Add mypy to pre-commit and fix all current typing issues (#414)

* Remove _RequireAttrsABCMeta metaclass and replace with simple check

* add mypy

* Fix some typing issues

* Fix some typing issues

* Fix some typing issues

* fix all Runner type issues

* fix all DataSaver type issues

* fix all IntegratorLearner type issues

* fix all SequenceLearner type issues

* some fixes

* some fixes

* some fixes

* Fix multiple issues

* Fix all mypy issues

* Make data a dict

* make BaseLearner a ABC

* remove BaseLearner._check_required_attributes()

* remove unused deps

* Wrap in TYPE_CHECKING

* pin ipython

* pin ipython

* Add NotImplemented methods

* remove unused import

Author: basnijholt

.pre-commit-config.yaml

@@ -25,3 +25,8 @@ repos:
       - id: nbqa
         args: ["ruff", "--fix", "--ignore=E402,B018,F704"]
         additional_dependencies: [jupytext, ruff]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.2.0"
+    hooks:
+      - id: mypy
+        exclude: ipynb_filter.py|docs/source/conf.py

adaptive/__init__.py

@@ -54,5 +54,5 @@
     __all__.append("SKOptLearner")
 
 # to avoid confusion with `notebook_extension` and `__version__`
-del _version  # noqa: F821
-del notebook_integration  # noqa: F821
+del _version  # type: ignore[name-defined] # noqa: F821
+del notebook_integration  # type: ignore[name-defined] # noqa: F821

adaptive/_version.py

@@ -1,5 +1,7 @@
 # This file is part of 'miniver': https://github.com/jbweston/miniver
 #
+from __future__ import annotations
+
 import os
 import subprocess
 from collections import namedtuple
@@ -10,7 +12,7 @@
 Version = namedtuple("Version", ("release", "dev", "labels"))
 
 # No public API
-__all__ = []
+__all__: list[str] = []
 
 package_root = os.path.dirname(os.path.realpath(__file__))
 package_name = os.path.basename(package_root)

adaptive/learner/average_learner.py

@@ -1,16 +1,14 @@
 from __future__ import annotations
 
 from math import sqrt
-from numbers import Integral as Int
-from numbers import Real
 from typing import Callable
 
 import cloudpickle
 import numpy as np
 
 from adaptive.learner.base_learner import BaseLearner
 from adaptive.notebook_integration import ensure_holoviews
-from adaptive.types import Float
+from adaptive.types import Float, Int, Real
 from adaptive.utils import (
     assign_defaults,
     cache_latest,
@@ -75,7 +73,6 @@ def __init__(
         self.min_npoints = max(min_npoints, 2)
         self.sum_f: Real = 0.0
         self.sum_f_sq: Real = 0.0
-        self._check_required_attributes()
 
     def new(self) -> AverageLearner:
         """Create a copy of `~adaptive.AverageLearner` without the data."""
@@ -89,7 +86,7 @@ def to_numpy(self):
         """Data as NumPy array of size (npoints, 2) with seeds and values."""
         return np.array(sorted(self.data.items()))
 
-    def to_dataframe(
+    def to_dataframe(  # type: ignore[override]
         self,
         with_default_function_args: bool = True,
         function_prefix: str = "function.",
@@ -129,7 +126,7 @@ def to_dataframe(
             assign_defaults(self.function, df, function_prefix)
         return df
 
-    def load_dataframe(
+    def load_dataframe(  # type: ignore[override]
         self,
         df: pandas.DataFrame,
         with_default_function_args: bool = True,

adaptive/learner/average_learner1D.py

@@ -5,8 +5,6 @@
 from collections import defaultdict
 from copy import deepcopy
 from math import hypot
-from numbers import Integral as Int
-from numbers import Real
 from typing import Callable, DefaultDict, Iterable, List, Sequence, Tuple
 
 import numpy as np
@@ -16,6 +14,7 @@
 
 from adaptive.learner.learner1D import Learner1D, _get_intervals
 from adaptive.notebook_integration import ensure_holoviews
+from adaptive.types import Int, Real
 from adaptive.utils import assign_defaults, partial_function_from_dataframe
 
 try:
@@ -99,7 +98,7 @@ def __init__(
         if min_samples > max_samples:
             raise ValueError("max_samples should be larger than min_samples.")
 
-        super().__init__(function, bounds, loss_per_interval)
+        super().__init__(function, bounds, loss_per_interval)  # type: ignore[arg-type]
 
         self.delta = delta
         self.alpha = alpha
@@ -110,7 +109,7 @@ def __init__(
 
         # Contains all samples f(x) for each
         # point x in the form {x0: {0: f_0(x0), 1: f_1(x0), ...}, ...}
-        self._data_samples = SortedDict()
+        self._data_samples: SortedDict[float, dict[int, Real]] = SortedDict()
         # Contains the number of samples taken
         # at each point x in the form {x0: n0, x1: n1, ...}
         self._number_samples = SortedDict()
@@ -124,15 +123,14 @@ def __init__(
         # form {xi: ((xii-xi)^2 + (yii-yi)^2)^0.5, ...}
         self._distances: dict[Real, float] = decreasing_dict()
         # {xii: error[xii]/min(_distances[xi], _distances[xii], ...}
-        self.rescaled_error: dict[Real, float] = decreasing_dict()
-        self._check_required_attributes()
+        self.rescaled_error: ItemSortedDict[Real, float] = decreasing_dict()
 
     def new(self) -> AverageLearner1D:
         """Create a copy of `~adaptive.AverageLearner1D` without the data."""
         return AverageLearner1D(
             self.function,
             self.bounds,
-            self.loss_per_interval,
+            self.loss_per_interval,  # type: ignore[arg-type]
             self.delta,
             self.alpha,
             self.neighbor_sampling,
@@ -164,7 +162,7 @@ def to_numpy(self, mean: bool = False) -> np.ndarray:
                 ]
             )
 
-    def to_dataframe(
+    def to_dataframe(  # type: ignore[override]
         self,
         mean: bool = False,
         with_default_function_args: bool = True,
@@ -202,10 +200,10 @@ def to_dataframe(
         if not with_pandas:
             raise ImportError("pandas is not installed.")
         if mean:
-            data = sorted(self.data.items())
+            data: list[tuple[Real, Real]] = sorted(self.data.items())
             columns = [x_name, y_name]
         else:
-            data = [
+            data: list[tuple[int, Real, Real]] = [  # type: ignore[no-redef]
                 (seed, x, y)
                 for x, seed_y in sorted(self._data_samples.items())
                 for seed, y in sorted(seed_y.items())
@@ -218,7 +216,7 @@ def to_dataframe(
             assign_defaults(self.function, df, function_prefix)
         return df
 
-    def load_dataframe(
+    def load_dataframe(  # type: ignore[override]
         self,
         df: pandas.DataFrame,
         with_default_function_args: bool = True,
@@ -258,7 +256,7 @@ def load_dataframe(
                 self.function, df, function_prefix
             )
 
-    def ask(self, n: int, tell_pending: bool = True) -> tuple[Points, list[float]]:
+    def ask(self, n: int, tell_pending: bool = True) -> tuple[Points, list[float]]:  # type: ignore[override]
         """Return 'n' points that are expected to maximally reduce the loss."""
         # If some point is undersampled, resample it
         if len(self._undersampled_points):
@@ -311,18 +309,18 @@ def _ask_for_new_point(self, n: int) -> tuple[Points, list[float]]:
         new point, since in general n << min_samples and this point will need
         to be resampled many more times"""
         points, (loss_improvement,) = self._ask_points_without_adding(1)
-        points = [(seed, x) for seed, x in zip(range(n), n * points)]
+        seed_points = [(seed, x) for seed, x in zip(range(n), n * points)]
         loss_improvements = [loss_improvement / n] * n
-        return points, loss_improvements
+        return seed_points, loss_improvements  # type: ignore[return-value]
 
-    def tell_pending(self, seed_x: Point) -> None:
+    def tell_pending(self, seed_x: Point) -> None:  # type: ignore[override]
         _, x = seed_x
         self.pending_points.add(seed_x)
         if x not in self.data:
             self._update_neighbors(x, self.neighbors_combined)
             self._update_losses(x, real=False)
 
-    def tell(self, seed_x: Point, y: Real) -> None:
+    def tell(self, seed_x: Point, y: Real) -> None:  # type: ignore[override]
         seed, x = seed_x
         if y is None:
             raise TypeError(
@@ -493,7 +491,7 @@ def _calc_error_in_mean(self, ys: Iterable[Real], y_avg: Real, n: int) -> float:
         t_student = scipy.stats.t.ppf(1 - self.alpha, df=n - 1)
         return t_student * (variance_in_mean / n) ** 0.5
 
-    def tell_many(
+    def tell_many(  # type: ignore[override]
         self, xs: Points | np.ndarray, ys: Sequence[Real] | np.ndarray
     ) -> None:
         # Check that all x are within the bounds
@@ -578,10 +576,10 @@ def tell_many_at_point(self, x: Real, seed_y_mapping: dict[int, Real]) -> None:
                     self._update_interpolated_loss_in_interval(*interval)
                 self._oldscale = deepcopy(self._scale)
 
-    def _get_data(self) -> dict[Real, dict[Int, Real]]:
+    def _get_data(self) -> dict[Real, dict[Int, Real]]:  # type: ignore[override]
         return self._data_samples
 
-    def _set_data(self, data: dict[Real, dict[Int, Real]]) -> None:
+    def _set_data(self, data: dict[Real, dict[Int, Real]]) -> None:  # type: ignore[override]
         if data:
             for x, samples in data.items():
                 self.tell_many_at_point(x, samples)
@@ -616,7 +614,7 @@ def plot(self):
         return p.redim(x={"range": plot_bounds})
 
 
-def decreasing_dict() -> dict:
+def decreasing_dict() -> ItemSortedDict:
     """This initialization orders the dictionary from large to small values"""
 
     def sorting_rule(key, value):