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

MatthewMiddlehurst · web-flow · commit 5a06ee067283 · 2024-11-27T08:51:49.000Z
* api part 1

* imports

* only takes 2d
diff --git a/aeon/base/_estimators/__init__.py b/aeon/base/_estimators/__init__.py
diff --git a/aeon/base/_estimators/compose/__init__.py b/aeon/base/_estimators/compose/__init__.py
diff --git a/aeon/base/_estimators/compose/collection_channel_ensemble.py b/aeon/base/_estimators/compose/collection_channel_ensemble.py
diff --git a/aeon/base/_estimators/compose/collection_ensemble.py b/aeon/base/_estimators/compose/collection_ensemble.py
diff --git a/aeon/base/_estimators/compose/collection_pipeline.py b/aeon/base/_estimators/compose/collection_pipeline.py
diff --git a/aeon/base/_estimators/hybrid/__init__.py b/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 b/aeon/base/_estimators/hybrid/base_rist.py
diff --git a/aeon/base/_estimators/hybrid/tests/__init__.py b/aeon/base/_estimators/hybrid/tests/__init__.py
diff --git a/aeon/base/_estimators/hybrid/tests/test_base_rist.py b/aeon/base/_estimators/hybrid/tests/test_base_rist.py
diff --git a/aeon/base/_estimators/interval_based/__init__.py b/aeon/base/_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/aeon/base/_estimators/interval_based/base_interval_forest.py b/aeon/base/_estimators/interval_based/base_interval_forest.py
diff --git a/aeon/base/_estimators/interval_based/tests/__init__.py b/aeon/base/_estimators/interval_based/tests/__init__.py
diff --git a/aeon/base/_estimators/interval_based/tests/test_base_interval_forest.py b/aeon/base/_estimators/interval_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
 -----------
 
diff --git a/docs/api_reference/clustering.rst b/docs/api_reference/clustering.rst

Original file line number	Diff line number	Diff line change
`@@ -2,4 +2,4 @@`
`2`	`2`
`3`	`3`	`__all__ = ["BaseRIST"]`
`4`	`4`
`5`		`-from aeon.base.estimators.hybrid.base_rist import BaseRIST`
	`5`	`+from aeon.base._estimators.hybrid.base_rist import BaseRIST`
Original file line number	Diff line number	Diff line change
`@@ -2,4 +2,4 @@`
`2`	`2`
`3`	`3`	`__all__ = ["BaseIntervalForest"]`
`4`	`4`
`5`		`-from aeon.base.estimators.interval_based.base_interval_forest import BaseIntervalForest`
	`5`	`+from aeon.base._estimators.interval_based.base_interval_forest import BaseIntervalForest`
Original file line number	Diff line number	Diff line change
`@@ -10,7 +10,7 @@`
`10`	`10`	`import numpy as np`
`11`	`11`	`from sklearn.utils import check_random_state`
`12`	`12`
`13`		`-from aeon.base.estimators.compose.collection_channel_ensemble import (`
	`13`	`+from aeon.base._estimators.compose.collection_channel_ensemble import (`
`14`	`14`	`BaseCollectionChannelEnsemble,`
`15`	`15`	`)`
`16`	`16`	`from aeon.classification.base import BaseClassifier`
Original file line number	Diff line number	Diff line change
`@@ -3,9 +3,11 @@`
`3`	`3`	`__all__ = [`
`4`	`4`	`"RotationForestClassifier",`
`5`	`5`	`"ContinuousIntervalTree",`
	`6`	`+ "SklearnClassifierWrapper",`
`6`	`7`	`]`
`7`	`8`
`8`	`9`	`from aeon.classification.sklearn._continuous_interval_tree import ContinuousIntervalTree`
`9`	`10`	`from aeon.classification.sklearn._rotation_forest_classifier import (`
`10`	`11`	`RotationForestClassifier,`
`11`	`12`	`)`
	`13`	`+from aeon.classification.sklearn._wrapper import SklearnClassifierWrapper`
Original file line number	Diff line number	Diff line change
`@@ -8,6 +8,7 @@`
`8`	`8`	`"VALID_BA_METRICS",`
`9`	`9`	`"shift_invariant_average",`
`10`	`10`	`]`
	`11`	`+`
`11`	`12`	`from aeon.clustering.averaging._averaging import mean_average`
`12`	`13`	`from aeon.clustering.averaging._ba_petitjean import petitjean_barycenter_average`
`13`	`14`	`from aeon.clustering.averaging._ba_subgradient import subgradient_barycenter_average`