Merge pull request #609 from MilesCranmer/cleanup

More extensive typing stubs and associated refactoring

.gitignore

@@ -23,3 +23,5 @@ site
 **/*.code-workspace
 **/*.tar.gz
 venv
+requirements-dev.lock
+requirements.lock

environment.yml

@@ -9,4 +9,3 @@ dependencies:
   - scikit-learn>=1.0.0,<2.0.0
   - pyjuliacall>=0.9.15,<0.10.0
   - click>=7.0.0,<9.0.0
-  - typing_extensions>=4.0.0,<5.0.0

pyproject.toml

@@ -35,4 +35,10 @@ dev-dependencies = [
     "pre-commit>=3.7.0",
     "ipython>=8.23.0",
     "ipykernel>=6.29.4",
+    "mypy>=1.10.0",
+    "jax[cpu]>=0.4.26",
+    "torch>=2.3.0",
+    "pandas-stubs>=2.2.1.240316",
+    "types-pytz>=2024.1.0.20240417",
+    "types-openpyxl>=3.1.0.20240428",
 ]

pysr/denoising.py

@@ -1,9 +1,17 @@
 """Functions for denoising data during preprocessing."""
 
+from typing import Optional, Tuple, cast
+
 import numpy as np
+from numpy import ndarray
 
 
-def denoise(X, y, Xresampled=None, random_state=None):
+def denoise(
+    X: ndarray,
+    y: ndarray,
+    Xresampled: Optional[ndarray] = None,
+    random_state: Optional[np.random.RandomState] = None,
+) -> Tuple[ndarray, ndarray]:
     """Denoise the dataset using a Gaussian process."""
     from sklearn.gaussian_process import GaussianProcessRegressor
     from sklearn.gaussian_process.kernels import RBF, ConstantKernel, WhiteKernel
@@ -15,12 +23,17 @@ def denoise(X, y, Xresampled=None, random_state=None):
     gpr.fit(X, y)
 
     if Xresampled is not None:
-        return Xresampled, gpr.predict(Xresampled)
+        return Xresampled, cast(ndarray, gpr.predict(Xresampled))
 
-    return X, gpr.predict(X)
+    return X, cast(ndarray, gpr.predict(X))
 
 
-def multi_denoise(X, y, Xresampled=None, random_state=None):
+def multi_denoise(
+    X: ndarray,
+    y: ndarray,
+    Xresampled: Optional[ndarray] = None,
+    random_state: Optional[np.random.RandomState] = None,
+):
     """Perform `denoise` along each column of `y` independently."""
     y = np.stack(
         [

pysr/export_latex.py

@@ -153,3 +153,15 @@ def sympy2multilatextable(
     ]
 
     return "\n\n".join(latex_tables)
+
+
+def with_preamble(table_string: str) -> str:
+    preamble_string = [
+        r"\usepackage{breqn}",
+        r"\usepackage{booktabs}",
+        "",
+        "...",
+        "",
+        table_string,
+    ]
+    return "\n".join(preamble_string)

pysr/export_numpy.py

@@ -1,10 +1,12 @@
 """Code for exporting discovered expressions to numpy"""
 
 import warnings
+from typing import List, Union
 
 import numpy as np
 import pandas as pd
-from sympy import lambdify
+from numpy.typing import NDArray
+from sympy import Expr, Symbol, lambdify
 
 
 def sympy2numpy(eqn, sympy_symbols, *, selection=None):
@@ -14,6 +16,10 @@ def sympy2numpy(eqn, sympy_symbols, *, selection=None):
 class CallableEquation:
     """Simple wrapper for numpy lambda functions built with sympy"""
 
+    _sympy: Expr
+    _sympy_symbols: List[Symbol]
+    _selection: Union[NDArray[np.bool_], None]
+
     def __init__(self, eqn, sympy_symbols, selection=None):
         self._sympy = eqn
         self._sympy_symbols = sympy_symbols
@@ -29,15 +35,17 @@ def __call__(self, X):
             return self._lambda(
                 **{k: X[k].values for k in map(str, self._sympy_symbols)}
             ) * np.ones(expected_shape)
+
         if self._selection is not None:
-            if X.shape[1] != len(self._selection):
+            if X.shape[1] != self._selection.sum():
                 warnings.warn(
                     "`X` should be of shape (n_samples, len(self._selection)). "
                     "Automatically filtering `X` to selection. "
                     "Note: Filtered `X` column order may not match column order in fit "
                     "this may lead to incorrect predictions and other errors."
                 )
                 X = X[:, self._selection]
+
         return self._lambda(*X.T) * np.ones(expected_shape)
 
     @property

pysr/export_sympy.py

@@ -5,6 +5,8 @@
 import sympy
 from sympy import sympify
 
+from .utils import ArrayLike
+
 sympy_mappings = {
     "div": lambda x, y: x / y,
     "mult": lambda x, y: x * y,
@@ -30,8 +32,8 @@
     "acosh": lambda x: sympy.acosh(x),
     "acosh_abs": lambda x: sympy.acosh(abs(x) + 1),
     "asinh": sympy.asinh,
-    "atanh": lambda x: sympy.atanh(sympy.Mod(x + 1, 2) - 1),
-    "atanh_clip": lambda x: sympy.atanh(sympy.Mod(x + 1, 2) - 1),
+    "atanh": lambda x: sympy.atanh(sympy.Mod(x + 1, 2) - sympy.S(1)),
+    "atanh_clip": lambda x: sympy.atanh(sympy.Mod(x + 1, 2) - sympy.S(1)),
     "abs": abs,
     "mod": sympy.Mod,
     "erf": sympy.erf,
@@ -60,21 +62,21 @@
 
 
 def create_sympy_symbols_map(
-    feature_names_in: List[str],
+    feature_names_in: ArrayLike[str],
 ) -> Dict[str, sympy.Symbol]:
     return {variable: sympy.Symbol(variable) for variable in feature_names_in}
 
 
 def create_sympy_symbols(
-    feature_names_in: List[str],
+    feature_names_in: ArrayLike[str],
 ) -> List[sympy.Symbol]:
     return [sympy.Symbol(variable) for variable in feature_names_in]
 
 
 def pysr2sympy(
     equation: str,
     *,
-    feature_names_in: Optional[List[str]] = None,
+    feature_names_in: Optional[ArrayLike[str]] = None,
     extra_sympy_mappings: Optional[Dict[str, Callable]] = None,
 ):
     if feature_names_in is None:

pysr/feature_selection.py

@@ -1,9 +1,20 @@
 """Functions for doing feature selection during preprocessing."""
 
+from typing import Optional, cast
+
 import numpy as np
+from numpy import ndarray
+from numpy.typing import NDArray
+
+from .utils import ArrayLike
 
 
-def run_feature_selection(X, y, select_k_features, random_state=None):
+def run_feature_selection(
+    X: ndarray,
+    y: ndarray,
+    select_k_features: int,
+    random_state: Optional[np.random.RandomState] = None,
+) -> NDArray[np.bool_]:
     """
     Find most important features.
 
@@ -21,11 +32,16 @@ def run_feature_selection(X, y, select_k_features, random_state=None):
     selector = SelectFromModel(
         clf, threshold=-np.inf, max_features=select_k_features, prefit=True
     )
-    return selector.get_support(indices=True)
+    return cast(NDArray[np.bool_], selector.get_support(indices=False))
 
 
 # Function has not been removed only due to usage in module tests
-def _handle_feature_selection(X, select_k_features, y, variable_names):
+def _handle_feature_selection(
+    X: ndarray,
+    select_k_features: Optional[int],
+    y: ndarray,
+    variable_names: ArrayLike[str],
+):
     if select_k_features is not None:
         selection = run_feature_selection(X, y, select_k_features)
         print(f"Using features {[variable_names[i] for i in selection]}")

pysr/julia_helpers.py

@@ -1,11 +1,16 @@
 """Functions for initializing the Julia environment and installing deps."""
 
+from typing import Any, Callable, Union, cast
+
 import numpy as np
 from juliacall import convert as jl_convert  # type: ignore
+from numpy.typing import NDArray
 
 from .deprecated import init_julia, install
 from .julia_import import jl
 
+jl_convert = cast(Callable[[Any, Any], Any], jl_convert)
+
 jl.seval("using Serialization: Serialization")
 jl.seval("using PythonCall: PythonCall")
 
@@ -22,24 +27,31 @@ def _escape_filename(filename):
     return str_repr
 
 
-def _load_cluster_manager(cluster_manager):
+def _load_cluster_manager(cluster_manager: str):
     jl.seval(f"using ClusterManagers: addprocs_{cluster_manager}")
     return jl.seval(f"addprocs_{cluster_manager}")
 
 
-def jl_array(x):
+def jl_array(x, dtype=None):
     if x is None:
         return None
-    return jl_convert(jl.Array, x)
+    elif dtype is None:
+        return jl_convert(jl.Array, x)
+    else:
+        return jl_convert(jl.Array[dtype], x)
+
+
+def jl_is_function(f) -> bool:
+    return cast(bool, jl.seval("op -> op isa Function")(f))
 
 
-def jl_serialize(obj):
+def jl_serialize(obj: Any) -> NDArray[np.uint8]:
     buf = jl.IOBuffer()
     Serialization.serialize(buf, obj)
     return np.array(jl.take_b(buf))
 
 
-def jl_deserialize(s):
+def jl_deserialize(s: Union[NDArray[np.uint8], None]):
     if s is None:
         return s
     buf = jl.IOBuffer()

pysr/julia_import.py

@@ -1,6 +1,8 @@
 import os
 import sys
 import warnings
+from types import ModuleType
+from typing import cast
 
 # Check if JuliaCall is already loaded, and if so, warn the user
 # about the relevant environment variables. If not loaded,
@@ -42,6 +44,9 @@
 
 from juliacall import Main as jl  # type: ignore
 
+jl = cast(ModuleType, jl)
+
+
 jl_version = (jl.VERSION.major, jl.VERSION.minor, jl.VERSION.patch)
 
 jl.seval("using SymbolicRegression")