remove reference np.float64

Author: Juan Orduz

pymc_bart/bart.py

@@ -132,7 +132,7 @@ def __new__(
         alpha: float = 0.95,
         beta: float = 2.0,
         response: str = "constant",
-        split_prior: Optional[npt.NDArray[np.float64]] = None,
+        split_prior: Optional[npt.NDArray] = None,
         split_rules: Optional[list[SplitRule]] = None,
         separate_trees: Optional[bool] = False,
         **kwargs,
@@ -203,9 +203,7 @@ def get_moment(cls, rv, size, *rv_inputs):
         return mean
 
 
-def preprocess_xy(
-    X: TensorLike, Y: TensorLike
-) -> tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]]:
+def preprocess_xy(X: TensorLike, Y: TensorLike) -> tuple[npt.NDArray, npt.NDArray]:
     if isinstance(Y, (Series, DataFrame)):
         Y = Y.to_numpy()
     if isinstance(X, (Series, DataFrame)):

pymc_bart/pgbart.py

@@ -325,7 +325,7 @@ def normalize(self, particles: list[ParticleTree]) -> float:
         return wei / wei.sum()
 
     def resample(
-        self, particles: list[ParticleTree], normalized_weights: npt.NDArray[np.float64]
+        self, particles: list[ParticleTree], normalized_weights: npt.NDArray
     ) -> list[ParticleTree]:
         """
         Use systematic resample for all but the first particle
@@ -347,7 +347,7 @@ def resample(
         return particles
 
     def get_particle_tree(
-        self, particles: list[ParticleTree], normalized_weights: npt.NDArray[np.float64]
+        self, particles: list[ParticleTree], normalized_weights: npt.NDArray
     ) -> tuple[ParticleTree, Tree]:
         """
         Sample a new particle and associated tree
@@ -359,7 +359,7 @@ def get_particle_tree(
 
         return new_particle, new_particle.tree
 
-    def systematic(self, normalized_weights: npt.NDArray[np.float64]) -> npt.NDArray[np.int_]:
+    def systematic(self, normalized_weights: npt.NDArray) -> npt.NDArray[np.int_]:
         """
         Systematic resampling.
 
@@ -411,7 +411,7 @@ def __init__(self, shape: tuple) -> None:
         self.mean = np.zeros(shape)  # running mean
         self.m_2 = np.zeros(shape)  # running second moment
 
-    def update(self, new_value: npt.NDArray[np.float64]) -> Union[float, npt.NDArray[np.float64]]:
+    def update(self, new_value: npt.NDArray) -> Union[float, npt.NDArray]:
         self.count = self.count + 1
         self.mean, self.m_2, std = _update(self.count, self.mean, self.m_2, new_value)
         return fast_mean(std)
@@ -420,21 +420,21 @@ def update(self, new_value: npt.NDArray[np.float64]) -> Union[float, npt.NDArray
 @njit
 def _update(
     count: int,
-    mean: npt.NDArray[np.float64],
-    m_2: npt.NDArray[np.float64],
-    new_value: npt.NDArray[np.float64],
-) -> tuple[npt.NDArray[np.float64], npt.NDArray[np.float64], Union[float, npt.NDArray[np.float64]]]:
+    mean: npt.NDArray,
+    m_2: npt.NDArray,
+    new_value: npt.NDArray,
+) -> tuple[npt.NDArray, npt.NDArray, Union[float, npt.NDArray]]:
     delta = new_value - mean
     mean += delta / count
     delta2 = new_value - mean
     m_2 += delta * delta2
 
     std = (m_2 / count) ** 0.5
-    return mean.astype(np.float64), m_2.astype(np.float64), std.astype(np.float64)
+    return mean, m_2, std
 
 
 class SampleSplittingVariable:
-    def __init__(self, alpha_vec: npt.NDArray[np.float64]) -> None:
+    def __init__(self, alpha_vec: npt.NDArray) -> None:
         """
         Sample splitting variables proportional to `alpha_vec`.
 
@@ -547,16 +547,16 @@ def filter_missing_values(available_splitting_values, idx_data_points, missing_d
 
 
 def draw_leaf_value(
-    y_mu_pred: npt.NDArray[np.float64],
-    x_mu: npt.NDArray[np.float64],
+    y_mu_pred: npt.NDArray,
+    x_mu: npt.NDArray,
     m: int,
-    norm: npt.NDArray[np.float64],
+    norm: npt.NDArray,
     shape: int,
     response: str,
-) -> tuple[npt.NDArray[np.float64], Optional[npt.NDArray[np.float64]]]:
+) -> tuple[npt.NDArray, Optional[npt.NDArray]]:
     """Draw Gaussian distributed leaf values."""
     linear_params = None
-    mu_mean: npt.NDArray[np.float64]
+    mu_mean: npt.NDArray
     if y_mu_pred.size == 0:
         return np.zeros(shape), linear_params
 
@@ -571,7 +571,7 @@ def draw_leaf_value(
 
 
 @njit
-def fast_mean(ari: npt.NDArray[np.float64]) -> Union[float, npt.NDArray[np.float64]]:
+def fast_mean(ari: npt.NDArray) -> Union[float, npt.NDArray]:
     """Use Numba to speed up the computation of the mean."""
     if ari.ndim == 1:
         count = ari.shape[0]
@@ -590,11 +590,11 @@ def fast_mean(ari: npt.NDArray[np.float64]) -> Union[float, npt.NDArray[np.float
 
 @njit
 def fast_linear_fit(
-    x: npt.NDArray[np.float64],
-    y: npt.NDArray[np.float64],
+    x: npt.NDArray,
+    y: npt.NDArray,
     m: int,
-    norm: npt.NDArray[np.float64],
-) -> tuple[npt.NDArray[np.float64], list[npt.NDArray[np.float64]]]:
+    norm: npt.NDArray,
+) -> tuple[npt.NDArray, list[npt.NDArray]]:
     n = len(x)
     y = (y / m + np.expand_dims(norm, axis=1)).astype(np.float64)
 
@@ -678,17 +678,17 @@ def update(self):
 
 @njit
 def inverse_cdf(
-    single_uniform: npt.NDArray[np.float64], normalized_weights: npt.NDArray[np.float64]
+    single_uniform: npt.NDArray, normalized_weights: npt.NDArray
 ) -> npt.NDArray[np.int_]:
     """
     Inverse CDF algorithm for a finite distribution.
 
     Parameters
     ----------
-    single_uniform: npt.NDArray[np.float64]
+    single_uniform: npt.NDArray
         Ordered points in [0,1]
 
-    normalized_weights: npt.NDArray[np.float64])
+    normalized_weights: npt.NDArray)
         Normalized weights
 
     Returns
@@ -711,7 +711,7 @@ def inverse_cdf(
 
 
 @njit
-def jitter_duplicated(array: npt.NDArray[np.float64], std: float) -> npt.NDArray[np.float64]:
+def jitter_duplicated(array: npt.NDArray, std: float) -> npt.NDArray:
     """
     Jitter duplicated values.
     """
@@ -727,7 +727,7 @@ def jitter_duplicated(array: npt.NDArray[np.float64], std: float) -> npt.NDArray
 
 
 @njit
-def are_whole_number(array: npt.NDArray[np.float64]) -> np.bool_:
+def are_whole_number(array: npt.NDArray) -> np.bool_:
     """Check if all values in array are whole numbers"""
     return np.all(np.mod(array[~np.isnan(array)], 1) == 0)
 

pymc_bart/tree.py

@@ -28,7 +28,7 @@ class Node:
 
     Attributes
     ----------
-    value : npt.NDArray[np.float64]
+    value : npt.NDArray
     idx_data_points : Optional[npt.NDArray[np.int_]]
     idx_split_variable : int
     linear_params: Optional[list[float]] = None
@@ -38,11 +38,11 @@ class Node:
 
     def __init__(
         self,
-        value: npt.NDArray[np.float64] = np.array([-1.0]),
+        value: npt.NDArray = np.array([-1.0]),
         nvalue: int = 0,
         idx_data_points: Optional[npt.NDArray[np.int_]] = None,
         idx_split_variable: int = -1,
-        linear_params: Optional[list[npt.NDArray[np.float64]]] = None,
+        linear_params: Optional[list[npt.NDArray]] = None,
     ) -> None:
         self.value = value
         self.nvalue = nvalue
@@ -53,11 +53,11 @@ def __init__(
     @classmethod
     def new_leaf_node(
         cls,
-        value: npt.NDArray[np.float64],
+        value: npt.NDArray,
         nvalue: int = 0,
         idx_data_points: Optional[npt.NDArray[np.int_]] = None,
         idx_split_variable: int = -1,
-        linear_params: Optional[list[npt.NDArray[np.float64]]] = None,
+        linear_params: Optional[list[npt.NDArray]] = None,
     ) -> "Node":
         return cls(
             value=value,
@@ -101,7 +101,7 @@ class Tree:
         The dictionary's keys are integers that represent the nodes position.
         The dictionary's values are objects of type Node that represent the split and leaf nodes
         of the tree itself.
-    output: Optional[npt.NDArray[np.float64]]
+    output: Optional[npt.NDArray]
         Array of shape number of observations, shape
     split_rules : list[SplitRule]
         List of SplitRule objects, one per column in input data.
@@ -122,7 +122,7 @@ class Tree:
     def __init__(
         self,
         tree_structure: dict[int, Node],
-        output: npt.NDArray[np.float64],
+        output: npt.NDArray,
         split_rules: list[SplitRule],
         idx_leaf_nodes: Optional[list[int]] = None,
     ) -> None:
@@ -134,7 +134,7 @@ def __init__(
     @classmethod
     def new_tree(
         cls,
-        leaf_node_value: npt.NDArray[np.float64],
+        leaf_node_value: npt.NDArray,
         idx_data_points: Optional[npt.NDArray[np.int_]],
         num_observations: int,
         shape: int,
@@ -190,7 +190,7 @@ def grow_leaf_node(
         self,
         current_node: Node,
         selected_predictor: int,
-        split_value: npt.NDArray[np.float64],
+        split_value: npt.NDArray,
         index_leaf_node: int,
     ) -> None:
         current_node.value = split_value
@@ -222,7 +222,7 @@ def get_split_variables(self) -> Generator[int, None, None]:
             if node.is_split_node():
                 yield node.idx_split_variable
 
-    def _predict(self) -> npt.NDArray[np.float64]:
+    def _predict(self) -> npt.NDArray:
         output = self.output
 
         if self.idx_leaf_nodes is not None:
@@ -233,23 +233,23 @@ def _predict(self) -> npt.NDArray[np.float64]:
 
     def predict(
         self,
-        x: npt.NDArray[np.float64],
+        x: npt.NDArray,
         excluded: Optional[list[int]] = None,
         shape: int = 1,
-    ) -> npt.NDArray[np.float64]:
+    ) -> npt.NDArray:
         """
         Predict output of tree for an (un)observed point x.
 
         Parameters
         ----------
-        x : npt.NDArray[np.float64]
+        x : npt.NDArray
             Unobserved point
         excluded: Optional[list[int]]
             Indexes of the variables to exclude when computing predictions
 
         Returns
         -------
-        npt.NDArray[np.float64]
+        npt.NDArray
             Value of the leaf value where the unobserved point lies.
         """
         if excluded is None:
@@ -259,16 +259,16 @@ def predict(
 
     def _traverse_tree(
         self,
-        X: npt.NDArray[np.float64],
+        X: npt.NDArray,
         excluded: Optional[list[int]] = None,
         shape: Union[int, tuple[int, ...]] = 1,
-    ) -> npt.NDArray[np.float64]:
+    ) -> npt.NDArray:
         """
         Traverse the tree starting from the root node given an (un)observed point.
 
         Parameters
         ----------
-        X : npt.NDArray[np.float64]
+        X : npt.NDArray
             (Un)observed point(s)
         node_index : int
             Index of the node to start the traversal from
@@ -279,7 +279,7 @@ def _traverse_tree(
 
         Returns
         -------
-        npt.NDArray[np.float64]
+        npt.NDArray
             Leaf node value or mean of leaf node values
         """
 
@@ -338,14 +338,14 @@ def _traverse_tree(
         return p_d
 
     def _traverse_leaf_values(
-        self, leaf_values: list[npt.NDArray[np.float64]], leaf_n_values: list[int], node_index: int
+        self, leaf_values: list[npt.NDArray], leaf_n_values: list[int], node_index: int
     ) -> None:
         """
         Traverse the tree appending leaf values starting from a particular node.
 
         Parameters
         ----------
-        leaf_values : list[npt.NDArray[np.float64]]
+        leaf_values : list[npt.NDArray]
         node_index : int
         """
         node = self.get_node(node_index)