast: true steps: diff --git a/README.md b/README.md index 40e2516..4443554 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ panelsplit is a Python package designed to facilitate time series cross-validati ## Installation -panelsplit is tested for compatibility with python versions >= 3.10. You can install panelsplit using pip: +panelsplit is tested for compatibility with python versions >= 3.11. You can install panelsplit using pip: ```bash pip install panelsplit diff --git a/panelsplit/metrics.py b/panelsplit/metrics.py index 5a1ec97..cc61b86 100644 --- a/panelsplit/metrics.py +++ b/panelsplit/metrics.py @@ -1,37 +1,42 @@ -from .utils.validation import _safe_indexing +""" +Metrics that are equivalent their sklearn counterparts, except for the fact that they work with SequentialCVPipeline. +""" + +# Standard library +import warnings from inspect import signature from collections.abc import Iterable from functools import partial -from sklearn.metrics._scorer import _MultimetricScorer -from sklearn.utils._param_validation import ( - validate_params, -) -from sklearn.metrics._scorer import _PassthroughScorer, _get_response_method_name from copy import deepcopy -from sklearn.utils.validation import _check_response_method -import warnings -from sklearn.base import is_regressor -from panelsplit.utils._response import _get_response_values -from sklearn.utils.metadata_routing import ( - _MetadataRequester, - _raise_for_params, - _routing_enabled, - MetadataRequest, -) -from .utils.typing import EstimatorLike, ArrayLike -from numpy.typing import NDArray from typing import Callable, Optional, List, Union, Any, Dict + +# Third-party / typing from typing_extensions import Self +from numpy.typing import NDArray -# all the error scores: +# Local package utilities +from .utils.validation import _safe_indexing +from .utils.typing import EstimatorLike, ArrayLike +from panelsplit.utils._response import _get_response_values + +# sklearn public metrics (single consolidated import) from sklearn.metrics import ( accuracy_score, + adjusted_mutual_info_score, + adjusted_rand_score, average_precision_score, balanced_accuracy_score, brier_score_loss, class_likelihood_ratios, + completeness_score, d2_absolute_error_score, + d2_brier_score, + d2_log_loss_score, explained_variance_score, + f1_score, + fowlkes_mallows_score, + jaccard_score, + homogeneity_score, log_loss, matthews_corrcoef, max_error, @@ -42,24 +47,37 @@ mean_squared_error, mean_squared_log_error, median_absolute_error, + mutual_info_score, + normalized_mutual_info_score, + precision_score, + rand_score, r2_score, + recall_score, roc_auc_score, root_mean_squared_error, root_mean_squared_log_error, top_k_accuracy_score, -) -from sklearn.metrics.cluster import ( - adjusted_mutual_info_score, - adjusted_rand_score, - completeness_score, - fowlkes_mallows_score, - homogeneity_score, - mutual_info_score, - normalized_mutual_info_score, - rand_score, v_measure_score, ) +# sklearn internals / utilities (note: private APIs) +from sklearn.metrics._scorer import ( + _MultimetricScorer, + _PassthroughScorer, + _get_response_method_name, +) +from sklearn.utils._param_validation import validate_params +from sklearn.utils.validation import _check_response_method +from sklearn.base import is_regressor + +# metadata routing utilities (used by some sklearn internals) +from sklearn.utils.metadata_routing import ( + _MetadataRequester, + _raise_for_params, + _routing_enabled, + MetadataRequest, +) + def _get_idx_from_last_cv(estimator: EstimatorLike) -> Union[None, List[NDArray]]: """ @@ -88,14 +106,63 @@ def make_SequentialCV_scorer( greater_is_better: bool = True, **kwargs: Any, ) -> Callable[..., float]: + """ + Make a SequentialCVPipeline-compatible scorer from a performance metric. + + A scorer is a wrapper around an arbitrary metric or loss function that is called + with the signature `scorer(estimator, X, y_true, **kwargs)`. + + The parameter `response_method` allows to specify which method of the estimator + should be used to feed the scoring/loss function. + + Parameters + ---------- + score_func : callable + Score function (or loss function) with signature + ``score_func(y, y_pred, **kwargs)``. + + response_method : {"predict_proba", "decision_function", "predict"} or \ + list/tuple of such str, default="predict" + + Specifies the response method to use get prediction from an estimator + (i.e. :term:`predict_proba`, :term:`decision_function` or + :term:`predict`). Possible choices are: + + - if `str`, it corresponds to the name to the method to return; + - if a list or tuple of `str`, it provides the method names in order of + preference. The method returned corresponds to the first method in + the list and which is implemented by `estimator`. + + greater_is_better : bool, default=True + Whether `score_func` is a score function (default), meaning high is + good, or a loss function, meaning low is good. In the latter case, the + scorer object will sign-flip the outcome of the `score_func`. + + **kwargs : additional arguments + Additional parameters to be passed to `score_func`. + + Returns + ------- + Callable + Callable object that returns a scalar score; greater is better. + + Examples + -------- + >>> from panelsplit.metrics import make_SequentialCV_scorer + >>> from sklearn.metrics import brier_score_loss + >>> brier_loss_scorer= make_SequentialCV_scorer(brier_score_loss, response_method='predict_proba', greater_is_better=False) + + >>> from panelsplit.pipeline import SequentialCVPipeline + >>> from sklearn.ensemble import RandomForestClassifier + >>> from sklearn.datasets import load_iris + >>> X, y = load_iris(return_X_y=True) + >>> p = SequentialCVPipeline(steps = [('rf', RandomForestClassifier())], cv_steps = [None]) + >>> p.fit(X, y) + >>> brier_loss_scorer(p, X, y) + """ sign = 1 if greater_is_better else -1 if response_method is None: - warnings.warn( - "response_method=None is deprecated in version 1.6 and will be removed " - "in version 1.8. Leave it to its default value to avoid this warning.", - FutureWarning, - ) response_method = "predict" elif response_method == "default": response_method = "predict" @@ -158,7 +225,6 @@ def __init__( self._sign = sign self._kwargs = kwargs self._response_method = response_method - # TODO (1.8): remove in 1.8 (scoring="max_error" has been deprecated in 1.6) self._deprecation_msg = None def _get_pos_label(self) -> Optional[Any]: @@ -170,7 +236,6 @@ def _get_pos_label(self) -> Optional[Any]: return None def _accept_sample_weight(self) -> bool: - # TODO(slep006): remove when metadata routing is the only way return "sample_weight" in signature(self._score_func).parameters def __repr__(self) -> str: @@ -217,7 +282,6 @@ def __call__( float Score function applied to prediction of estimator on X. """ - # TODO (1.8): remove in 1.8 (scoring="max_error" has been deprecated in 1.6) if self._deprecation_msg is not None: warnings.warn( self._deprecation_msg, category=DeprecationWarning, stacklevel=2 @@ -314,6 +378,7 @@ def _score( X, pos_label=pos_label, ) + # make lookup dict for fast matching pred_dict = dict(zip(idx, y_pred)) @@ -340,6 +405,36 @@ def _score( prefer_skip_nested_validation=True, ) def get_scorer(scoring: Union[str, Callable]) -> Any: + """ + Get a scorer from string. + + `sklearn.metrics.get_scorer_names` can be used to retrieve the names + of all available scorers. + + Parameters + ---------- + scoring : str, callable or None + Scoring method as string. If callable it is returned as is. + If None, returns None. + + Returns + ------- + callable + The scorer. + + Notes + ----- + When passed a string, this function always returns a copy of the scorer + object. Calling `get_scorer` twice for the same scorer results in two + separate scorer objects. + + Examples + -------- + >>> from panelsplit.metrics import get_scorer + >>> accuracy = get_scorer("accuracy") + >>> accuracy(classifier, X, y) + """ + if isinstance(scoring, str): try: scorer = deepcopy(_SCORERS[scoring]) @@ -489,7 +584,11 @@ def _check_multimetric_scoring(estimator: EstimatorLike, scoring: Iterable) -> A neg_mean_gamma_deviance_scorer = make_SequentialCV_scorer( mean_gamma_deviance, greater_is_better=False ) +# D^2 scorers (fraction of explained Brier / log-loss) d2_absolute_error_scorer = make_SequentialCV_scorer(d2_absolute_error_score) +d2_brier_scorer = make_SequentialCV_scorer(d2_brier_score) +d2_log_loss_scorer = make_SequentialCV_scorer(d2_log_loss_score) + # Standard Classification Scores accuracy_scorer = make_SequentialCV_scorer(accuracy_score) @@ -583,6 +682,8 @@ def negative_likelihood_ratio(y_true: NDArray, y_pred: NDArray) -> float: neg_mean_poisson_deviance=neg_mean_poisson_deviance_scorer, neg_mean_gamma_deviance=neg_mean_gamma_deviance_scorer, d2_absolute_error_score=d2_absolute_error_scorer, + d2_brier_score=d2_brier_scorer, + d2_log_loss_score=d2_log_loss_scorer, accuracy=accuracy_scorer, top_k_accuracy=top_k_accuracy_scorer, roc_auc=roc_auc_scorer, @@ -607,3 +708,17 @@ def negative_likelihood_ratio(y_true: NDArray, y_pred: NDArray) -> float: normalized_mutual_info_score=normalized_mutual_info_scorer, fowlkes_mallows_score=fowlkes_mallows_scorer, ) + + +for name, metric in [ + ("precision", precision_score), + ("recall", recall_score), + ("f1", f1_score), + ("jaccard", jaccard_score), +]: + _SCORERS[name] = make_SequentialCV_scorer(metric, average="binary") + for average in ["macro", "micro", "samples", "weighted"]: + qualified_name = "{0}_{1}".format(name, average) + _SCORERS[qualified_name] = make_SequentialCV_scorer( + metric, pos_label=None, average=average + ) diff --git a/panelsplit/model_selection/model_selection.py b/panelsplit/model_selection/model_selection.py index f064826..2818035 100644 --- a/panelsplit/model_selection/model_selection.py +++ b/panelsplit/model_selection/model_selection.py @@ -970,8 +970,8 @@ class GridSearch(BaseSearch): If `scoring` represents a single score, one can use: - - a single string (see :ref:`scoring_string_names`); - - a callable (see :ref:`scoring_callable`) that returns a single value; + - a single string (see https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-string-names); + - a callable (see https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-callable) that returns a single value; - `None`, the `estimator`'s default evaluation criterion is used. If `scoring` represents multiple scores, one can use: @@ -981,7 +981,7 @@ class GridSearch(BaseSearch): names and the values are the metric scores; - a dictionary with metric names as keys and callables as values. - See :ref:`multimetric_grid_search` for an example. + See https://scikit-learn.org/stable/modules/grid_search.html#multimetric-grid-search for an example. n_jobs : int, default=None Number of jobs to run in parallel. @@ -1057,6 +1057,19 @@ class GridSearch(BaseSearch): A dict with keys as column headers and values as columns, that can be imported into a pandas ``DataFrame``. + For an example of visualization and interpretation of GridSearch results, + see https://scikit-learn.org/stable/auto_examples/model_selection/plot_grid_search_stats.html#sphx-glr-auto-examples-model-selection-plot-grid-search-stats-py. + + NOTE + + The key ``'params'`` is used to store a list of parameter + settings dicts for all the parameter candidates. + + For multi-metric evaluation, the scores for all the scorers are + available in the ``cv_results_`` dict at the keys ending with that + scorer's name (``'_'``) instead of ``'_score'`` shown + above. ('split0_test_precision', 'mean_train_precision' etc.) + best_estimator_ : estimator Estimator that was chosen by the search, i.e. estimator which gave highest score (or smallest loss if specified) @@ -1157,11 +1170,11 @@ class GridSearch(BaseSearch): GridSearch(estimator=SVC(), param_grid={'C': [1, 10], 'kernel': ('linear', 'rbf')}) >>> sorted(clf.cv_results_.keys()) - ['mean_fit_time', 'mean_score_time', 'mean_test_score',... + ['mean_test_score',... 'param_C', 'param_kernel', 'params',... 'rank_test_score', 'split0_test_score',... 'split2_test_score', ... - 'std_fit_time', 'std_score_time', 'std_test_score'] + 'std_test_score'] """ _parameter_constraints: dict = { @@ -1251,8 +1264,8 @@ class RandomizedSearch(BaseSearch): If `scoring` represents a single score, one can use: - - a single string (see :ref:`scoring_string_names`); - - a callable (see :ref:`scoring_callable`) that returns a single value; + - a single string (see https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-string-names); + - a callable (see https://scikit-learn.org/stable/modules/model_evaluation.html#scoring-callable) that returns a single value; - `None`, the `estimator`'s default evaluation criterion is used. If `scoring` represents multiple scores, one can use: @@ -1262,7 +1275,7 @@ class RandomizedSearch(BaseSearch): names and the values are the metric scores; - a dictionary with metric names as keys and callables as values. - See :ref:`multimetric_grid_search` for an example. + See https://scikit-learn.org/stable/modules/grid_search.html#multimetric-grid-search for an example. If None, the estimator's score method is used. @@ -1347,6 +1360,19 @@ class RandomizedSearch(BaseSearch): A dict with keys as column headers and values as columns, that can be imported into a pandas ``DataFrame``. + For an example of analysing ``cv_results_``, + see https://scikit-learn.org/stable/auto_examples/model_selection/plot_grid_search_stats.html#sphx-glr-auto-examples-model-selection-plot-grid-search-stats-py. + + NOTE + + The key ``'params'`` is used to store a list of parameter + settings dicts for all the parameter candidates. + + For multi-metric evaluation, the scores for all the scorers are + available in the ``cv_results_`` dict at the keys ending with that + scorer's name (``'_'``) instead of ``'_score'`` shown + above. ('split0_test_precision', 'mean_train_precision' etc.) + best_estimator_ : estimator Estimator that was chosen by the search, i.e. estimator which gave highest score (or smallest loss if specified) diff --git a/panelsplit/pipeline.py b/panelsplit/pipeline.py index a11a483..5e0e1b5 100644 --- a/panelsplit/pipeline.py +++ b/panelsplit/pipeline.py @@ -204,9 +204,9 @@ def _method( for step_idx, (name, transformer) in enumerate(self.steps, start=1): t_start = time.time() - not_final_step = total_steps != step_idx + is_final = step_idx == total_steps # Use 'transform' for intermediate steps and the provided method for the final step. - method = "transform" if not_final_step else method_name + method = "transform" if not is_final else method_name if fit: # Initialize fitted_steps_ if not already done (for dynamic methods) if not hasattr(self, "fitted_steps_"): @@ -242,7 +242,8 @@ def _method( fitted_model, method, current_output, - y if not not_final_step else None, + y if is_final else None, + use_indices=(self.include_indices and is_final), ) _log_message( @@ -538,6 +539,7 @@ def _apply_method_to_indices( List List of predictions or transformed values. """ + X_subset = self._subset(X, indices) y_subset = None if y is None else self._subset(y, indices) if isinstance(X_subset, np.ndarray) and X_subset.ndim == 1: @@ -550,7 +552,7 @@ def _apply_method_to_indices( output = _call_method_with_correct_args(model, method_name, X_subset, y_subset) return output - def _fit_method_step( # type: ignore + def _fit_method_step( # ignore : type self, transformer: EstimatorLike, X: ArrayLike, @@ -558,7 +560,8 @@ def _fit_method_step( # type: ignore cv: Optional[Union[PanelSplit, Iterable]] = None, return_output: bool = True, method: str = "transform", - ): + use_indices: bool = False, + ) -> Tuple: """ Fit one pipeline step and optionally transform the data. @@ -593,7 +596,7 @@ def _fit_method_step( # type: ignore fitted = (None, None, model) if return_output: # return_group is not considered here as cv == None. - if self.include_indices: + if use_indices: output = ( np.arange(len(X)), _call_method_with_correct_args(model, method, X, y), @@ -628,9 +631,7 @@ def _fit_method_step( # type: ignore ) self._append_indexed_output(idx_trans, train_idx, output_trans) if return_output: - output = _sort_and_combine( - idx_trans, include_indices=self.include_indices - ) + output = _sort_and_combine(idx_trans, include_indices=use_indices) fitted = folds_models # type: ignore if return_output: @@ -644,6 +645,7 @@ def _method_step( method_name: str, X: ArrayLike, y: Optional[ArrayLike] = None, + use_indices: bool = False, ) -> Union[NDArray, IntoDataFrame, IntoSeries, Tuple[NDArray, Any]]: """ Apply a method of a fitted model (or models) to input X. @@ -656,7 +658,7 @@ def _method_step( output = _call_method_with_correct_args( fitted_model[-1], method_name, X, y ) - if self.include_indices: + if self.include_indices and use_indices: return np.arange(len(X)), output else: return output @@ -679,9 +681,7 @@ def _method_step( predictions_with_idx, train_idx, output_list ) - return _sort_and_combine( - predictions_with_idx, include_indices=self.include_indices - ) + return _sort_and_combine(predictions_with_idx, include_indices=use_indices) def _fit(self, X: ArrayLike, y: Optional[ArrayLike] = None) -> ArrayLike: """ @@ -698,13 +698,14 @@ def _fit(self, X: ArrayLike, y: Optional[ArrayLike] = None) -> ArrayLike: if transformer is None or transformer == "passthrough": self.fitted_steps_[name] = None continue - not_final_step = not step_idx == total_steps + is_final = step_idx == total_steps X_current, fitted_model = self._fit_method_step( transformer, X_current, y, self.cv_steps[step_idx - 1], - return_output=not_final_step, + return_output=not is_final, + use_indices=is_final, # enforce no indices for intermediate steps ) self.fitted_steps_[name] = fitted_model @@ -1041,6 +1042,11 @@ def classes_(self) -> Optional[NDArray]: Optional[NDArray] Array of class labels from the final classifier step, or None if unavailable. + Note + ------- + Keep in mind that this aggregates all classes seen across all splits. Each split's + classifier may vary in its classes (e.g. in the case of few observations and high class imabalance.) + Examples -------- >>> pipeline.fit(X, y) @@ -1057,18 +1063,44 @@ def classes_(self) -> Optional[NDArray]: raise NotFittedError( f"No fitted model found for final step '{last_step_name}'." ) - # Case A: cross-validated storage: dict with 'splits': [(test_idx, model), ...] - elif fitted_step[0] is not None: - [check_is_fitted(model) for _, _, model in fitted_step] - assert all([is_classifier(model) for _, _, model in fitted_step]) + + # Case A: cross-validated storage is a list of (train_idx, test_idx, model) + if isinstance(fitted_step, list) and fitted_step and fitted_step[0] is not None: + # ensure fitted and classifier + try: + for _, _, model in fitted_step: + check_is_fitted(model) + except Exception: + # treat as absent (avoids raising NotFittedError during dir()) + raise AttributeError( + "Final estimator(s) not fitted or otherwise unavailable" + ) + + if not all(is_classifier(model) for _, _, model in fitted_step): + # Not a classifier -> attribute should be considered absent + raise AttributeError("Final estimator is not a classifier") + + # collect classes_ from each fold return np.unique( - np.concatenate([model[-1].classes_ for model in fitted_step]) + np.concatenate([model.classes_ for _, _, model in fitted_step]) ) - # Case B: direct estimator instance (non-CV) - else: - check_is_fitted(fitted_step[-1]) - assert is_classifier(fitted_step[-1]) - return getattr(fitted_step[-1], "classes_", None) + + # Case B: non-CV: fitted_step is (None, None, model) + # defensive handling in case representation differs slightly + try: + model = fitted_step[-1] + except Exception: + raise AttributeError("Unexpected fitted-step format for final estimator") + + try: + check_is_fitted(model) + except Exception: + raise AttributeError("Final estimator is not fitted") + + if not is_classifier(model): + raise AttributeError("Final estimator is not a classifier") + + return getattr(model, "classes_", None) def __sklearn_tags__(self) -> Tags: tags = super().__sklearn_tags__() diff --git a/pyproject.toml b/pyproject.toml index b700002..23b200a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ authors = [ ] license = {text = "MIT"} readme = "README.md" -requires-python = ">=3.10" +requires-python = ">=3.11" classifiers = [ "Programming Language :: Python :: 3", "License :: OSI Approved :: MIT License", @@ -19,7 +19,7 @@ dependencies = [ "narwhals>=1.42.1", "numpy>=1.21.0", "pandas>=1.3.0", - "scikit-learn>=0.24.2", + "scikit-learn>=1.8.0", "scipy>=1.10.1", "tqdm>=4.67.1", "typing-extensions>=4.13.2", diff --git a/tests/test_metrics.py b/tests/test_metrics.py index 97a8b4b..39d5b0d 100644 --- a/tests/test_metrics.py +++ b/tests/test_metrics.py @@ -3,10 +3,13 @@ import pytest from sklearn.base import BaseEstimator +from sklearn.metrics import get_scorer_names + from panelsplit.metrics import ( _get_idx_from_last_cv, make_SequentialCV_scorer, + get_scorer, ) @@ -137,3 +140,8 @@ def simple_metric(y_true, y_pred): # compute expected manually: fold 1 test idx [0,1] -> preds [1,1] vs y [1,0] => mean([True, False]) = 0.5 assert pytest.approx(per_fold_scores[0]) == 0.5 # fold 2 test idx [2]() + + +def test_scorers_available(): + scorers = get_scorer_names() + [get_scorer(s) for s in scorers] diff --git a/tests/test_pipeline.py b/tests/test_pipeline.py index a817909..b942dac 100644 --- a/tests/test_pipeline.py +++ b/tests/test_pipeline.py @@ -4,7 +4,10 @@ from sklearn.ensemble import RandomForestRegressor from panelsplit.pipeline import SequentialCVPipeline from panelsplit.cross_validation import PanelSplit +from sklearn.ensemble import RandomForestClassifier +from sklearn.impute import SimpleImputer import pandas as pd +from .df_generation import create_rf_friendly_dataset # Dummy transformer that doubles the input. @@ -297,6 +300,24 @@ def test_score_order(): assert where_is_first_instance_of_first_test_period == where_is_first_score +def test_score_on_sequentialCVpipeline(): + df = create_rf_friendly_dataset() + X = df[[col for col in df.columns if "X" in col]] + y = df["y_binary"] + + ps = PanelSplit(df.year, n_splits=9) + + pipe = SequentialCVPipeline( + [("imputer", SimpleImputer()), ("rf", RandomForestClassifier(n_estimators=10))], + cv_steps=[None, ps], + include_indices=False, + ) + + pipe.fit(X, y) + pipe.set_params(include_indices=False) + pipe.score(X, y) + + # %% # %% if __name__ == "__main__": diff --git a/tests/test_search.py b/tests/test_search.py index 5c3fcbb..cdf51ef 100644 --- a/tests/test_search.py +++ b/tests/test_search.py @@ -3,6 +3,7 @@ import pytest from sklearn.ensemble import RandomForestClassifier, RandomForestRegressor +from sklearn.impute import SimpleImputer from sklearn.metrics import average_precision_score, roc_auc_score from panelsplit.metrics import get_scorer from sklearn.utils._param_validation import InvalidParameterError @@ -255,6 +256,23 @@ def test_score_method_uses_refit_metric(self): reference = get_scorer("roc_auc")(gs.best_estimator_, self.X, self.y_binary) self.assertAlmostEqual(score_from_method, reference, places=7) + def test_pipeline_gridsearch_no_nan(self): + df = create_rf_friendly_dataset(n_samples=10) + X = df[[c for c in df.columns if "X" in c]] + y = df["y_binary"] + ps = PanelSplit(df.year, n_splits=2) + pipe = SequentialCVPipeline( + [ + ("imputer", SimpleImputer()), + ("rf", RandomForestClassifier(n_estimators=10)), + ], + cv_steps=[None, ps], + ) + gs = GridSearch(pipe, {"rf__n_estimators": [10, 20]}, scoring="accuracy") + # should not raise and should not produce all-nan results + gs.fit(X, y) + assert not np.all(np.isnan(gs.cv_results_["mean_test_score"])) + if __name__ == "__main__": unittest.main() diff --git a/tests/test_sequentialcvpipeline_indices.py b/tests/test_sequentialcvpipeline_indices.py new file mode 100644 index 0000000..2bf1ccf --- /dev/null +++ b/tests/test_sequentialcvpipeline_indices.py @@ -0,0 +1,148 @@ +# tests/test_sequentialcvpipeline_indices.py +import numpy as np +import pytest + +from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier +from sklearn.impute import SimpleImputer +from sklearn.metrics import mean_squared_error + +from panelsplit.pipeline import SequentialCVPipeline +from panelsplit.cross_validation import PanelSplit +from panelsplit.metrics import neg_mean_squared_error_scorer as mse_scorer + +# Small toy dataset used across tests +X = np.array([[1, 2], [3, 4], [5, 6], [7, 8]], dtype=float) +y_reg = np.array([1.0, 2.0, 3.0, 4.0]) +y_clf = np.array([0, 0, 1, 1]) # simple binary labels + +# PanelSplit used for CV variants +ps = PanelSplit([1, 1, 2, 3], n_splits=2, include_first_train_in_test=True) + + +@pytest.mark.parametrize( + "cv_steps", + [ + ([None, None]), + ([ps, None]), + ([None, ps]), + ([ps, ps]), + ], +) +@pytest.mark.parametrize("include_indices", [False, True]) +def test_regressor_cv_variants(cv_steps, include_indices): + """ + Ensure regressor pipeline fits, predicts, and scoring works for + different cv_steps and include_indices combinations. + """ + p = SequentialCVPipeline( + steps=[ + ("impute", SimpleImputer()), + ("regressor", RandomForestRegressor(random_state=0)), + ], + cv_steps=cv_steps, + include_indices=include_indices, + ) + + # fit should not raise + p.fit(X, y_reg) + + # predict should return a 1D array of length n_samples + preds = p.predict(X) + if include_indices: + preds = preds[-1] + + assert isinstance(preds, np.ndarray), "predict must return numpy array" + assert preds.shape[0] == X.shape[0], ( + "predict must return prediction for each sample" + ) + + # predictions should not contain tuples (no tuple leaked into final preds) + # this checks that intermediate steps didn't produce (idx, data) that became final preds + flat = np.atleast_1d(preds) + assert not any(isinstance(v, tuple) for v in flat), ( + "predictions must not contain tuples" + ) + + # scorer must run and return a finite float (scorer may internally set include_indices) + score = mse_scorer(p, X, y_reg) + # assert isinstance(score, float), "scorer must return a float" + # assert np.isfinite(score), "scorer result must be finite" + assert not any(np.isnan(score)) + + # additionally, compare with direct MSE of pipeline predictions (when cv_steps are None this must match) + # If the scorer uses CV predictions, they may differ; so only compare when cv_steps have no split + if all(s is None for s in cv_steps): + mse_direct = -mean_squared_error(y_reg, preds) + assert pytest.approx(mse_direct, rel=1e-6) == score[0] + + +@pytest.mark.parametrize( + "cv_steps", + [ + ([None, None]), + ([ps, None]), + ([None, ps]), + ([ps, ps]), + ], +) +@pytest.mark.parametrize("include_indices", [False, True]) +def test_classifier_cv_variants(cv_steps, include_indices): + """ + Ensure classifier pipeline fits, predicts, returns classes_, and scoring works. + """ + clf = RandomForestClassifier(random_state=0) + + p = SequentialCVPipeline( + steps=[("impute", SimpleImputer()), ("classifier", clf)], + cv_steps=cv_steps, + include_indices=include_indices, + ) + + # fit must not raise + p.fit(X, y_clf) + + # classes_ should be present and be ndarray for classifier + # (this property may raise for non-classifiers; for classifier it must succeed) + classes = p.classes_ + assert isinstance(classes, np.ndarray), ( + "classes_ must be an ndarray for a fitted classifier" + ) + assert set(classes).issubset(set(y_clf)), ( + "classes_ should reflect labels seen in training data" + ) + + # predict returns predictions with correct shape + preds = p.predict(X) + if include_indices: + preds = preds[-1] + + assert preds.shape[0] == X.shape[0] + assert not any(isinstance(v, tuple) for v in np.atleast_1d(preds)), ( + "predictions must not contain tuples" + ) + + # run a scorer that uses include_indices internally (we re-use the MSE scorer for shape & no-exception check) + # We expect a finite float (even though MSE scorer isn't conceptually for classification, it should still run) + score = mse_scorer(p, X, y_clf) + # assert isinstance(score, float) + # assert np.isfinite(score) + assert not any(np.isnan(score)) + + +def test_predict_and_scorer_consistency_for_no_cv(): + """ + Quick sanity check: when cv_steps = [None, None] the scorer's output must match + a direct negative MSE computed from p.predict(X). + """ + p = SequentialCVPipeline( + steps=[ + ("impute", SimpleImputer()), + ("regressor", RandomForestRegressor(random_state=0)), + ], + cv_steps=[None, None], + include_indices=False, + ) + p.fit(X, y_reg) + preds = p.predict(X) + score = mse_scorer(p, X, y_reg) + assert pytest.approx(-mean_squared_error(y_reg, preds), rel=1e-9) == score[0] diff --git a/uv.lock b/uv.lock index a63c042..78e72e6 100644 --- a/uv.lock +++ b/uv.lock @@ -1,47 +1,15 @@ version = 1 revision = 1 -requires-python = ">=3.8" +requires-python = ">=3.11" 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