Merge branch 'main' into doc_build, fix library import conflicts

Author: jay-m-dev

ImputerExperiments/data/r/.DS_Store

@@ -6,4 +6,4 @@ mkdocs-jupyter==0.25.0
 mkdocs-material==9.5.35
 mkdocstrings==0.26.1
 mkdocstrings-python==1.11.1
-nbconvert==7.16.4
+nbconvert==7.16.5

docs/requirements_docs.txt

@@ -3,7 +3,6 @@
 #TODO update this
 from setuptools import setup, find_packages
 
-
 def calculate_version():
     initpy = open('tpot/_version.py').read().split('\n')
     version = list(filter(lambda x: '__version__' in x, initpy))[0].split('\'')[1]

setup.py

@@ -32,4 +32,4 @@
 License along with TPOT. If not, see <http://www.gnu.org/licenses/>.
 
 """
-__version__ = '1.0.0'
+__version__ = '0.1.9a0'

tpot/_version.py

@@ -1,6 +1,6 @@
 from .feature_set_selector import FeatureSetSelector
 from .zero_count import ZeroCount
-from .column_one_hot_encoder import ColumnOneHotEncoder
+from .column_one_hot_encoder import ColumnOneHotEncoder, ColumnOrdinalEncoder
 from .arithmetictransformer import ArithmeticTransformer
 from .arithmetictransformer import AddTransformer, mul_neg_1_Transformer, MulTransformer, SafeReciprocalTransformer, EQTransformer, NETransformer, GETransformer, GTTransformer, LETransformer, LTTransformer, MinTransformer, MaxTransformer, ZeroTransformer, OneTransformer, NTransformer
 from .passthrough import Passthrough, SkipTransformer

tpot/builtin_modules/__init__.py

@@ -37,7 +37,7 @@
 
 from sklearn.base import BaseEstimator, TransformerMixin
 from sklearn.utils import check_array
-from sklearn.preprocessing import OneHotEncoder
+from sklearn.preprocessing import OneHotEncoder, OrdinalEncoder
 import sklearn
 
 import pandas as pd
@@ -203,3 +203,138 @@ def transform(self, X):
                 return pd.concat([X_not_sel.reset_index(drop=True), X_sel.reset_index(drop=True)], axis=1)
             else:
                 return np.hstack((X_not_sel, X_sel))
+
+class ColumnOrdinalEncoder(BaseEstimator, TransformerMixin):
+
+
+    def __init__(self, columns='auto', handle_unknown='error', unknown_value = -1, encoded_missing_value = np.nan, min_frequency=None,max_categories=None):
+        '''
+        
+        Parameters
+        ----------
+
+        columns : str, list, default='auto'
+            Determines which columns to onehot encode with sklearn.preprocessing.OneHotEncoder.
+            - 'auto' : Automatically select categorical features based on columns with less than 10 unique values
+            - 'categorical' : Automatically select categorical features
+            - 'numeric' : Automatically select numeric features
+            - 'all' : Select all features
+            - list : A list of columns to select
+        
+        drop, handle_unknown, sparse_output, min_frequency, max_categories : see sklearn.preprocessing.OneHotEncoder
+
+        '''
+
+        self.columns = columns
+        self.handle_unknown = handle_unknown
+        self.unknown_value = unknown_value
+        self.encoded_missing_value = encoded_missing_value
+        self.min_frequency = min_frequency
+        self.max_categories = max_categories
+
+
+
+    def fit(self, X, y=None):
+        """Fit OneHotEncoder to X, then transform X.
+
+        Equivalent to self.fit(X).transform(X), but more convenient and more
+        efficient. See fit for the parameters, transform for the return value.
+
+        Parameters
+        ----------
+        X : array-like or sparse matrix, shape=(n_samples, n_features)
+            Dense array or sparse matrix.
+        y: array-like {n_samples,} (Optional, ignored)
+            Feature labels
+        """
+        
+        if (self.columns == "categorical" or self.columns == "numeric") and not isinstance(X, pd.DataFrame):
+            raise ValueError(f"Invalid value for columns: {self.columns}. "
+                             "Only 'all' or <list> is supported for np arrays")
+
+        if self.columns == "categorical":
+            self.columns_ = list(X.select_dtypes(exclude='number').columns)
+        elif self.columns == "numeric":
+            self.columns_ =  [col for col in X.columns if is_numeric_dtype(X[col])]
+        elif self.columns == "auto":
+            self.columns_ = auto_select_categorical_features(X)
+        elif self.columns == "all":
+            if isinstance(X, pd.DataFrame):
+                self.columns_ = X.columns
+            else:
+                self.columns_ = list(range(X.shape[1]))
+        elif isinstance(self.columns, list):
+            self.columns_ = self.columns
+        else:
+            raise ValueError(f"Invalid value for columns: {self.columns}")
+
+        if len(self.columns_) == 0:
+            return self
+        
+        self.enc = sklearn.preprocessing.OrdinalEncoder(categories='auto',   
+                                                        handle_unknown = self.handle_unknown,
+                                                        unknown_value = self.unknown_value, 
+                                                        encoded_missing_value = self.encoded_missing_value,
+                                                        min_frequency = self.min_frequency,
+                                                        max_categories = self.max_categories)
+        #TODO make this more consistent with sklearn baseimputer/baseencoder
+        '''
+        if isinstance(X, pd.DataFrame):
+            self.enc.set_output(transform="pandas")
+            for col in X.columns:
+                # check if the column name is not a string
+                if not isinstance(col, str):
+                    # if it's not a string, rename the column with "X" prefix
+                    X.rename(columns={col: f"X{col}"}, inplace=True)
+        '''
+
+        if len(self.columns_) == X.shape[1]:
+            X_sel = self.enc.fit(X)
+        else:
+            X_sel, X_not_sel = _X_selected(X, self.columns_)
+            X_sel = self.enc.fit(X_sel)
+        
+        return self
+  
+    def transform(self, X):
+        """Transform X using one-hot encoding.
+
+        Parameters
+        ----------
+        X : array-like or sparse matrix, shape=(n_samples, n_features)
+            Dense array or sparse matrix.
+
+        Returns
+        -------
+        X_out : sparse matrix if sparse=True else a 2-d array, dtype=int
+            Transformed input.
+        """
+
+    
+        if len(self.columns_) == 0:
+            return X
+        
+        #TODO make this more consistent with sklearn baseimputer/baseencoder
+        '''
+        if isinstance(X, pd.DataFrame):
+            for col in X.columns:
+                # check if the column name is not a string
+                if not isinstance(col, str):
+                    # if it's not a string, rename the column with "X" prefix
+                    X.rename(columns={col: f"X{col}"}, inplace=True)
+        '''
+
+        if len(self.columns_) == X.shape[1]:
+            return self.enc.transform(X)
+        else:
+
+            X_sel, X_not_sel= _X_selected(X, self.columns_)
+            X_sel = self.enc.transform(X_sel)
+            
+            #If X is dataframe
+            if isinstance(X, pd.DataFrame):
+            
+                X_sel = pd.DataFrame(X_sel, columns=self.enc.get_feature_names_out())
+                return pd.concat([X_not_sel.reset_index(drop=True), X_sel.reset_index(drop=True)], axis=1)
+            else:
+                return np.hstack((X_not_sel, X_sel))

tpot/builtin_modules/column_one_hot_encoder.py

@@ -60,7 +60,7 @@
 from tpot.builtin_modules import genetic_encoders, feature_encoding_frequency_selector
 from tpot.builtin_modules import AddTransformer, mul_neg_1_Transformer, MulTransformer, SafeReciprocalTransformer, EQTransformer, NETransformer, GETransformer, GTTransformer, LETransformer, LTTransformer, MinTransformer, MaxTransformer, ZeroTransformer, OneTransformer, NTransformer
 from tpot.builtin_modules.genetic_encoders import DominantEncoder, RecessiveEncoder, HeterosisEncoder, UnderDominanceEncoder, OverDominanceEncoder 
-from tpot.builtin_modules import ZeroCount, ColumnOneHotEncoder, PassKBinsDiscretizer
+from tpot.builtin_modules import ZeroCount, ColumnOneHotEncoder, ColumnOrdinalEncoder, PassKBinsDiscretizer
 from tpot.builtin_modules import Passthrough, SkipTransformer
 from sklearn.linear_model import SGDClassifier, LogisticRegression, SGDRegressor, Ridge, Lasso, ElasticNet, Lars, LassoLars, LassoLarsCV, RidgeCV, ElasticNetCV, PassiveAggressiveClassifier, ARDRegression
 from sklearn.ensemble import BaggingClassifier, RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, ExtraTreesRegressor, ExtraTreesClassifier, AdaBoostRegressor, AdaBoostClassifier, GradientBoostingRegressor,RandomForestRegressor, BaggingRegressor, ExtraTreesRegressor, HistGradientBoostingClassifier, HistGradientBoostingRegressor
@@ -86,7 +86,7 @@
 import sklearn.calibration
 
 
-all_methods = [SGDClassifier, RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, MLPClassifier, DecisionTreeClassifier, XGBClassifier, KNeighborsClassifier, SVC, LogisticRegression, LGBMClassifier, LinearSVC, GaussianNB, BernoulliNB, MultinomialNB, ExtraTreesRegressor, RandomForestRegressor, GradientBoostingRegressor, BaggingRegressor, DecisionTreeRegressor, KNeighborsRegressor, XGBRegressor,  ZeroCount, ColumnOneHotEncoder, Binarizer, FastICA, FeatureAgglomeration, MaxAbsScaler, MinMaxScaler, Normalizer, Nystroem, PCA, PolynomialFeatures, RBFSampler, RobustScaler, StandardScaler, SelectFwe, SelectPercentile, VarianceThreshold, SGDRegressor, Ridge, Lasso, ElasticNet, Lars, LassoLars, LassoLarsCV, RidgeCV, SVR, LinearSVR, AdaBoostRegressor, GradientBoostingRegressor, RandomForestRegressor, BaggingRegressor, ExtraTreesRegressor, DecisionTreeRegressor, KNeighborsRegressor, ElasticNetCV,
+all_methods = [SGDClassifier, RandomForestClassifier, ExtraTreesClassifier, GradientBoostingClassifier, MLPClassifier, DecisionTreeClassifier, XGBClassifier, KNeighborsClassifier, SVC, LogisticRegression, LGBMClassifier, LinearSVC, GaussianNB, BernoulliNB, MultinomialNB, ExtraTreesRegressor, RandomForestRegressor, GradientBoostingRegressor, BaggingRegressor, DecisionTreeRegressor, KNeighborsRegressor, XGBRegressor,  ZeroCount, ColumnOneHotEncoder, ColumnOrdinalEncoder, Binarizer, FastICA, FeatureAgglomeration, MaxAbsScaler, MinMaxScaler, Normalizer, Nystroem, PCA, PolynomialFeatures, RBFSampler, RobustScaler, StandardScaler, SelectFwe, SelectPercentile, VarianceThreshold, SGDRegressor, Ridge, Lasso, ElasticNet, Lars, LassoLars, LassoLarsCV, RidgeCV, SVR, LinearSVR, AdaBoostRegressor, GradientBoostingRegressor, RandomForestRegressor, BaggingRegressor, ExtraTreesRegressor, DecisionTreeRegressor, KNeighborsRegressor, ElasticNetCV,
                AdaBoostClassifier,MLPRegressor,
                GaussianProcessRegressor, HistGradientBoostingClassifier, HistGradientBoostingRegressor,
                AddTransformer, mul_neg_1_Transformer, MulTransformer, SafeReciprocalTransformer, EQTransformer, NETransformer, GETransformer, GTTransformer, LETransformer, LTTransformer, MinTransformer, MaxTransformer, ZeroTransformer, OneTransformer, NTransformer,
@@ -155,19 +155,17 @@
         "selectors": ["SelectFwe", "SelectPercentile", "VarianceThreshold",],
         "selectors_classification": ["SelectFwe", "SelectPercentile", "VarianceThreshold", "RFE_classification", "SelectFromModel_classification"],
         "selectors_regression": ["SelectFwe", "SelectPercentile", "VarianceThreshold", "RFE_regression", "SelectFromModel_regression"],
+ 
         "classifiers" :  ["LGBMClassifier", "BaggingClassifier", 'AdaBoostClassifier', 'BernoulliNB', 'DecisionTreeClassifier', 'ExtraTreesClassifier', 'GaussianNB', 'HistGradientBoostingClassifier', 'KNeighborsClassifier','LinearDiscriminantAnalysis', 'LogisticRegression', 'MLPClassifier', 'MultinomialNB',  "QuadraticDiscriminantAnalysis", 'RandomForestClassifier', 'SGDClassifier', 'XGBClassifier'],
         "regressors" : ["LGBMRegressor", 'AdaBoostRegressor', "ARDRegression", 'DecisionTreeRegressor', 'ExtraTreesRegressor', 'HistGradientBoostingRegressor', 'KNeighborsRegressor',  'LinearSVR', "MLPRegressor", 'RandomForestRegressor', 'SGDRegressor', 'XGBRegressor'],
-        
-        
-        "transformers":  ["KBinsDiscretizer", "Binarizer", "PCA", "ZeroCount", "ColumnOneHotEncoder", "FastICA", "FeatureAgglomeration", "Nystroem", "RBFSampler", "QuantileTransformer", "PowerTransformer"],
+        "transformers":  ["KBinsDiscretizer", "Binarizer", "PCA", "ZeroCount", "FastICA", "FeatureAgglomeration", "Nystroem", "RBFSampler", "QuantileTransformer", "PowerTransformer", "ColumnOneHotEncoder", "ColumnOrdinalEncoder"],
+
         "scalers": ["MinMaxScaler", "RobustScaler", "StandardScaler", "MaxAbsScaler", "Normalizer", ],
         "all_transformers" : ["transformers", "scalers"],
-
         "arithmatic": ["AddTransformer", "mul_neg_1_Transformer", "MulTransformer", "SafeReciprocalTransformer", "EQTransformer", "NETransformer", "GETransformer", "GTTransformer", "LETransformer", "LTTransformer", "MinTransformer", "MaxTransformer"],
         "imputers": ["SimpleImputer", "IterativeImputer", "KNNImputer"],
         "skrebate": ["ReliefF", "SURF", "SURFstar", "MultiSURF"],
         "genetic_encoders": ["DominantEncoder", "RecessiveEncoder", "HeterosisEncoder", "UnderDominanceEncoder", "OverDominanceEncoder"],
-
         "classifiers_sklearnex" : ["RandomForestClassifier_sklearnex", "LogisticRegression_sklearnex", "KNeighborsClassifier_sklearnex", "SVC_sklearnex","NuSVC_sklearnex"],
         "regressors_sklearnex" : ["LinearRegression_sklearnex", "Ridge_sklearnex", "Lasso_sklearnex", "ElasticNet_sklearnex", "SVR_sklearnex", "NuSVR_sklearnex", "RandomForestRegressor_sklearnex", "KNeighborsRegressor_sklearnex"],
         "genetic encoders" : ["DominantEncoder", "RecessiveEncoder", "HeterosisEncoder", "UnderDominanceEncoder", "OverDominanceEncoder"],
@@ -352,8 +350,6 @@ def get_configspace(name, n_classes=3, n_samples=1000, n_features=100, random_st
             return transformers.get_QuantileTransformer_configspace(n_samples=n_samples, random_state=random_state)
         case "RobustScaler":
             return transformers.RobustScaler_configspace
-        case "ColumnOneHotEncoder":
-            return {}
         case "MaxAbsScaler":
             return {}
         case "PolynomialFeatures":
@@ -364,6 +360,10 @@ def get_configspace(name, n_classes=3, n_samples=1000, n_features=100, random_st
             return transformers.get_passkbinsdiscretizer_configspace(random_state=random_state)
         case "KBinsDiscretizer":
             return transformers.get_passkbinsdiscretizer_configspace(random_state=random_state)
+        case "ColumnOneHotEncoder":
+            return {}
+        case "ColumnOrdinalEncoder":
+            return {}
 
         #selectors.py
         case "SelectFwe":

tpot/config/get_configspace.py

@@ -51,7 +51,7 @@
         # and can cause errors. gk
     }
 )
-
+#test
 def get_IterativeImputer_config_space(n_features, random_state):
     space = { 'initial_strategy' : Categorical('initial_strategy', 
                                              ['mean', 'median', 

tpot/config/imputers.py

@@ -62,6 +62,8 @@
 
 OneHotEncoder_configspace = {} #TODO include the parameter for max unique values
 
+OrdinalEncoder_configspace = {} #TODO include the parameter for max unique values
+
 def get_FastICA_configspace(n_features=100, random_state=None):
 
     space = {