MAINT honest API with a multi view (#231)

* Ensure HonestForest and HonestTree inherit fitted attributes from any decision tree we can use in scikit-tree

---------

Signed-off-by: Adam Li <adam2392@gmail.com>

pyproject.toml

@@ -15,9 +15,6 @@ requires = [
   "numpy>=1.25; python_version>='3.9'"
 ]
 
-[lint.per-file-ignores]
-'__init__.py' = ['F401']
-
 [project]
 name = "scikit-tree"
 version = "0.7.0dev0"
@@ -266,10 +263,12 @@ extend-exclude = [
   'validation'
 ]
 line-length = 88
-lint.ignore = ['E731']
 
-[tool.ruff.per-file-ignores]
-"__init__.py" = ["F401"]
+[tool.ruff.lint]
+ignore = ['E731']
+
+[tool.ruff.lint.per-file-ignores]
+'__init__.py' = ['F401']
 
 [tool.spin]
 package = 'sktree'

sktree/ensemble/_honest_forest.py

@@ -277,9 +277,6 @@ class labels (multi-output problem).
         The number of classes (single output problem), or a list containing the
         number of classes for each output (multi-output problem).
 
-    n_features_ : int
-        The number of features when ``fit`` is performed.
-
     n_features_in_ : int
         Number of features seen during :term:`fit`.
 
@@ -508,6 +505,9 @@ def fit(self, X, y, sample_weight=None, classes=None, **fit_params):
 
         super().fit(X, y, sample_weight=sample_weight, classes=classes, **fit_params)
 
+        # Inherit attributes from the tree estimator
+        self._inherit_estimator_attributes()
+
         # Compute honest decision function
         self.honest_decision_function_ = self._predict_proba(
             X, indices=self.honest_indices_, impute_missing=np.nan
@@ -536,6 +536,12 @@ def _make_estimator(self, append=True, random_state=None):
 
         return estimator
 
+    def _inherit_estimator_attributes(self):
+        """Initialize necessary attributes from the provided tree estimator"""
+        if hasattr(self.tree_estimator, "_inheritable_fitted_attribute"):
+            for attr in self.tree_estimator._inheritable_fitted_attribute:
+                setattr(self, attr, getattr(self.estimators_[0], attr))
+
     def predict_proba(self, X):
         """
         Predict class probabilities for X.
@@ -638,25 +644,6 @@ def oob_samples_(self):
     def _more_tags(self):
         return {"multioutput": False}
 
-    def apply(self, X):
-        """
-        Apply trees in the forest to X, return leaf indices.
-
-        Parameters
-        ----------
-        X : {array-like, sparse matrix} of shape (n_samples, n_features)
-            The input samples. Internally, its dtype will be converted to
-            ``dtype=np.float32``. If a sparse matrix is provided, it will be
-            converted into a sparse ``csr_matrix``.
-
-        Returns
-        -------
-        X_leaves : ndarray of shape (n_samples, n_estimators)
-            For each datapoint x in X and for each tree in the forest,
-            return the index of the leaf x ends up in.
-        """
-        return self.estimator_.apply(X)
-
     def decision_path(self, X):
         """
         Return the decision path in the forest.

sktree/stats/tests/test_forestht.py

@@ -838,6 +838,69 @@ def test_build_coleman_forest():
     assert forest_result.observe_stat < 0.05, f"{forest_result.observe_stat}"
 
 
+def test_build_coleman_forest_multiview():
+    """Simple test for building a Coleman forest.
+
+    Test the function under alternative and null hypothesis for a very simple dataset.
+    """
+    n_estimators = 40
+    n_samples = 30
+    n_features = 5
+    rng = np.random.default_rng(seed)
+
+    _X = rng.uniform(size=(n_samples, n_features))
+    _X = rng.uniform(size=(n_samples // 2, n_features))
+    X2 = _X + 3
+    X = np.vstack([_X, X2])
+    y = np.vstack(
+        [np.zeros((n_samples // 2, 1)), np.ones((n_samples // 2, 1))]
+    )  # Binary classification
+
+    clf = HonestForestClassifier(
+        n_estimators=n_estimators,
+        random_state=seed,
+        n_jobs=-1,
+        honest_fraction=0.5,
+        bootstrap=True,
+        max_samples=1.6,
+        max_features=[1, 1],
+        tree_estimator=MultiViewDecisionTreeClassifier(),
+        feature_set_ends=[2, 5],
+    )
+    perm_clf = PermutationHonestForestClassifier(
+        n_estimators=n_estimators,
+        random_state=seed,
+        n_jobs=-1,
+        honest_fraction=0.5,
+        bootstrap=True,
+        max_samples=1.6,
+        max_features=[1, 1],
+        tree_estimator=MultiViewDecisionTreeClassifier(),
+        feature_set_ends=[2, 5],
+    )
+    with pytest.raises(
+        RuntimeError, match="Permutation forest must be a PermutationHonestForestClassifier"
+    ):
+        build_coleman_forest(clf, clf, X, y)
+
+    forest_result, orig_forest_proba, perm_forest_proba, clf_fitted, perm_clf_fitted = (
+        build_coleman_forest(clf, perm_clf, X, y, metric="s@98", n_repeats=1000, seed=seed)
+    )
+    assert clf_fitted._n_samples_bootstrap == round(n_samples * 1.6)
+    assert perm_clf_fitted._n_samples_bootstrap == round(n_samples * 1.6)
+    assert_array_equal(perm_clf_fitted.permutation_indices_.shape, (n_samples, 1))
+
+    assert forest_result.pvalue <= 0.05, f"{forest_result.pvalue}"
+    assert forest_result.observe_stat > 0.1, f"{forest_result.observe_stat}"
+    assert_array_equal(orig_forest_proba.shape, perm_forest_proba.shape)
+
+    X = np.vstack([_X, _X])
+    forest_result, _, _, clf_fitted, perm_clf_fitted = build_coleman_forest(
+        clf, perm_clf, X, y, metric="s@98"
+    )
+    assert forest_result.pvalue > 0.05, f"{forest_result.pvalue}"
+
+
 def test_build_permutation_forest():
     """Simple test for building a permutation forest."""
     n_estimators = 30

sktree/tests/test_honest_forest.py

@@ -437,33 +437,51 @@ def test_honest_forest_with_sklearn_trees_with_mi():
     assert_allclose(np.mean(sk_scores), np.mean(scores), atol=0.005)
 
 
-def test_honest_forest_with_tree_estimator_params():
+@pytest.mark.parametrize(
+    "tree, tree_kwargs",
+    [
+        (MultiViewDecisionTreeClassifier(), {"feature_set_ends": [10, 20]}),
+        (ObliqueDecisionTreeClassifier(), {"feature_combinations": 2}),
+        (PatchObliqueDecisionTreeClassifier(), {"max_patch_dims": 5}),
+    ],
+)
+def test_honest_forest_with_tree_estimator_params(tree, tree_kwargs):
+    """Test that honest forest inherits all the fitted parameters of the tree estimator."""
     X = np.ones((20, 4))
     X[10:] *= -1
     y = [0] * 10 + [1] * 10
 
     # test with a parameter that is a repeat of an init parameter
     clf = HonestForestClassifier(
-        tree_estimator=DecisionTreeClassifier(),
-        random_state=0,
-        feature_set_ends=[10, 20],
+        tree_estimator=DecisionTreeClassifier(), random_state=0, **tree_kwargs
     )
     with pytest.raises(ValueError, match=r"Invalid parameter\(s\)"):
         clf.fit(X, y)
 
     # test with a parameter that is not in any init signature
     clf = HonestForestClassifier(
-        tree_estimator=MultiViewDecisionTreeClassifier(),
+        tree_estimator=tree,
         random_state=0,
         blah=0,
     )
     with pytest.raises(ValueError, match=r"Invalid parameter\(s\)"):
         clf.fit(X, y)
 
     # passing in a valid argument to the tree_estimator should work
-    clf = HonestForestClassifier(
-        tree_estimator=MultiViewDecisionTreeClassifier(),
-        random_state=0,
-        feature_set_ends=[10, 20],
-    )
+    clf = HonestForestClassifier(tree_estimator=tree, random_state=0, **tree_kwargs)
     clf.fit(X, y)
+    checked_attrs = [
+        "classes_",
+        "n_classes_",
+        "n_features_in_",
+        "n_outputs_",
+    ]
+    checked_attrs + getattr(tree, "_inheritable_fitted_attribute", [])
+    for attr_name in checked_attrs:
+        if not attr_name.startswith("_") and attr_name.endswith("_"):
+            if isinstance(getattr(clf, attr_name), np.ndarray):
+                np.testing.assert_array_equal(
+                    getattr(clf, attr_name), getattr(clf.estimators_[0], attr_name)
+                )
+            else:
+                assert getattr(clf, attr_name) == getattr(clf.estimators_[0], attr_name)

sktree/tree/_classes.py

@@ -990,6 +990,12 @@ def _build_tree(
 
         return self
 
+    @property
+    def _inheritable_fitted_attribute(self):
+        return [
+            "feature_combinations_",
+        ]
+
 
 class ObliqueDecisionTreeRegressor(SimMatrixMixin, DecisionTreeRegressor):
     """An oblique decision tree Regressor.
@@ -1852,6 +1858,16 @@ def _more_tags(self):
         allow_nan = False
         return {"multilabel": True, "allow_nan": allow_nan}
 
+    @property
+    def _inheritable_fitted_attribute(self):
+        return [
+            "feature_combinations_",
+            "min_patch_dims_",
+            "max_patch_dims_",
+            "dim_contiguous_",
+            "data_dims_",
+        ]
+
 
 class PatchObliqueDecisionTreeRegressor(SimMatrixMixin, DecisionTreeRegressor):
     """A oblique decision tree regressor that operates over patches of data.
@@ -2747,6 +2763,12 @@ def _build_tree(
             self.classes_ = self.classes_[0]
         return self
 
+    @property
+    def _inheritable_fitted_attribute(self):
+        return [
+            "feature_combinations_",
+        ]
+
 
 class ExtraObliqueDecisionTreeRegressor(SimMatrixMixin, DecisionTreeRegressor):
     """An oblique decision tree Regressor.

sktree/tree/_honest_tree.py

@@ -730,13 +730,21 @@ def _set_leaf_nodes(self, leaf_ids, y):
 
     def _inherit_estimator_attributes(self):
         """Initialize necessary attributes from the provided tree estimator"""
+        if hasattr(self.estimator_, "_inheritable_fitted_attribute"):
+            for attr in self.estimator_._inheritable_fitted_attribute:
+                setattr(self, attr, getattr(self.estimator_, attr))
+
         self.classes_ = self.estimator_.classes_
         self.max_features_ = self.estimator_.max_features_
         self.n_classes_ = self.estimator_.n_classes_
         self.n_features_in_ = self.estimator_.n_features_in_
         self.n_outputs_ = self.estimator_.n_outputs_
         self.tree_ = self.estimator_.tree_
 
+        # XXX: scikit-learn trees do not store their builder, or min_samples_split_
+        self.builder_ = getattr(self.estimator_, "builder_", None)
+        self.min_samples_split_ = getattr(self.estimator_, "min_samples_split_", None)
+
     def _empty_leaf_correction(self, proba, pos=0):
         """Leaves with empty posteriors are assigned values.
 

sktree/tree/_multiview.py

@@ -476,7 +476,6 @@ def _build_tree(
                     max_features = 0
 
             self.max_features_ = max_features
-            print(self.max_features_, self.max_features_per_set_)
 
         if not isinstance(self.splitter, ObliqueSplitter):
             splitter = SPLITTERS[self.splitter](
@@ -576,3 +575,18 @@ def _fit(
         super()._fit(X, y, sample_weight, check_input, missing_values_in_feature_mask, classes)
         self.max_features = self._max_features_arr
         return self
+
+    @property
+    def _inheritable_fitted_attribute(self):
+        """Define additional attributes to pass onto a parent meta tree-estimator.
+
+        Used for passing parameters to HonestTreeClassifier.
+        """
+        return [
+            "max_features_",
+            "feature_combinations_",
+            "feature_set_ends_",
+            "n_feature_sets_",
+            "n_features_in_set_",
+            "max_features_per_set_",
+        ]

sktree/tree/tests/test_honest_tree.py

@@ -63,36 +63,47 @@ def test_toy_accuracy():
     np.testing.assert_array_equal(clf.predict(X), y)
 
 
-def test_honest_tree_with_tree_estimator_params():
+@pytest.mark.parametrize(
+    "tree, tree_kwargs",
+    [
+        (MultiViewDecisionTreeClassifier(), {"feature_set_ends": [10, 20]}),
+        (ObliqueDecisionTreeClassifier(), {"feature_combinations": 2}),
+        (PatchObliqueDecisionTreeClassifier(), {"max_patch_dims": 5}),
+    ],
+)
+def test_honest_tree_with_tree_estimator_params(tree, tree_kwargs):
+    """Test that honest tree inherits all the fitted parameters of the tree estimator."""
     X = np.ones((20, 4))
     X[10:] *= -1
     y = [0] * 10 + [1] * 10
 
     # test with a parameter that is a repeat of an init parameter
     clf = HonestTreeClassifier(
-        tree_estimator=DecisionTreeClassifier(),
-        random_state=0,
-        feature_set_ends=[10, 20],
+        tree_estimator=DecisionTreeClassifier(), random_state=0, **tree_kwargs
     )
     with pytest.raises(ValueError, match=r"Invalid parameter\(s\)"):
         clf.fit(X, y)
 
     # test with a parameter that is not in any init signature
     clf = HonestTreeClassifier(
-        tree_estimator=MultiViewDecisionTreeClassifier(),
+        tree_estimator=tree,
         random_state=0,
         blah=0,
     )
     with pytest.raises(ValueError, match=r"Invalid parameter\(s\)"):
         clf.fit(X, y)
 
     # passing in a valid argument to the tree_estimator should work
-    clf = HonestTreeClassifier(
-        tree_estimator=MultiViewDecisionTreeClassifier(),
-        random_state=0,
-        feature_set_ends=[10, 20],
-    )
+    clf = HonestTreeClassifier(tree_estimator=tree, random_state=0, **tree_kwargs)
     clf.fit(X, y)
+    for attr_name in dir(clf.estimator_):
+        if not attr_name.startswith("_") and attr_name.endswith("_"):
+            if isinstance(getattr(clf, attr_name), np.ndarray):
+                np.testing.assert_array_equal(
+                    getattr(clf, attr_name), getattr(clf.estimator_, attr_name)
+                )
+            else:
+                assert getattr(clf, attr_name) == getattr(clf.estimator_, attr_name)
 
 
 @pytest.mark.parametrize(