Update pyproject.toml, including stricter linting rules

.github/workflows/ci.yml

@@ -24,9 +24,9 @@ jobs:
       - name: Setup environment
         run: pip install -e .[test]
       - name: Run doctests
-        run: pytest --doctest-modules --ignore=causalpy/tests/ causalpy/ --config-file=causalpy/tests/conftest.py
+        run: pytest --doctest-modules --ignore=causalpy/tests/ causalpy/ --config-file=causalpy/tests/conftest.py --no-cov
       - name: Run extra tests
-        run: pytest docs/source/.codespell/test_notebook_to_markdown.py
+        run: pytest docs/source/.codespell/test_notebook_to_markdown.py --no-cov
       - name: Run tests
         run: pytest --cov-report=xml --no-cov-on-fail
       - name: Check codespell for notebooks

.pre-commit-config.yaml

@@ -36,6 +36,9 @@ repos:
       - id: ruff
         types_or: [ python, pyi, jupyter ]
         args: [ --fix ]
+        # Exclude docs/ to avoid applying strict linting rules to example notebooks
+        # Remove this exclusion if you want to enforce strict rules on documentation
+        exclude: ^docs/
       # Run the formatter
       - id: ruff-format
         types_or: [ python, pyi, jupyter ]

causalpy/data/simulate_data.py

@@ -308,7 +308,7 @@ def impact(x: np.ndarray) -> np.ndarray:
 
 def generate_ancova_data(
     N: int = 200,
-    pre_treatment_means: np.ndarray = np.array([10, 12]),
+    pre_treatment_means: np.ndarray | None = None,
     treatment_effect: int = 2,
     sigma: int = 1,
 ) -> pd.DataFrame:
@@ -324,6 +324,8 @@ def generate_ancova_data(
     ... )
     >>> df.to_csv(pathlib.Path.cwd() / "ancova_data.csv", index=False)  # doctest: +SKIP
     """
+    if pre_treatment_means is None:
+        pre_treatment_means = np.array([10, 12])
     group = np.random.choice(2, size=N)
     pre = np.random.normal(loc=pre_treatment_means[group])
     post = pre + treatment_effect * group + np.random.normal(size=N) * sigma

causalpy/experiments/base.py

@@ -16,7 +16,7 @@
 """
 
 from abc import abstractmethod
-from typing import Any, Literal, Union
+from typing import Any, Literal
 
 import arviz as az
 import matplotlib.pyplot as plt
@@ -54,7 +54,7 @@ class BaseExperiment:
     supports_bayes: bool
     supports_ols: bool
 
-    def __init__(self, model: Union[PyMCModel, RegressorMixin] | None = None) -> None:
+    def __init__(self, model: PyMCModel | RegressorMixin | None = None) -> None:
         # Ensure we've made any provided Scikit Learn model (as identified as being type
         # RegressorMixin) compatible with CausalPy by appending our custom methods.
         if isinstance(model, RegressorMixin):
@@ -141,7 +141,7 @@ def get_plot_data_ols(self, *args: Any, **kwargs: Any) -> pd.DataFrame:
 
     def effect_summary(
         self,
-        window: Union[Literal["post"], tuple, slice] = "post",
+        window: Literal["post"] | tuple | slice = "post",
         direction: Literal["increase", "decrease", "two-sided"] = "increase",
         alpha: float = 0.05,
         cumulative: bool = True,

causalpy/experiments/diff_in_diff.py

@@ -15,8 +15,6 @@
 Difference in differences
 """
 
-from typing import Union
-
 import arviz as az
 import numpy as np
 import pandas as pd
@@ -98,7 +96,7 @@ def __init__(
         time_variable_name: str,
         group_variable_name: str,
         post_treatment_variable_name: str = "post_treatment",
-        model: Union[PyMCModel, RegressorMixin] | None = None,
+        model: PyMCModel | RegressorMixin | None = None,
         **kwargs: dict,
     ) -> None:
         super().__init__(model=model)
@@ -234,7 +232,7 @@ def __init__(
         elif isinstance(self.model, RegressorMixin):
             # This is the coefficient on the interaction term
             # Store the coefficient into dictionary {intercept:value}
-            coef_map = dict(zip(self.labels, self.model.get_coeffs()))
+            coef_map = dict(zip(self.labels, self.model.get_coeffs(), strict=False))
             # Create and find the interaction term based on the values user provided
             interaction_term = (
                 f"{self.group_variable_name}:{self.post_treatment_variable_name}"

causalpy/experiments/instrumental_variable.py

@@ -161,7 +161,9 @@ def input_validation(self) -> None:
                 """Warning. The treatment variable is not Binary.
                 This is not necessarily a problem but it violates
                 the assumption of a simple IV experiment.
-                The coefficients should be interpreted appropriately."""
+                The coefficients should be interpreted appropriately.""",
+                UserWarning,
+                stacklevel=2,
             )
 
     def get_2SLS_fit(self) -> None:
@@ -195,7 +197,9 @@ def get_naive_OLS_fit(self) -> None:
         ols_reg = sk_lin_reg().fit(self.X, self.y)
         beta_params = list(ols_reg.coef_[0][1:])
         beta_params.insert(0, ols_reg.intercept_[0])
-        self.ols_beta_params = dict(zip(self._x_design_info.column_names, beta_params))
+        self.ols_beta_params = dict(
+            zip(self._x_design_info.column_names, beta_params, strict=False)
+        )
         self.ols_reg = ols_reg
 
     def plot(self, *args, **kwargs) -> None:  # type: ignore[override]

causalpy/experiments/interrupted_time_series.py

@@ -15,7 +15,7 @@
 Interrupted Time Series Analysis
 """
 
-from typing import Any, List, Union
+from typing import Any
 
 import arviz as az
 import numpy as np
@@ -91,9 +91,9 @@ class InterruptedTimeSeries(BaseExperiment):
     def __init__(
         self,
         data: pd.DataFrame,
-        treatment_time: Union[int, float, pd.Timestamp],
+        treatment_time: int | float | pd.Timestamp,
         formula: str,
-        model: Union[PyMCModel, RegressorMixin] | None = None,
+        model: PyMCModel | RegressorMixin | None = None,
         **kwargs: dict,
     ) -> None:
         super().__init__(model=model)
@@ -155,7 +155,7 @@ def __init__(
         # fit the model to the observed (pre-intervention) data
         if isinstance(self.model, PyMCModel):
             is_bsts_like = isinstance(
-                self.model, (BayesianBasisExpansionTimeSeries, StateSpaceTimeSeries)
+                self.model, BayesianBasisExpansionTimeSeries | StateSpaceTimeSeries
             )
 
             if is_bsts_like:
@@ -183,7 +183,7 @@ def __init__(
         # score the goodness of fit to the pre-intervention data
         if isinstance(self.model, PyMCModel):
             is_bsts_like = isinstance(
-                self.model, (BayesianBasisExpansionTimeSeries, StateSpaceTimeSeries)
+                self.model, BayesianBasisExpansionTimeSeries | StateSpaceTimeSeries
             )
             if is_bsts_like:
                 X_score = self.pre_X.values if self.pre_X.shape[1] > 0 else None  # type: ignore[attr-defined]
@@ -202,7 +202,7 @@ def __init__(
         # get the model predictions of the observed (pre-intervention) data
         if isinstance(self.model, PyMCModel):
             is_bsts_like = isinstance(
-                self.model, (BayesianBasisExpansionTimeSeries, StateSpaceTimeSeries)
+                self.model, BayesianBasisExpansionTimeSeries | StateSpaceTimeSeries
             )
             if is_bsts_like:
                 X_pre_predict = self.pre_X.values if self.pre_X.shape[1] > 0 else None  # type: ignore[attr-defined]
@@ -220,7 +220,7 @@ def __init__(
         # calculate the counterfactual (post period)
         if isinstance(self.model, PyMCModel):
             is_bsts_like = isinstance(
-                self.model, (BayesianBasisExpansionTimeSeries, StateSpaceTimeSeries)
+                self.model, BayesianBasisExpansionTimeSeries | StateSpaceTimeSeries
             )
             if is_bsts_like:
                 X_post_predict = (
@@ -244,7 +244,7 @@ def __init__(
         # calculate impact - use appropriate y data format for each model type
         if isinstance(self.model, PyMCModel):
             is_bsts_like = isinstance(
-                self.model, (BayesianBasisExpansionTimeSeries, StateSpaceTimeSeries)
+                self.model, BayesianBasisExpansionTimeSeries | StateSpaceTimeSeries
             )
             if is_bsts_like:
                 pre_y_for_impact = self.pre_y.isel(treated_units=0)
@@ -275,7 +275,7 @@ def __init__(
         )
 
     def input_validation(
-        self, data: pd.DataFrame, treatment_time: Union[int, float, pd.Timestamp]
+        self, data: pd.DataFrame, treatment_time: int | float | pd.Timestamp
     ) -> None:
         """Validate the input data and model formula for correctness"""
         if isinstance(data.index, pd.DatetimeIndex) and not isinstance(
@@ -303,7 +303,7 @@ def summary(self, round_to: int | None = None) -> None:
 
     def _bayesian_plot(
         self, round_to: int | None = 2, **kwargs: dict
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """
         Plot the results
 
@@ -481,7 +481,7 @@ def _bayesian_plot(
 
     def _ols_plot(
         self, round_to: int | None = 2, **kwargs: dict
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """
         Plot the results
 

causalpy/experiments/inverse_propensity_weighting.py

@@ -15,8 +15,6 @@
 Inverse propensity weighting
 """
 
-from typing import List
-
 import arviz as az
 import matplotlib.pyplot as plt
 import numpy as np
@@ -263,7 +261,7 @@ def plot_ate(
         method: str | None = None,
         prop_draws: int = 100,
         ate_draws: int = 300,
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         if idata is None:
             idata = self.model.idata
         if method is None:
@@ -325,7 +323,7 @@ def make_hists(idata, i, axs, method=method):
                     BBBBCC"""
 
         fig, axs = plt.subplot_mosaic(mosaic, figsize=(20, 13))
-        axs = [axs[k] for k in axs.keys()]
+        axs = [axs[k] for k in axs]
         axs[0].axvline(
             0.1, linestyle="--", label="Low Extreme Propensity Scores", color="black"
         )
@@ -412,7 +410,7 @@ def plot_balance_ecdf(
         covariate: str,
         idata: az.InferenceData | None = None,
         weighting_scheme: str | None = None,
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """
         Plotting function takes a single covariate and shows the
         differences in the ECDF between the treatment and control

causalpy/experiments/prepostnegd.py

@@ -15,8 +15,6 @@
 Pretest/posttest nonequivalent group design
 """
 
-from typing import List
-
 import arviz as az
 import numpy as np
 import pandas as pd
@@ -227,7 +225,7 @@ def summary(self, round_to: int | None = None) -> None:
 
     def _bayesian_plot(
         self, round_to: int | None = None, **kwargs: dict
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """Generate plot for ANOVA-like experiments with non-equivalent group designs."""
         fig, ax = plt.subplots(
             2, 1, figsize=(7, 9), gridspec_kw={"height_ratios": [3, 1]}

causalpy/experiments/regression_discontinuity.py

@@ -16,7 +16,6 @@
 """
 
 import warnings  # noqa: I001
-from typing import Union
 
 
 import numpy as np
@@ -88,7 +87,7 @@ def __init__(
         data: pd.DataFrame,
         formula: str,
         treatment_threshold: float,
-        model: Union[PyMCModel, RegressorMixin] | None = None,
+        model: PyMCModel | RegressorMixin | None = None,
         running_variable_name: str = "x",
         epsilon: float = 0.001,
         bandwidth: float = np.inf,
@@ -112,6 +111,7 @@ def __init__(
                 warnings.warn(
                     f"Choice of bandwidth parameter has lead to only {len(filtered_data)} remaining datapoints. Consider increasing the bandwidth parameter.",  # noqa: E501
                     UserWarning,
+                    stacklevel=2,
                 )
             y, X = dmatrices(formula, filtered_data)
         else:
@@ -218,7 +218,7 @@ def input_validation(self) -> None:
             self.data = self.data.copy()
             self.data["treated"] = self.data["treated"].astype(bool)
 
-    def _is_treated(self, x: Union[np.ndarray, pd.Series]) -> np.ndarray:
+    def _is_treated(self, x: np.ndarray | pd.Series) -> np.ndarray:
         """Returns ``True`` if `x` is greater than or equal to the treatment threshold.
 
         .. warning::

causalpy/experiments/regression_kink.py

@@ -17,7 +17,6 @@
 """
 
 import warnings  # noqa: I001
-from typing import Union
 
 
 from matplotlib import pyplot as plt
@@ -75,6 +74,7 @@ def __init__(
                 warnings.warn(
                     f"Choice of bandwidth parameter has lead to only {len(filtered_data)} remaining datapoints. Consider increasing the bandwidth parameter.",  # noqa: E501
                     UserWarning,
+                    stacklevel=2,
                 )
             y, X = dmatrices(formula, filtered_data)
         else:
@@ -192,7 +192,7 @@ def _probe_kink_point(self) -> tuple[xr.DataArray, xr.DataArray, xr.DataArray]:
         mu_kink_right = predicted["posterior_predictive"].sel(obs_ind=2)["mu"]
         return mu_kink_left, mu_kink, mu_kink_right
 
-    def _is_treated(self, x: Union[np.ndarray, pd.Series]) -> np.ndarray:
+    def _is_treated(self, x: np.ndarray | pd.Series) -> np.ndarray:
         """Returns ``True`` if `x` is greater than or equal to the treatment threshold."""  # noqa: E501
         return np.greater_equal(x, self.kink_point)
 

causalpy/experiments/synthetic_control.py

@@ -15,8 +15,6 @@
 Synthetic Control Experiment
 """
 
-from typing import List, Union
-
 import arviz as az
 import numpy as np
 import pandas as pd
@@ -83,10 +81,10 @@ class SyntheticControl(BaseExperiment):
     def __init__(
         self,
         data: pd.DataFrame,
-        treatment_time: Union[int, float, pd.Timestamp],
+        treatment_time: int | float | pd.Timestamp,
         control_units: list[str],
         treated_units: list[str],
-        model: Union[PyMCModel, RegressorMixin] | None = None,
+        model: PyMCModel | RegressorMixin | None = None,
         **kwargs: dict,
     ) -> None:
         super().__init__(model=model)
@@ -186,7 +184,7 @@ def __init__(
         )
 
     def input_validation(
-        self, data: pd.DataFrame, treatment_time: Union[int, float, pd.Timestamp]
+        self, data: pd.DataFrame, treatment_time: int | float | pd.Timestamp
     ) -> None:
         """Validate the input data and model formula for correctness"""
         if isinstance(data.index, pd.DatetimeIndex) and not isinstance(
@@ -221,7 +219,7 @@ def _bayesian_plot(
         round_to: int | None = None,
         treated_unit: str | None = None,
         **kwargs: dict,
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """
         Plot the results for a specific treated unit
 
@@ -375,7 +373,7 @@ def _ols_plot(
         round_to: int | None = None,
         treated_unit: str | None = None,
         **kwargs: dict,
-    ) -> tuple[plt.Figure, List[plt.Axes]]:
+    ) -> tuple[plt.Figure, list[plt.Axes]]:
         """
         Plot the results for OLS model for a specific treated unit
 

causalpy/plot_utils.py

@@ -15,7 +15,7 @@
 Plotting utility functions.
 """
 
-from typing import Any, Dict, Tuple, Union
+from typing import Any
 
 import arviz as az
 import matplotlib.pyplot as plt
@@ -28,13 +28,13 @@
 
 
 def plot_xY(
-    x: Union[pd.DatetimeIndex, np.ndarray, pd.Index, pd.Series, ExtensionArray],
+    x: pd.DatetimeIndex | np.ndarray | pd.Index | pd.Series | ExtensionArray,
     Y: xr.DataArray,
     ax: plt.Axes,
-    plot_hdi_kwargs: Dict[str, Any] | None = None,
+    plot_hdi_kwargs: dict[str, Any] | None = None,
     hdi_prob: float = 0.94,
     label: str | None = None,
-) -> Tuple[Line2D, PolyCollection]:
+) -> tuple[Line2D, PolyCollection]:
     """Plot HDI intervals.
 
     Parameters