[python-package] Fix inconsistency in predict() output shape for 1-…

…tree models (microsoft#6753)

python-package/lightgbm/basic.py

@@ -1248,7 +1248,7 @@ def predict(
         if pred_leaf:
             preds = preds.astype(np.int32)
         is_sparse = isinstance(preds, (list, scipy.sparse.spmatrix))
-        if not is_sparse and preds.size != nrow:
+        if not is_sparse and (preds.size != nrow or pred_leaf or pred_contrib):
             if preds.size % nrow == 0:
                 preds = preds.reshape(nrow, -1)
             else:

tests/python_package_test/test_engine.py

@@ -15,7 +15,7 @@
 import psutil
 import pytest
 from scipy.sparse import csr_matrix, isspmatrix_csc, isspmatrix_csr
-from sklearn.datasets import load_svmlight_file, make_blobs, make_multilabel_classification
+from sklearn.datasets import load_svmlight_file, make_blobs, make_classification, make_multilabel_classification
 from sklearn.metrics import average_precision_score, log_loss, mean_absolute_error, mean_squared_error, roc_auc_score
 from sklearn.model_selection import GroupKFold, TimeSeriesSplit, train_test_split
 
@@ -2314,6 +2314,33 @@ def test_refit():
     assert err_pred > new_err_pred
 
 
+def test_refit_with_one_tree_regression():
+    X, y = make_synthetic_regression(n_samples=1_000, n_features=2)
+    lgb_train = lgb.Dataset(X, label=y)
+    params = {"objective": "regression", "verbosity": -1}
+    model = lgb.train(params, lgb_train, num_boost_round=1)
+    model_refit = model.refit(X, y)
+    assert isinstance(model_refit, lgb.Booster)
+
+
+def test_refit_with_one_tree_binary_classification():
+    X, y = load_breast_cancer(return_X_y=True)
+    lgb_train = lgb.Dataset(X, label=y)
+    params = {"objective": "binary", "verbosity": -1}
+    model = lgb.train(params, lgb_train, num_boost_round=1)
+    model_refit = model.refit(X, y)
+    assert isinstance(model_refit, lgb.Booster)
+
+
+def test_refit_with_one_tree_multiclass_classification():
+    X, y = load_iris(return_X_y=True)
+    lgb_train = lgb.Dataset(X, y)
+    params = {"objective": "multiclass", "num_class": 3, "verbose": -1}
+    model = lgb.train(params, lgb_train, num_boost_round=1)
+    model_refit = model.refit(X, y)
+    assert isinstance(model_refit, lgb.Booster)
+
+
 def test_refit_dataset_params(rng):
     # check refit accepts dataset_params
     X, y = load_breast_cancer(return_X_y=True)
@@ -3872,6 +3899,67 @@ def test_predict_stump(rng, use_init_score):
         np.testing.assert_allclose(preds_all, np.full_like(preds_all, fill_value=y_avg))
 
 
+def test_predict_regression_output_shape():
+    n_samples = 1_000
+    n_features = 4
+    X, y = make_synthetic_regression(n_samples=n_samples, n_features=n_features)
+    dtrain = lgb.Dataset(X, label=y)
+    params = {"objective": "regression", "verbosity": -1}
+
+    # 1-round model
+    bst = lgb.train(params, dtrain, num_boost_round=1)
+    assert bst.predict(X).shape == (n_samples,)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_features + 1)
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, 1)
+
+    # 2-round model
+    bst = lgb.train(params, dtrain, num_boost_round=2)
+    assert bst.predict(X).shape == (n_samples,)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_features + 1)
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, 2)
+
+
+def test_predict_binary_classification_output_shape():
+    n_samples = 1_000
+    n_features = 4
+    X, y = make_classification(n_samples=n_samples, n_features=n_features, n_classes=2)
+    dtrain = lgb.Dataset(X, label=y)
+    params = {"objective": "binary", "verbosity": -1}
+
+    # 1-round model
+    bst = lgb.train(params, dtrain, num_boost_round=1)
+    assert bst.predict(X).shape == (n_samples,)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_features + 1)
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, 1)
+
+    # 2-round model
+    bst = lgb.train(params, dtrain, num_boost_round=2)
+    assert bst.predict(X).shape == (n_samples,)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_features + 1)
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, 2)
+
+
+def test_predict_multiclass_classification_output_shape():
+    n_samples = 1_000
+    n_features = 10
+    n_classes = 3
+    X, y = make_classification(n_samples=n_samples, n_features=n_features, n_classes=n_classes, n_informative=6)
+    dtrain = lgb.Dataset(X, label=y)
+    params = {"objective": "multiclass", "verbosity": -1, "num_class": n_classes}
+
+    # 1-round model
+    bst = lgb.train(params, dtrain, num_boost_round=1)
+    assert bst.predict(X).shape == (n_samples, n_classes)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_classes * (n_features + 1))
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, n_classes)
+
+    # 2-round model
+    bst = lgb.train(params, dtrain, num_boost_round=2)
+    assert bst.predict(X).shape == (n_samples, n_classes)
+    assert bst.predict(X, pred_contrib=True).shape == (n_samples, n_classes * (n_features + 1))
+    assert bst.predict(X, pred_leaf=True).shape == (n_samples, n_classes * 2)
+
+
 def test_average_precision_metric():
     # test against sklearn average precision metric
     X, y = load_breast_cancer(return_X_y=True)