[DOC] Update API webpages to include new classes and functions (#2397)

* api part 1 * imports * only takes 2d
aeon-toolkit · Nov 27, 2024 · 5a06ee0 · 5a06ee0
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diff --git a/aeon/base/estimators/__init__.py → aeon/base/_estimators/__init__.py b/aeon/base/estimators/__init__.py → aeon/base/_estimators/__init__.py
diff --git a/aeon/base/estimators/compose/__init__.py → aeon/base/_estimators/compose/__init__.py b/aeon/base/estimators/compose/__init__.py → aeon/base/_estimators/compose/__init__.py
diff --git a/...rs/compose/collection_channel_ensemble.py → ...rs/compose/collection_channel_ensemble.py b/...rs/compose/collection_channel_ensemble.py → ...rs/compose/collection_channel_ensemble.py
diff --git a/...estimators/compose/collection_ensemble.py → ...estimators/compose/collection_ensemble.py b/...estimators/compose/collection_ensemble.py → ...estimators/compose/collection_ensemble.py
diff --git a/...estimators/compose/collection_pipeline.py → ...estimators/compose/collection_pipeline.py b/...estimators/compose/collection_pipeline.py → ...estimators/compose/collection_pipeline.py
diff --git a/aeon/base/estimators/hybrid/__init__.py → aeon/base/_estimators/hybrid/__init__.py b/aeon/base/estimators/hybrid/__init__.py → aeon/base/_estimators/hybrid/__init__.py
@@ -2,4 +2,4 @@
 
 __all__ = ["BaseRIST"]
 
-from aeon.base.estimators.hybrid.base_rist import BaseRIST
+from aeon.base._estimators.hybrid.base_rist import BaseRIST
diff --git a/aeon/base/estimators/hybrid/base_rist.py → aeon/base/_estimators/hybrid/base_rist.py b/aeon/base/estimators/hybrid/base_rist.py → aeon/base/_estimators/hybrid/base_rist.py
diff --git a/.../base/estimators/hybrid/tests/__init__.py → ...base/_estimators/hybrid/tests/__init__.py b/.../base/estimators/hybrid/tests/__init__.py → ...base/_estimators/hybrid/tests/__init__.py
diff --git a/...estimators/hybrid/tests/test_base_rist.py → ...estimators/hybrid/tests/test_base_rist.py b/...estimators/hybrid/tests/test_base_rist.py → ...estimators/hybrid/tests/test_base_rist.py
diff --git a/...ase/estimators/interval_based/__init__.py → ...se/_estimators/interval_based/__init__.py b/...ase/estimators/interval_based/__init__.py → ...se/_estimators/interval_based/__init__.py
@@ -2,4 +2,4 @@
 
 __all__ = ["BaseIntervalForest"]
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
diff --git a/...rs/interval_based/base_interval_forest.py → ...rs/interval_based/base_interval_forest.py b/...rs/interval_based/base_interval_forest.py → ...rs/interval_based/base_interval_forest.py
diff --git a/...timators/interval_based/tests/__init__.py → ...timators/interval_based/tests/__init__.py b/...timators/interval_based/tests/__init__.py → ...timators/interval_based/tests/__init__.py
diff --git a/..._based/tests/test_base_interval_forest.py → ..._based/tests/test_base_interval_forest.py b/..._based/tests/test_base_interval_forest.py → ..._based/tests/test_base_interval_forest.py
diff --git a/aeon/classification/compose/_channel_ensemble.py b/aeon/classification/compose/_channel_ensemble.py
@@ -10,7 +10,7 @@
 import numpy as np
 from sklearn.utils import check_random_state
 
-from aeon.base.estimators.compose.collection_channel_ensemble import (
+from aeon.base._estimators.compose.collection_channel_ensemble import (
     BaseCollectionChannelEnsemble,
 )
 from aeon.classification.base import BaseClassifier

diff --git a/aeon/classification/compose/_ensemble.py b/aeon/classification/compose/_ensemble.py
@@ -7,7 +7,7 @@
 import numpy as np
 from sklearn.utils import check_random_state
 
-from aeon.base.estimators.compose.collection_ensemble import BaseCollectionEnsemble
+from aeon.base._estimators.compose.collection_ensemble import BaseCollectionEnsemble
 from aeon.classification.base import BaseClassifier
 from aeon.classification.sklearn._wrapper import SklearnClassifierWrapper
 from aeon.utils.sklearn import is_sklearn_classifier

diff --git a/aeon/classification/compose/_pipeline.py b/aeon/classification/compose/_pipeline.py
@@ -4,7 +4,7 @@
 __all__ = ["ClassifierPipeline"]
 
 
-from aeon.base.estimators.compose.collection_pipeline import BaseCollectionPipeline
+from aeon.base._estimators.compose.collection_pipeline import BaseCollectionPipeline
 from aeon.classification.base import BaseClassifier
 
 

diff --git a/aeon/classification/hybrid/_rist.py b/aeon/classification/hybrid/_rist.py
@@ -6,7 +6,7 @@
 from sklearn.ensemble import ExtraTreesClassifier
 from sklearn.preprocessing import FunctionTransformer
 
-from aeon.base.estimators.hybrid import BaseRIST
+from aeon.base._estimators.hybrid import BaseRIST
 from aeon.classification import BaseClassifier
 from aeon.utils.numba.general import first_order_differences_3d
 

diff --git a/aeon/classification/interval_based/_cif.py b/aeon/classification/interval_based/_cif.py
@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based import BaseIntervalForest
+from aeon.base._estimators.interval_based import BaseIntervalForest
 from aeon.classification import BaseClassifier
 from aeon.classification.sklearn import ContinuousIntervalTree
 from aeon.transformations.collection.feature_based import Catch22

diff --git a/aeon/classification/interval_based/_drcif.py b/aeon/classification/interval_based/_drcif.py
@@ -10,7 +10,7 @@
 import numpy as np
 from sklearn.preprocessing import FunctionTransformer
 
-from aeon.base.estimators.interval_based import BaseIntervalForest
+from aeon.base._estimators.interval_based import BaseIntervalForest
 from aeon.classification.base import BaseClassifier
 from aeon.classification.sklearn._continuous_interval_tree import ContinuousIntervalTree
 from aeon.transformations.collection import PeriodogramTransformer

diff --git a/aeon/classification/interval_based/_interval_forest.py b/aeon/classification/interval_based/_interval_forest.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.classification.base import BaseClassifier
 
 

diff --git a/aeon/classification/interval_based/_rise.py b/aeon/classification/interval_based/_rise.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.classification import BaseClassifier
 from aeon.classification.sklearn import ContinuousIntervalTree
 from aeon.transformations.collection import (

diff --git a/aeon/classification/interval_based/_stsf.py b/aeon/classification/interval_based/_stsf.py
@@ -11,7 +11,7 @@
 import numpy as np
 from sklearn.preprocessing import FunctionTransformer
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.classification.base import BaseClassifier
 from aeon.transformations.collection import PeriodogramTransformer
 from aeon.utils.numba.general import first_order_differences_3d

diff --git a/aeon/classification/interval_based/_tsf.py b/aeon/classification/interval_based/_tsf.py
@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.classification import BaseClassifier
 from aeon.classification.sklearn import ContinuousIntervalTree
 

diff --git a/aeon/classification/sklearn/__init__.py b/aeon/classification/sklearn/__init__.py
@@ -3,9 +3,11 @@
 __all__ = [
     "RotationForestClassifier",
     "ContinuousIntervalTree",
+    "SklearnClassifierWrapper",
 ]
 
 from aeon.classification.sklearn._continuous_interval_tree import ContinuousIntervalTree
 from aeon.classification.sklearn._rotation_forest_classifier import (
     RotationForestClassifier,
 )
+from aeon.classification.sklearn._wrapper import SklearnClassifierWrapper
diff --git a/aeon/classification/sklearn/_wrapper.py b/aeon/classification/sklearn/_wrapper.py
@@ -26,7 +26,7 @@ class SklearnClassifierWrapper(BaseClassifier):
     """
 
     _tags = {
-        "X_inner_type": ["np-list", "numpy3D"],
+        "X_inner_type": "numpy2D",
     }
 
     def __init__(self, classifier, random_state=None):
@@ -35,7 +35,7 @@ def __init__(self, classifier, random_state=None):
 
         super().__init__()
 
-    def _fit(self, X, y=None):
+    def _fit(self, X, y):
         self.classifier_ = _clone_estimator(self.classifier, self.random_state)
         self.classifier_.fit(X, y)
         return self

diff --git a/aeon/clustering/averaging/__init__.py b/aeon/clustering/averaging/__init__.py
@@ -8,6 +8,7 @@
     "VALID_BA_METRICS",
     "shift_invariant_average",
 ]
+
 from aeon.clustering.averaging._averaging import mean_average
 from aeon.clustering.averaging._ba_petitjean import petitjean_barycenter_average
 from aeon.clustering.averaging._ba_subgradient import subgradient_barycenter_average

diff --git a/aeon/clustering/compose/_pipeline.py b/aeon/clustering/compose/_pipeline.py
@@ -4,7 +4,7 @@
 __all__ = ["ClustererPipeline"]
 
 
-from aeon.base.estimators.compose.collection_pipeline import BaseCollectionPipeline
+from aeon.base._estimators.compose.collection_pipeline import BaseCollectionPipeline
 from aeon.clustering import BaseClusterer
 
 

diff --git a/aeon/regression/compose/_ensemble.py b/aeon/regression/compose/_ensemble.py
@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.compose.collection_ensemble import BaseCollectionEnsemble
+from aeon.base._estimators.compose.collection_ensemble import BaseCollectionEnsemble
 from aeon.regression import BaseRegressor
 from aeon.regression.sklearn._wrapper import SklearnRegressorWrapper
 from aeon.utils.sklearn import is_sklearn_regressor

diff --git a/aeon/regression/compose/_pipeline.py b/aeon/regression/compose/_pipeline.py
@@ -3,7 +3,7 @@
 __maintainer__ = ["MatthewMiddlehurst"]
 __all__ = ["RegressorPipeline"]
 
-from aeon.base.estimators.compose.collection_pipeline import BaseCollectionPipeline
+from aeon.base._estimators.compose.collection_pipeline import BaseCollectionPipeline
 from aeon.regression.base import BaseRegressor
 
 

diff --git a/aeon/regression/hybrid/_rist.py b/aeon/regression/hybrid/_rist.py
@@ -1,7 +1,7 @@
 from sklearn.ensemble import ExtraTreesRegressor
 from sklearn.preprocessing import FunctionTransformer
 
-from aeon.base.estimators.hybrid import BaseRIST
+from aeon.base._estimators.hybrid import BaseRIST
 from aeon.regression import BaseRegressor
 from aeon.utils.numba.general import first_order_differences_3d
 

diff --git a/aeon/regression/interval_based/_cif.py b/aeon/regression/interval_based/_cif.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based import BaseIntervalForest
+from aeon.base._estimators.interval_based import BaseIntervalForest
 from aeon.regression import BaseRegressor
 from aeon.transformations.collection.feature_based import Catch22
 from aeon.utils.numba.stats import row_mean, row_slope, row_std

diff --git a/aeon/regression/interval_based/_drcif.py b/aeon/regression/interval_based/_drcif.py
@@ -7,7 +7,7 @@
 import numpy as np
 from sklearn.preprocessing import FunctionTransformer
 
-from aeon.base.estimators.interval_based import BaseIntervalForest
+from aeon.base._estimators.interval_based import BaseIntervalForest
 from aeon.regression import BaseRegressor
 from aeon.transformations.collection import PeriodogramTransformer
 from aeon.transformations.collection.feature_based import Catch22

diff --git a/aeon/regression/interval_based/_interval_forest.py b/aeon/regression/interval_based/_interval_forest.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.regression.base import BaseRegressor
 
 

diff --git a/aeon/regression/interval_based/_rise.py b/aeon/regression/interval_based/_rise.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.regression import BaseRegressor
 from aeon.transformations.collection import (
     AutocorrelationFunctionTransformer,

diff --git a/aeon/regression/interval_based/_tsf.py b/aeon/regression/interval_based/_tsf.py
@@ -8,7 +8,7 @@
 
 import numpy as np
 
-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest
 from aeon.regression import BaseRegressor
 
 

diff --git a/aeon/transformations/collection/compose/_pipeline.py b/aeon/transformations/collection/compose/_pipeline.py
@@ -4,7 +4,7 @@
 __all__ = ["CollectionTransformerPipeline"]
 
 
-from aeon.base.estimators.compose.collection_pipeline import BaseCollectionPipeline
+from aeon.base._estimators.compose.collection_pipeline import BaseCollectionPipeline
 from aeon.transformations.collection import BaseCollectionTransformer
 from aeon.transformations.collection.compose import CollectionId
 

diff --git a/docs/api_reference/anomaly_detection.rst b/docs/api_reference/anomaly_detection.rst
@@ -69,16 +69,26 @@ Detectors
     :toctree: auto_generated/
     :template: class.rst
 
-
     CBLOF
     COPOD
     DWT_MLEAD
     IsolationForest
-    LOF
     KMeansAD
     LeftSTAMPi
+    LOF
     MERLIN
+    OneClassSVM
     PyODAdapter
-    STRAY
     STOMP
-    OneClassSVM
+    STRAY
+
+Base
+----
+
+.. currentmodule:: aeon.anomaly_detection.base
+
+.. autosummary::
+    :toctree: auto_generated/
+    :template: class.rst
+
+    BaseAnomalyDetector
diff --git a/docs/api_reference/base.rst b/docs/api_reference/base.rst
@@ -17,3 +17,4 @@ Base classes
     BaseAeonEstimator
     BaseCollectionEstimator
     BaseSeriesEstimator
+    ComposableEstimatorMixin
diff --git a/docs/api_reference/classification.rst b/docs/api_reference/classification.rst
@@ -34,7 +34,6 @@ Deep learning
     :toctree: auto_generated/
     :template: class.rst
 
-    BaseDeepClassifier
     TimeCNNClassifier
     EncoderClassifier
     FCNClassifier
@@ -59,6 +58,7 @@ Dictionary-based
     ContractableBOSS
     IndividualBOSS
     IndividualTDE
+    MrSEQLClassifier
     MrSQMClassifier
     MUSE
     REDCOMETS
@@ -140,6 +140,7 @@ Shapelet-based
     LearningShapeletClassifier
     RDSTClassifier
     SASTClassifier
+    RSASTClassifier
     ShapeletTransformClassifier
 
 sklearn
@@ -153,6 +154,7 @@ sklearn
 
     ContinuousIntervalTree
     RotationForestClassifier
+    SklearnClassifierWrapper
 
 Early classification
 --------------------
@@ -179,13 +181,6 @@ Ordinal classification
     IndividualOrdinalTDE
     OrdinalTDE
 
-
-.. autosummary::
-    :toctree: auto_generated/
-    :template: function.rst
-
-    histogram_intersection
-
 Composition
 -----------
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,4 @@

		__all__ = ["BaseRIST"]

		from aeon.base.estimators.hybrid.base_rist import BaseRIST
		from aeon.base._estimators.hybrid.base_rist import BaseRIST
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,4 @@

		__all__ = ["BaseIntervalForest"]

		from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest
		from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest