[pull] main from mne-tools:main

.github/workflows/autofix.yml

@@ -12,7 +12,7 @@ jobs:
     name: Autoupdate changelog entry and headers
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
       - uses: actions/setup-python@v5

.github/workflows/codeql-analysis.yml

@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         persist-credentials: false
 

.github/workflows/credit.yml

@@ -17,7 +17,7 @@ jobs:
       GH_TOKEN: ${{ github.token }}
       GITHUB_TOKEN: ${{ github.token }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: true
       - uses: actions/setup-python@v5

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
   package:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
       - uses: actions/setup-python@v5

.github/workflows/tests.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 3
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           persist-credentials: false
       - uses: actions/setup-python@v5
@@ -91,7 +91,7 @@ jobs:
             python: '3.10'
             kind: old
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
           persist-credentials: false

doc/changes/dev/13361.bugfix.rst

@@ -0,0 +1,8 @@
+``model`` parameter of :class:`mne.decoding.LinearModel` 
+will not be modified, use ``model_`` attribute to access the fitted model.
+To be compatible with all MNE-Python versions you can use 
+``getattr(clf, "model_", getattr(clf, "model"))``
+The provided ``model`` is expected to be a supervised predictor, 
+i.e. classifier or regressor (or :class:`sklearn.multiclass.OneVsRestClassifier`), 
+otherwise an error will be raised.
+by `Gennadiy Belonosov`_.

mne/decoding/base.py

@@ -17,15 +17,25 @@
     TransformerMixin,
     clone,
     is_classifier,
+    is_regressor,
 )
 from sklearn.linear_model import LogisticRegression
 from sklearn.metrics import check_scoring
 from sklearn.model_selection import KFold, StratifiedKFold, check_cv
-from sklearn.utils import check_array, check_X_y, indexable
+from sklearn.utils import indexable
 from sklearn.utils.validation import check_is_fitted
 
 from ..parallel import parallel_func
-from ..utils import _check_option, _pl, _validate_type, logger, pinv, verbose, warn
+from ..utils import (
+    _check_option,
+    _pl,
+    _validate_type,
+    logger,
+    pinv,
+    verbose,
+    warn,
+)
+from ._fixes import validate_data
 from ._ged import (
     _handle_restr_mat,
     _is_cov_pos_semidef,
@@ -340,7 +350,8 @@ class LinearModel(MetaEstimatorMixin, BaseEstimator):
     model : object | None
         A linear model from scikit-learn with a fit method
         that updates a ``coef_`` attribute.
-        If None the model will be LogisticRegression.
+        If None the model will be
+        :class:`sklearn.linear_model.LogisticRegression`.
 
     Attributes
     ----------
@@ -364,46 +375,66 @@ class LinearModel(MetaEstimatorMixin, BaseEstimator):
     .. footbibliography::
     """
 
-    # TODO: Properly refactor this using
-    # https://github.com/scikit-learn/scikit-learn/issues/30237#issuecomment-2465572885
     _model_attr_wrap = (
         "transform",
+        "fit_transform",
         "predict",
         "predict_proba",
-        "_estimator_type",
-        "__tags__",
+        "predict_log_proba",
+        "_estimator_type",  # remove after sklearn 1.6
         "decision_function",
         "score",
         "classes_",
     )
 
     def __init__(self, model=None):
-        # TODO: We need to set this to get our tag checking to work properly
-        if model is None:
-            model = LogisticRegression(solver="liblinear")
         self.model = model
 
     def __sklearn_tags__(self):
         """Get sklearn tags."""
-        from sklearn.utils import get_tags  # added in 1.6
-
-        # fit method below does not allow sparse data via check_data, we could
-        # eventually make it smarter if we had to
-        tags = get_tags(self.model)
-        tags.input_tags.sparse = False
+        tags = super().__sklearn_tags__()
+        model = self.model if self.model is not None else LogisticRegression()
+        model_tags = model.__sklearn_tags__()
+        tags.estimator_type = model_tags.estimator_type
+        if tags.estimator_type is not None:
+            model_type_tags = getattr(model_tags, f"{tags.estimator_type}_tags")
+            setattr(tags, f"{tags.estimator_type}_tags", model_type_tags)
         return tags
 
     def __getattr__(self, attr):
         """Wrap to model for some attributes."""
         if attr in LinearModel._model_attr_wrap:
-            return getattr(self.model, attr)
-        elif attr == "fit_transform" and hasattr(self.model, "fit_transform"):
-            return super().__getattr__(self, "_fit_transform")
-        return super().__getattr__(self, attr)
+            model = self.model_ if "model_" in self.__dict__ else self.model
+            if attr == "fit_transform" and hasattr(model, "fit_transform"):
+                return self._fit_transform
+            else:
+                return getattr(model, attr)
+        else:
+            raise AttributeError(
+                f"'{type(self).__name__}' object has no attribute '{attr}'"
+            )
 
     def _fit_transform(self, X, y):
         return self.fit(X, y).transform(X)
 
+    def _validate_params(self, X):
+        if self.model is not None:
+            model = self.model
+            if isinstance(model, MetaEstimatorMixin):
+                model = model.estimator
+            is_predictor = is_regressor(model) or is_classifier(model)
+            if not is_predictor:
+                raise ValueError(
+                    "Linear model should be a supervised predictor "
+                    "(classifier or regressor)"
+                )
+
+        # For sklearn < 1.6
+        try:
+            self._check_n_features(X, reset=True)
+        except AttributeError:
+            pass
+
     def fit(self, X, y, **fit_params):
         """Estimate the coefficients of the linear model.
 
@@ -424,25 +455,18 @@ def fit(self, X, y, **fit_params):
         self : instance of LinearModel
             Returns the modified instance.
         """
-        if y is not None:
-            X = check_array(X)
-        else:
-            X, y = check_X_y(X, y)
-        self.n_features_in_ = X.shape[1]
-        if y is not None:
-            y = check_array(y, dtype=None, ensure_2d=False, input_name="y")
-            if y.ndim > 2:
-                raise ValueError(
-                    f"LinearModel only accepts up to 2-dimensional y, got {y.shape} "
-                    "instead."
-                )
+        self._validate_params(X)
+        X, y = validate_data(self, X, y, multi_output=True)
 
         # fit the Model
-        self.model.fit(X, y, **fit_params)
-        self.model_ = self.model  # for better sklearn compat
+        self.model_ = (
+            clone(self.model)
+            if self.model is not None
+            else LogisticRegression(solver="liblinear")
+        )
+        self.model_.fit(X, y, **fit_params)
 
         # Computes patterns using Haufe's trick: A = Cov_X . W . Precision_Y
-
         inv_Y = 1.0
         X = X - X.mean(0, keepdims=True)
         if y.ndim == 2 and y.shape[1] != 1:
@@ -454,12 +478,17 @@ def fit(self, X, y, **fit_params):
 
     @property
     def filters_(self):
-        if hasattr(self.model, "coef_"):
+        if hasattr(self.model_, "coef_"):
             # Standard Linear Model
-            filters = self.model.coef_
-        elif hasattr(self.model.best_estimator_, "coef_"):
+            filters = self.model_.coef_
+        elif hasattr(self.model_, "estimators_"):
+            # Linear model with OneVsRestClassifier
+            filters = np.vstack([est.coef_ for est in self.model_.estimators_])
+        elif hasattr(self.model_, "best_estimator_") and hasattr(
+            self.model_.best_estimator_, "coef_"
+        ):
             # Linear Model with GridSearchCV
-            filters = self.model.best_estimator_.coef_
+            filters = self.model_.best_estimator_.coef_
         else:
             raise ValueError("model does not have a `coef_` attribute.")
         if filters.ndim == 2 and filters.shape[0] == 1:

mne/decoding/tests/test_base.py

@@ -28,13 +28,15 @@
     is_classifier,
     is_regressor,
 )
+from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
 from sklearn.linear_model import LinearRegression, LogisticRegression, Ridge
 from sklearn.model_selection import (
     GridSearchCV,
     KFold,
     StratifiedKFold,
     cross_val_score,
 )
+from sklearn.multiclass import OneVsRestClassifier
 from sklearn.pipeline import make_pipeline
 from sklearn.preprocessing import StandardScaler
 from sklearn.utils.estimator_checks import parametrize_with_checks
@@ -93,12 +95,11 @@ def _make_data(n_samples=1000, n_features=5, n_targets=3):
     return X, Y, A
 
 
-@pytest.mark.filterwarnings("ignore:invalid value encountered in cast.*:RuntimeWarning")
 def test_get_coef():
     """Test getting linear coefficients (filters/patterns) from estimators."""
-    lm_classification = LinearModel()
+    lm_classification = LinearModel(LogisticRegression(solver="liblinear"))
     assert hasattr(lm_classification, "__sklearn_tags__")
-    if check_version("sklearn", "1.4"):
+    if check_version("sklearn", "1.6"):
         print(lm_classification.__sklearn_tags__())
     assert is_classifier(lm_classification.model)
     assert is_classifier(lm_classification)
@@ -200,19 +201,19 @@ def inverse_transform(self, X):
         # Retrieve final linear model
         filters = get_coef(clf, "filters_", False)
         if hasattr(clf, "steps"):
-            if hasattr(clf.steps[-1][-1].model, "best_estimator_"):
+            if hasattr(clf.steps[-1][-1].model_, "best_estimator_"):
                 # Linear Model with GridSearchCV
-                coefs = clf.steps[-1][-1].model.best_estimator_.coef_
+                coefs = clf.steps[-1][-1].model_.best_estimator_.coef_
             else:
                 # Standard Linear Model
-                coefs = clf.steps[-1][-1].model.coef_
+                coefs = clf.steps[-1][-1].model_.coef_
         else:
-            if hasattr(clf.model, "best_estimator_"):
+            if hasattr(clf.model_, "best_estimator_"):
                 # Linear Model with GridSearchCV
-                coefs = clf.model.best_estimator_.coef_
+                coefs = clf.model_.best_estimator_.coef_
             else:
                 # Standard Linear Model
-                coefs = clf.model.coef_
+                coefs = clf.model_.coef_
         if coefs.ndim == 2 and coefs.shape[0] == 1:
             coefs = coefs[0]
         assert_array_equal(filters, coefs)
@@ -280,9 +281,7 @@ def test_get_coef_multiclass(n_features, n_targets):
     lm = LinearModel(LinearRegression())
     assert not hasattr(lm, "model_")
     lm.fit(X, Y)
-    # TODO: modifying non-underscored `model` is a sklearn no-no, maybe should be a
-    # metaestimator?
-    assert lm.model is lm.model_
+    assert lm.model is not lm.model_
     assert_array_equal(lm.filters_.shape, lm.patterns_.shape)
     if n_targets == 1:
         want_shape = (n_features,)
@@ -328,9 +327,6 @@ def test_get_coef_multiclass(n_features, n_targets):
         (3, 1, 2),
     ],
 )
-# TODO: Need to fix this properly in LinearModel
-@pytest.mark.filterwarnings("ignore:'multi_class' was depr.*:FutureWarning")
-@pytest.mark.filterwarnings("ignore:lbfgs failed to converge.*:")
 def test_get_coef_multiclass_full(n_classes, n_channels, n_times):
     """Test a full example with pattern extraction."""
     data = np.zeros((10 * n_classes, n_channels, n_times))
@@ -345,7 +341,7 @@ def test_get_coef_multiclass_full(n_classes, n_channels, n_times):
     clf = make_pipeline(
         Scaler(epochs.info),
         Vectorizer(),
-        LinearModel(LogisticRegression(random_state=0, multi_class="ovr")),
+        LinearModel(OneVsRestClassifier(LogisticRegression(random_state=0))),
     )
     scorer = "roc_auc_ovr_weighted"
     time_gen = GeneralizingEstimator(clf, scorer, verbose=True)
@@ -382,6 +378,20 @@ def test_linearmodel():
         wrong_X = rng.rand(n, n_features, 99)
         clf.fit(wrong_X, y)
 
+    # check fit_transform call
+    clf = LinearModel(LinearDiscriminantAnalysis())
+    _ = clf.fit_transform(X, y)
+
+    # check that model has to have coef_, RBF-SVM doesn't
+    clf = LinearModel(svm.SVC(kernel="rbf"))
+    with pytest.raises(ValueError, match="does not have a `coef_`"):
+        clf.fit(X, y)
+
+    # check that model has to be a predictor
+    clf = LinearModel(StandardScaler())
+    with pytest.raises(ValueError, match="classifier or regressor"):
+        clf.fit(X, y)
+
     # check categorical target fit in standard linear model with GridSearchCV
     parameters = {"kernel": ["linear"], "C": [1, 10]}
     clf = LinearModel(
@@ -481,11 +491,4 @@ def test_cross_val_multiscore():
 @parametrize_with_checks([LinearModel(LogisticRegression())])
 def test_sklearn_compliance(estimator, check):
     """Test LinearModel compliance with sklearn."""
-    ignores = (
-        "check_estimators_overwrite_params",  # self.model changes!
-        "check_dont_overwrite_parameters",
-        "check_parameters_default_constructible",
-    )
-    if any(ignore in str(check) for ignore in ignores):
-        return
     check(estimator)