switch to use NDArray

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.2
+  hooks:
+    - id: ruff
+      args: [ --fix ]
+    - id: ruff-format
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v1.10.0
+  hooks:
+    - id: mypy
+      files: ^src

src/mrtool/core/cov_model.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 import xspline
+from numpy.typing import NDArray
 
 from . import utils
 from .data import MRData
@@ -438,7 +439,7 @@ def has_data(self):
             return True
 
     def create_spline(
-        self, data: MRData, spline_knots: np.ndarray = None
+        self, data: MRData, spline_knots: NDArray | None = None
     ) -> xspline.XSpline:
         """Create spline given current spline parameters.
         Parameters
@@ -525,7 +526,7 @@ def create_spline(
 
         return spline
 
-    def create_design_mat(self, data) -> tuple[np.ndarray, np.ndarray]:
+    def create_design_mat(self, data) -> tuple[NDArray, NDArray]:
         """Create design matrix.
         Parameters
         ----------
@@ -564,7 +565,7 @@ def create_z_mat(self, data):
             "Cannot use create_z_mat directly in CovModel class."
         )
 
-    def create_constraint_mat(self) -> tuple[np.ndarray, np.ndarray]:
+    def create_constraint_mat(self) -> tuple[NDArray, NDArray]:
         """Create constraint matrix.
         Returns:
             tuple{numpy.ndarray, numpy.ndarray}:
@@ -679,7 +680,7 @@ def create_constraint_mat(self) -> tuple[np.ndarray, np.ndarray]:
 
         return c_mat, c_val
 
-    def create_regularization_mat(self) -> tuple[np.ndarray, np.ndarray]:
+    def create_regularization_mat(self) -> tuple[NDArray, NDArray]:
         """Create constraint matrix.
         Returns:
             tuple{numpy.ndarray, numpy.ndarray}:

src/mrtool/core/data.py

@@ -12,6 +12,7 @@
 
 import numpy as np
 import pandas as pd
+from numpy.typing import NDArray
 
 from .utils import empty_array, expand_array, is_numeric_array, to_list
 
@@ -20,11 +21,11 @@
 class MRData:
     """Data for simple linear mixed effects model."""
 
-    obs: np.ndarray = field(default_factory=empty_array)
-    obs_se: np.ndarray = field(default_factory=empty_array)
-    covs: dict[str, np.ndarray] = field(default_factory=dict)
-    study_id: np.ndarray = field(default_factory=empty_array)
-    data_id: np.ndarray = field(default_factory=empty_array)
+    obs: NDArray = field(default_factory=empty_array)
+    obs_se: NDArray = field(default_factory=empty_array)
+    covs: dict[str, NDArray] = field(default_factory=dict)
+    study_id: NDArray = field(default_factory=empty_array)
+    data_id: NDArray = field(default_factory=empty_array)
     cov_scales: dict[str, float] = field(init=False, default_factory=dict)
 
     def __post_init__(self):
@@ -121,7 +122,7 @@ def _get_study_structure(self):
         )
         self._sort_by_study_id()
 
-    def _sort_data(self, index: np.ndarray):
+    def _sort_data(self, index: NDArray):
         """Sort the object.
 
         Parameters
@@ -166,7 +167,7 @@ def _remove_nan_in_covs(self):
                 index = index | cov_index
             self._remove_data(index)
 
-    def _remove_data(self, index: np.ndarray):
+    def _remove_data(self, index: NDArray):
         """Remove the data point by index.
 
         Parameters
@@ -186,7 +187,7 @@ def _remove_data(self, index: np.ndarray):
         self.study_id = self.study_id[keep_index]
         self.data_id = self.data_id[keep_index]
 
-    def _get_data(self, index: np.ndarray) -> "MRData":
+    def _get_data(self, index: NDArray) -> "MRData":
         """Get the data point by index.
 
         Parameters
@@ -383,7 +384,7 @@ def _assert_has_studies(self, studies: list[Any] | Any):
                 f"MRData object do not contain studies: {missing_studies}."
             )
 
-    def get_covs(self, covs: list[str] | str) -> np.ndarray:
+    def get_covs(self, covs: list[str] | str) -> NDArray:
         """Get covariate matrix.
 
         Parameters
@@ -393,7 +394,7 @@ def get_covs(self, covs: list[str] | str) -> np.ndarray:
 
         Returns
         -------
-        np.ndarray
+        NDArray
             Covariates matrix, in the column fashion.
 
         """

src/mrtool/core/model.py

@@ -7,6 +7,7 @@
 """
 
 from copy import deepcopy
+from typing import Sequence
 
 import numpy as np
 import pandas as pd
@@ -22,7 +23,10 @@ class MRBRT:
     """MR-BRT Object"""
 
     def __init__(
-        self, data: MRData, cov_models: list[CovModel], inlier_pct: float = 1.0
+        self,
+        data: MRData,
+        cov_models: Sequence[CovModel],
+        inlier_pct: float = 1.0,
     ):
         """Constructor of MRBRT.
 
@@ -80,12 +84,12 @@ def __init__(
         )
 
         # place holder for the limetr objective
-        self.lt = None
-        self.beta_soln = None
-        self.gamma_soln = None
-        self.u_soln = None
-        self.w_soln = None
-        self.re_soln = None
+        self.lt: LimeTr
+        self.beta_soln: NDArray
+        self.gamma_soln: NDArray
+        self.u_soln: NDArray
+        self.w_soln: NDArray
+        self.re_soln: NDArray
 
     def attach_data(self, data=None):
         """Attach data to cov_model."""

src/mrtool/core/utils.py

@@ -9,6 +9,7 @@
 
 import numpy as np
 import pandas as pd
+from numpy.typing import NDArray
 
 
 def get_cols(df, cols):
@@ -124,7 +125,7 @@ def sizes_to_indices(sizes):
 
     Returns
     -------
-    list[np.ndarray]
+    list[NDArray]
         list the indices.
 
     """
@@ -325,29 +326,29 @@ def avg_integral(mat, spline=None, use_spline_intercept=False):
 # random knots
 def sample_knots(
     num_knots: int,
-    knot_bounds: np.ndarray,
-    min_dist: float | np.ndarray,
+    knot_bounds: NDArray,
+    min_dist: float | NDArray,
     num_samples: int = 1,
-) -> np.ndarray:
+) -> NDArray:
     """Sample knot vectors given a set of rules.
 
     Parameters
     ----------
     num_knots : int
         Number of interior knots.
-    knot_bounds : np.ndarray, shape(2,) or shape(`num_knots`,2)
+    knot_bounds : NDArray, shape(2,) or shape(`num_knots`,2)
         Lower and upper bounds for knots. If shape(2,), boundary knots
         placed at `knot_bounds[0]` and `knot_bounds[1]`. If
         shape(`num_knots`,2), boundary knots placed at
         `knot_bounds[0, 0]` and `knot_bounds[-1, 1]`.
-    min_dist : float or np.ndarray, shape(`num_knots`+1,)
+    min_dist : float or NDArray, shape(`num_knots`+1,)
         Minimum distances between knots.
     num_samples : int, optional
         Number of knot vectors to sample. Default is 1.
 
     Returns
     -------
-    np.ndarray, shape(`num_samples`,`num_knots`+2)
+    NDArray, shape(`num_samples`,`num_knots`+2)
         Sampled knot vectors.
 
     """
@@ -380,7 +381,7 @@ def _check_nums(num_name: str, num_val: int) -> None:
         raise ValueError(f"{num_name} must be at least 1")
 
 
-def _check_knot_bounds(num_knots: int, knot_bounds: np.ndarray) -> np.ndarray:
+def _check_knot_bounds(num_knots: int, knot_bounds: NDArray) -> NDArray:
     """Check knot_bounds."""
     try:
         knot_bounds = np.asarray(knot_bounds, dtype=float)
@@ -399,7 +400,7 @@ def _check_knot_bounds(num_knots: int, knot_bounds: np.ndarray) -> np.ndarray:
     return knot_bounds
 
 
-def _check_min_dist(num_knots: int, min_dist: float | np.ndarray) -> np.ndarray:
+def _check_min_dist(num_knots: int, min_dist: float | NDArray) -> NDArray:
     """Check knot min_dist."""
     if np.isscalar(min_dist):
         min_dist = np.tile(min_dist, num_knots + 1)
@@ -415,8 +416,8 @@ def _check_min_dist(num_knots: int, min_dist: float | np.ndarray) -> np.ndarray:
 
 
 def _check_feasibility(
-    num_knots: int, knot_bounds: np.ndarray, min_dist: np.ndarray
-) -> tuple[np.ndarray, np.ndarray]:
+    num_knots: int, knot_bounds: NDArray, min_dist: NDArray
+) -> tuple[NDArray, NDArray]:
     """Check knot feasibility and get left and right boundaries."""
     if np.sum(min_dist) > knot_bounds[-1, 1] - knot_bounds[0, 0]:
         raise ValueError("min_dist cannot exceed knot_bounds")
@@ -561,7 +562,7 @@ def to_list(obj: Any) -> list[Any]:
         return [obj]
 
 
-def is_numeric_array(array: np.ndarray) -> bool:
+def is_numeric_array(array: NDArray) -> bool:
     """Check if an array is numeric.
 
     Parameters
@@ -590,8 +591,8 @@ def is_numeric_array(array: np.ndarray) -> bool:
 
 
 def expand_array(
-    array: np.ndarray, shape: tuple[int], value: Any, name: str
-) -> np.ndarray:
+    array: NDArray, shape: tuple[int], value: Any, name: str
+) -> NDArray:
     """Expand array when it is empty.
 
     Parameters
@@ -608,7 +609,7 @@ def expand_array(
 
     Returns
     -------
-    np.ndarray
+    NDArray
         Expanded array.
 
     """
@@ -630,7 +631,7 @@ def expand_array(
 def ravel_dict(x: dict) -> dict:
     """Ravel dictionary."""
     assert all([isinstance(k, str) for k in x.keys()])
-    assert all([isinstance(v, np.ndarray) for v in x.values()])
+    assert all([isinstance(v, NDArray) for v in x.values()])
     new_x = {}
     for k, v in x.items():
         if v.size == 1:

src/mrtool/cov_selection/covfinder.py

@@ -30,7 +30,7 @@ def __init__(
         power_step_size: float = 0.5,
         inlier_pct: float = 1.0,
         alpha: float = 0.05,
-        beta_gprior: dict[str, np.ndarray] = None,
+        beta_gprior: dict[str, np.ndarray] | None = None,
         beta_gprior_std: float = 1.0,
         bias_zero: bool = False,
         use_re: dict | None = None,
@@ -106,7 +106,7 @@ def __init__(
         self.power_step_size = power_step_size
         self.powers = np.arange(*self.power_range, self.power_step_size)
 
-        self.num_covs = len(pre_selected_covs) + len(covs)
+        self.num_covs = len(self.all_covs)
         if len(covs) == 0:
             warnings.warn(
                 "There is no covariates to select, will return the pre-selected covariates."
@@ -117,7 +117,7 @@ def create_model(
         self,
         covs: list[str],
         prior_type: str = "Laplace",
-        laplace_std: float = None,
+        laplace_std: float | None = None,
     ) -> MRBRT:
         """Create Gaussian or Laplace model.