black formatting and imports

bamt/external/pyitlib/DiscreteRandomVariableUtils.py

@@ -8,17 +8,17 @@
 
 
 def information_mutual_conditional(
-        x,
-        y,
-        z,
-        cartesian_product=False,
-        base=2,
-        fill_value=-1,
-        estimator="ML",
-        alphabet_x=None,
-        alphabet_y=None,
-        Alphabet_Z=None,
-        keep_dims=False,
+    x,
+    y,
+    z,
+    cartesian_product=False,
+    base=2,
+    fill_value=-1,
+    estimator="ML",
+    alphabet_x=None,
+    alphabet_y=None,
+    Alphabet_Z=None,
+    keep_dims=False,
 ):
     x, fill_value_X = _sanitise_array_input(x, fill_value)
     y, fill_value_Y = _sanitise_array_input(y, fill_value)
@@ -113,6 +113,7 @@ def information_mutual_conditional(
         Alphabet_Z = np.reshape(Alphabet_Z, (-1, Alphabet_Z.shape[-1]))
         I = []
         for i in range(z.shape[0]):
+
             def f(X, Y, Alphabet_X, Alphabet_Y):
                 return information_mutual_conditional(
                     X,
@@ -150,28 +151,28 @@ def f(X, Y, Alphabet_X, Alphabet_Y):
 
     for i in range(x.shape[0]):
         I_ = (
-                entropy_joint(
-                    np.vstack((x[i], z[i])),
-                    base,
-                    fill_value,
-                    estimator,
-                    _vstack_pad((alphabet_x[i], Alphabet_Z[i]), fill_value),
-                )
-                + entropy_joint(
-            np.vstack((y[i], z[i])),
-            base,
-            fill_value,
-            estimator,
-            _vstack_pad((alphabet_y[i], Alphabet_Z[i]), fill_value),
-        )
-                - entropy_joint(
-            np.vstack((x[i], y[i], z[i])),
-            base,
-            fill_value,
-            estimator,
-            _vstack_pad((alphabet_x[i], alphabet_y[i], Alphabet_Z[i]), fill_value),
-        )
-                - entropy_joint(z[i], base, fill_value, estimator, Alphabet_Z[i])
+            entropy_joint(
+                np.vstack((x[i], z[i])),
+                base,
+                fill_value,
+                estimator,
+                _vstack_pad((alphabet_x[i], Alphabet_Z[i]), fill_value),
+            )
+            + entropy_joint(
+                np.vstack((y[i], z[i])),
+                base,
+                fill_value,
+                estimator,
+                _vstack_pad((alphabet_y[i], Alphabet_Z[i]), fill_value),
+            )
+            - entropy_joint(
+                np.vstack((x[i], y[i], z[i])),
+                base,
+                fill_value,
+                estimator,
+                _vstack_pad((alphabet_x[i], alphabet_y[i], Alphabet_Z[i]), fill_value),
+            )
+            - entropy_joint(z[i], base, fill_value, estimator, Alphabet_Z[i])
         )
         I[i] = I_
 
@@ -185,15 +186,15 @@ def f(X, Y, Alphabet_X, Alphabet_Y):
 
 
 def information_mutual(
-        X,
-        Y=None,
-        cartesian_product=False,
-        base=2,
-        fill_value=-1,
-        estimator="ML",
-        Alphabet_X=None,
-        Alphabet_Y=None,
-        keep_dims=False,
+    X,
+    Y=None,
+    cartesian_product=False,
+    base=2,
+    fill_value=-1,
+    estimator="ML",
+    Alphabet_X=None,
+    Alphabet_Y=None,
+    keep_dims=False,
 ):
     H_conditional = entropy_conditional(
         X, Y, cartesian_product, base, fill_value, estimator, Alphabet_X, Alphabet_Y
@@ -236,7 +237,7 @@ def entropy_pmf(P, base=2, require_valid_pmf=True, keep_dims=False):
 
 
 def entropy_joint(
-        X, base=2, fill_value=-1, estimator="ML", Alphabet_X=None, keep_dims=False
+    X, base=2, fill_value=-1, estimator="ML", Alphabet_X=None, keep_dims=False
 ):
     X, fill_value_X = _sanitise_array_input(X, fill_value)
     if Alphabet_X is not None:
@@ -302,15 +303,15 @@ def entropy_joint(
 
 
 def entropy_conditional(
-        X,
-        Y=None,
-        cartesian_product=False,
-        base=2,
-        fill_value=-1,
-        estimator="ML",
-        Alphabet_X=None,
-        Alphabet_Y=None,
-        keep_dims=False,
+    X,
+    Y=None,
+    cartesian_product=False,
+    base=2,
+    fill_value=-1,
+    estimator="ML",
+    Alphabet_X=None,
+    Alphabet_Y=None,
+    keep_dims=False,
 ):
     if Y is None:
         Y = X
@@ -485,10 +486,10 @@ def entropy(X, base=2, fill_value=-1, estimator="ML", Alphabet_X=None, keep_dims
         # P_0 is the probability mass assigned to each additional empty bin
         P, P_0 = _estimate_probabilities(L, estimator, n_additional_empty_bins)
         H_0 = (
-                n_additional_empty_bins
-                * P_0
-                * -np.log2(P_0 + np.spacing(0))
-                / np.log2(base)
+            n_additional_empty_bins
+            * P_0
+            * -np.log2(P_0 + np.spacing(0))
+            / np.log2(base)
         )
         H[i] = entropy_pmf(P, base, require_valid_pmf=False) + H_0
 
@@ -571,7 +572,7 @@ def _map_observations_to_integers(Symbol_matrices, Fill_values):
     assert len(Symbol_matrices) == len(Fill_values)
     FILL_VALUE = -1
     if np.any([A.dtype != "int" for A in Symbol_matrices]) or np.any(
-            np.array(Fill_values) != FILL_VALUE
+        np.array(Fill_values) != FILL_VALUE
     ):
         L = sklearn.preprocessing.LabelEncoder()
         F = [np.atleast_1d(v) for v in Fill_values]
@@ -606,7 +607,7 @@ def _isnan_element(x):
 
 
 def _determine_number_additional_empty_bins(
-        Counts, Alphabet, Full_Alphabet, fill_value
+    Counts, Alphabet, Full_Alphabet, fill_value
 ):
     alphabet_sizes = np.sum(np.atleast_2d(Full_Alphabet) != fill_value, axis=-1)
     if np.any(alphabet_sizes != fill_value):
@@ -630,34 +631,35 @@ def _estimate_probabilities(Counts, estimator, n_additional_empty_bins=0):
     # 2) James-Stein approach may be used as an alternative
     # 3) Dirichlet prior may be used in all other cases
 
-    assert (np.sum(Counts) > 0)
-    assert (np.all(Counts.astype('int') == Counts))
-    assert (n_additional_empty_bins >= 0)
-    Counts = Counts.astype('int')
+    assert np.sum(Counts) > 0
+    assert np.all(Counts.astype("int") == Counts)
+    assert n_additional_empty_bins >= 0
+    Counts = Counts.astype("int")
 
     if isinstance(estimator, str):
-        estimator = estimator.upper().replace(' ', '')
+        estimator = estimator.upper().replace(" ", "")
 
-    if np.isreal(estimator) or estimator in ('ML', 'PERKS', 'MINIMAX'):
+    if np.isreal(estimator) or estimator in ("ML", "PERKS", "MINIMAX"):
         if np.isreal(estimator):
             alpha = estimator
-        elif estimator == 'PERKS':
+        elif estimator == "PERKS":
             alpha = 1.0 / (Counts.size + n_additional_empty_bins)
-        elif estimator == 'MINIMAX':
-            alpha = np.sqrt(np.sum(Counts)) / \
-                    (Counts.size + n_additional_empty_bins)
+        elif estimator == "MINIMAX":
+            alpha = np.sqrt(np.sum(Counts)) / (Counts.size + n_additional_empty_bins)
         else:
             alpha = 0
-        Theta = (Counts + alpha) / \
-                (1.0 * np.sum(Counts) + alpha * (Counts.size + n_additional_empty_bins))
+        Theta = (Counts + alpha) / (
+            1.0 * np.sum(Counts) + alpha * (Counts.size + n_additional_empty_bins)
+        )
         # Theta_0 is the probability mass assigned to each additional empty bin
         if n_additional_empty_bins > 0:
-            Theta_0 = alpha / (1.0 * np.sum(Counts) +
-                               alpha * (Counts.size + n_additional_empty_bins))
+            Theta_0 = alpha / (
+                1.0 * np.sum(Counts) + alpha * (Counts.size + n_additional_empty_bins)
+            )
         else:
             Theta_0 = 0
 
-    elif estimator == 'GOOD-TURING':
+    elif estimator == "GOOD-TURING":
         # TODO We could also add a Chen-Chao vocabulary size estimator (See
         # Bhat Suma's thesis)
 
@@ -679,34 +681,35 @@ def _estimate_probabilities(Counts, estimator, n_additional_empty_bins=0):
 
         # Fit least squares regression line to plot of log(Z_r) versus log(r)
         x = np.log10(np.arange(1, Z_r.size))
-        with np.errstate(invalid='ignore', divide='ignore'):
+        with np.errstate(invalid="ignore", divide="ignore"):
             y = np.log10(Z_r[1:])
         x = x[np.isfinite(y)]
         y = y[np.isfinite(y)]
-        m, c = np.linalg.lstsq(np.vstack([x, np.ones(x.size)]).T, y,
-                               rcond=None)[0]
+        m, c = np.linalg.lstsq(np.vstack([x, np.ones(x.size)]).T, y, rcond=None)[0]
         if m >= -1:
-            warnings.warn("Regression slope < -1 requirement in linear "
-                          "Good-Turing estimate not satisfied")
+            warnings.warn(
+                "Regression slope < -1 requirement in linear "
+                "Good-Turing estimate not satisfied"
+            )
         # Compute smoothed value of N_r based on interpolation
         # We need to refer to SmoothedN_{r+1} for all observed values of r
         SmoothedN_r = np.zeros(N_r.size + 1)
-        SmoothedN_r[1:] = 10 ** (np.log10(np.arange(1, SmoothedN_r.size)) *
-                                 m + c)
+        SmoothedN_r[1:] = 10 ** (np.log10(np.arange(1, SmoothedN_r.size)) * m + c)
 
         # Determine threshold value of r at which to use smoothed values of N_r
         # (SmoothedN_r), as apposed to straightforward N_r.
         # Variance of Turing estimate
-        with np.errstate(invalid='ignore', divide='ignore'):
-            VARr_T = (np.arange(N_r.size) + 1) ** 2 * \
-                     (1.0 * np.append(N_r[1:], 0) / (N_r ** 2)) * \
-                     (1 + np.append(N_r[1:], 0) / N_r)
+        with np.errstate(invalid="ignore", divide="ignore"):
+            VARr_T = (
+                (np.arange(N_r.size) + 1) ** 2
+                * (1.0 * np.append(N_r[1:], 0) / (N_r**2))
+                * (1 + np.append(N_r[1:], 0) / N_r)
+            )
             x = (np.arange(N_r.size) + 1) * 1.0 * np.append(N_r[1:], 0) / N_r
-            y = (np.arange(N_r.size) + 1) * \
-                1.0 * SmoothedN_r[1:] / (SmoothedN_r[:-1])
-            assert (np.isinf(VARr_T[0]) or np.isnan(VARr_T[0]))
+            y = (np.arange(N_r.size) + 1) * 1.0 * SmoothedN_r[1:] / (SmoothedN_r[:-1])
+            assert np.isinf(VARr_T[0]) or np.isnan(VARr_T[0])
             turing_is_sig_diff = np.abs(x - y) > 1.96 * np.sqrt(VARr_T)
-        assert (turing_is_sig_diff[0] == np.array(False))
+        assert turing_is_sig_diff[0] == np.array(False)
         # NB: 0th element can be safely ignored, since always 0
         T = np.where(turing_is_sig_diff == np.array(False))[0]
         if T.size > 1:
@@ -722,8 +725,12 @@ def _estimate_probabilities(Counts, estimator, n_additional_empty_bins=0):
         # objects observed r times, r>0
         p_r = np.zeros(N_r.size)
         N = np.sum(Counts)
-        p_r[1:] = (np.arange(1, N_r.size) + 1) * \
-                  1.0 * SmoothedN_r[2:] / (SmoothedN_r[1:-1] * N)
+        p_r[1:] = (
+            (np.arange(1, N_r.size) + 1)
+            * 1.0
+            * SmoothedN_r[2:]
+            / (SmoothedN_r[1:-1] * N)
+        )
         # Estimate probability of observing any unseen symbol
         p_r[0] = 1.0 * N_r[1] / N
 
@@ -735,30 +742,34 @@ def _estimate_probabilities(Counts, estimator, n_additional_empty_bins=0):
         if np.any(Counts == 0) or n_additional_empty_bins > 0:
             Theta = (1 - p_r[0]) * Theta / np.sum(Theta)
         else:
-            warnings.warn("No unobserved outcomes specified. Disregarding the "
-                          "probability mass allocated to any unobserved "
-                          "outcomes.")
+            warnings.warn(
+                "No unobserved outcomes specified. Disregarding the "
+                "probability mass allocated to any unobserved "
+                "outcomes."
+            )
             Theta = Theta / np.sum(Theta)
 
         # Divide p_0 among unobserved symbols
-        with np.errstate(invalid='ignore', divide='ignore'):
-            p_emptybin = p_r[0] / (np.sum(Counts == 0) +
-                                   n_additional_empty_bins)
+        with np.errstate(invalid="ignore", divide="ignore"):
+            p_emptybin = p_r[0] / (np.sum(Counts == 0) + n_additional_empty_bins)
         Theta[Counts == 0] = p_emptybin
         # Theta_0 is the probability mass assigned to each additional empty bin
         if n_additional_empty_bins > 0:
             Theta_0 = p_emptybin
         else:
             Theta_0 = 0
 
-    elif estimator == 'JAMES-STEIN':
-        Theta, _ = _estimate_probabilities(Counts, 'ML')
+    elif estimator == "JAMES-STEIN":
+        Theta, _ = _estimate_probabilities(Counts, "ML")
         p_uniform = 1.0 / (Counts.size + n_additional_empty_bins)
-        with np.errstate(invalid='ignore', divide='ignore'):
-            Lambda = (1 - np.sum(Theta ** 2)) / \
-                     ((np.sum(Counts) - 1) *
-                      (np.sum((p_uniform - Theta) ** 2) +
-                       n_additional_empty_bins * p_uniform ** 2))
+        with np.errstate(invalid="ignore", divide="ignore"):
+            Lambda = (1 - np.sum(Theta**2)) / (
+                (np.sum(Counts) - 1)
+                * (
+                    np.sum((p_uniform - Theta) ** 2)
+                    + n_additional_empty_bins * p_uniform**2
+                )
+            )
 
         if Lambda > 1:
             Lambda = 1

bamt/log.py

@@ -39,7 +39,9 @@ def switch_console_out(self, value: bool):
         for logger in self.loggers.values():
             if self.has_handler(logger, handler_class):
                 self.remove_handler_type(logger, handler_class)
-                logger.addHandler(logging.NullHandler() if not value else logging.root.handlers[0])
+                logger.addHandler(
+                    logging.NullHandler() if not value else logging.root.handlers[0]
+                )
 
     def switch_file_out(self, value: bool, log_file: str):
         """

bamt/nodes/conditional_mixture_gaussian_node.py

@@ -165,11 +165,11 @@ def choose(
         mean, covariance, w = self.get_dist(node_info, pvals)
 
         # check if w is nan or list of weights
-        if not isinstance(w,  np.ndarray):
+        if not isinstance(w, np.ndarray):
             return np.nan
-            
+
         n_comp = len(w)
-        
+
         gmm = GMM(
             n_components=n_comp,
             priors=w,

bamt/utils/composite_utils/MLUtils.py

@@ -1,9 +1,8 @@
 import json
 from random import choice
-
-import pkg_resources
 from typing import Union
 
+import pkg_resources
 from catboost import CatBoostClassifier, CatBoostRegressor
 from golem.core.dag.graph_node import GraphNode
 from sklearn.cluster import KMeans

docs/source/conf.py

@@ -9,7 +9,6 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 
-import datetime
 import sys
 from pathlib import Path
 

tests/sendingRegressors.py

@@ -4,7 +4,6 @@
 from catboost import CatBoostRegressor
 from sklearn import preprocessing as pp
 from sklearn.ensemble import RandomForestRegressor
-
 # from sklearn.linear_model import ElasticNet
 from sklearn.tree import DecisionTreeRegressor