Address security warnings (#183)

fortuna/calib_model/classification.py

@@ -182,9 +182,11 @@ def calibrate(
             self._check_output_dim(val_data_loader)
         return self._calibrate(
             calib_data_loader=calib_data_loader,
-            uncertainty_fn=config.monitor.uncertainty_fn
-            if config.monitor.uncertainty_fn is not None
-            else self.prob_output_layer.mean,
+            uncertainty_fn=(
+                config.monitor.uncertainty_fn
+                if config.monitor.uncertainty_fn is not None
+                else self.prob_output_layer.mean
+            ),
             val_data_loader=val_data_loader,
             loss_fn=loss_fn,
             config=config,

fortuna/calib_model/loss.py

@@ -95,12 +95,16 @@ def __call__(
         aux = dict()
         if self.likelihood.output_calib_manager is not None:
             outs = self.likelihood.output_calib_manager.apply(
-                params=calib_params["output_calibrator"]
-                if calib_params is not None
-                else None,
-                mutable=calib_mutable["output_calibrator"]
-                if calib_mutable is not None
-                else None,
+                params=(
+                    calib_params["output_calibrator"]
+                    if calib_params is not None
+                    else None
+                ),
+                mutable=(
+                    calib_mutable["output_calibrator"]
+                    if calib_mutable is not None
+                    else None
+                ),
                 outputs=outputs,
                 calib="calib_mutable" in return_aux,
             )

fortuna/calib_model/predictive/regression.py

@@ -146,9 +146,7 @@ def credible_interval(
         q = (
             jnp.array([0.5 * error, 1 - 0.5 * error])
             if interval_type == "two-tailed"
-            else error
-            if interval_type == "left-tailed"
-            else 1 - error
+            else error if interval_type == "left-tailed" else 1 - error
         )
         qq = self.quantile(
             q=q,

fortuna/calib_model/regression.py

@@ -128,9 +128,11 @@ def calibrate(
             self._check_output_dim(val_data_loader)
         return self._calibrate(
             calib_data_loader=calib_data_loader,
-            uncertainty_fn=config.monitor.uncertainty_fn
-            if config.monitor.uncertainty_fn is not None
-            else self.prob_output_layer.variance,
+            uncertainty_fn=(
+                config.monitor.uncertainty_fn
+                if config.monitor.uncertainty_fn is not None
+                else self.prob_output_layer.variance
+            ),
             val_data_loader=val_data_loader,
             loss_fn=loss_fn,
             config=config,

fortuna/calib_model/state.py

@@ -37,9 +37,11 @@ def init(
         return cls(
             apply_fn=None,
             params=params,
-            opt_state=kwargs["opt_state"]
-            if optimizer is None and "opt_state" in kwargs
-            else optimizer.init(params),
+            opt_state=(
+                kwargs["opt_state"]
+                if optimizer is None and "opt_state" in kwargs
+                else optimizer.init(params)
+            ),
             mutable=mutable,
             step=kwargs.get("step", 0),
             tx=optimizer,
@@ -78,11 +80,15 @@ def init_from_dict(
             FrozenDict(d["params"]),
             FrozenDict(d["mutable"]) if d["mutable"] is not None else None,
             optimizer,
-            FrozenDict(d.get("calib_params"))
-            if d["calib_params"] is not None
-            else None,
-            FrozenDict(d.get("calib_mutable"))
-            if d["calib_mutable"] is not None
-            else None,
+            (
+                FrozenDict(d.get("calib_params"))
+                if d["calib_params"] is not None
+                else None
+            ),
+            (
+                FrozenDict(d.get("calib_mutable"))
+                if d["calib_mutable"] is not None
+                else None
+            ),
             **kwargs,
         )

fortuna/likelihood/base.py

@@ -223,12 +223,16 @@ def _batched_log_joint_prob(
         aux = dict()
         if self.output_calib_manager is not None:
             outs = self.output_calib_manager.apply(
-                params=calib_params["output_calibrator"]
-                if calib_params is not None
-                else None,
-                mutable=calib_mutable["output_calibrator"]
-                if calib_mutable is not None
-                else None,
+                params=(
+                    calib_params["output_calibrator"]
+                    if calib_params is not None
+                    else None
+                ),
+                mutable=(
+                    calib_mutable["output_calibrator"]
+                    if calib_mutable is not None
+                    else None
+                ),
                 outputs=outputs,
                 calib="calib_mutable" in return_aux,
             )
@@ -407,12 +411,16 @@ def get_calibrated_outputs(
             and self.output_calib_manager.output_calibrator is not None
         ):
             outputs = self.output_calib_manager.apply(
-                params=calib_params["output_calibrator"]
-                if calib_params is not None
-                else None,
-                mutable=calib_mutable["output_calibrator"]
-                if calib_mutable is not None
-                else None,
+                params=(
+                    calib_params["output_calibrator"]
+                    if calib_params is not None
+                    else None
+                ),
+                mutable=(
+                    calib_mutable["output_calibrator"]
+                    if calib_mutable is not None
+                    else None
+                ),
                 outputs=outputs,
                 **kwargs,
             )
@@ -434,12 +442,16 @@ def _get_batched_calibrated_outputs(
             and self.output_calib_manager.output_calibrator is not None
         ):
             outputs = self.output_calib_manager.apply(
-                params=calib_params["output_calibrator"]
-                if calib_params is not None
-                else None,
-                mutable=calib_mutable["output_calibrator"]
-                if calib_mutable is not None
-                else None,
+                params=(
+                    calib_params["output_calibrator"]
+                    if calib_params is not None
+                    else None
+                ),
+                mutable=(
+                    calib_mutable["output_calibrator"]
+                    if calib_mutable is not None
+                    else None
+                ),
                 outputs=outputs,
                 **kwargs,
             )

fortuna/model/constant.py

@@ -19,6 +19,7 @@ class ConstantModel(nn.Module):
         Function to initialize the model parameters.
         This must be one of the available options in :code:`flax.linen.initializers`.
     """
+
     output_dim: int
     initializer_fun: Optional[Initializer] = nn.initializers.zeros
 

fortuna/model/hyper.py

@@ -13,6 +13,7 @@ class HyperparameterModel(nn.Module):
     value: Union[float, Array]
         Value of the hyperparameter.
     """
+
     value: Array
 
     def setup(self) -> None:

fortuna/model/model_manager/regression.py

@@ -120,9 +120,9 @@ def apply_fn(p, x, m_mutable, llv_mutable):
                     p,
                     x,
                     m_mutable=mutable["model"] if mutable is not None else False,
-                    llv_mutable=mutable["lik_log_var"]
-                    if mutable is not None
-                    else False,
+                    llv_mutable=(
+                        mutable["lik_log_var"] if mutable is not None else False
+                    ),
                 ),
                 model_params=params,
                 x=inputs,

fortuna/model/scalar_constant.py

@@ -20,6 +20,7 @@ class ScalarConstantModel(nn.Module):
         Function to initialize the model parameters.
         This must be one of the available options in :code:`flax.linen.initializers`.
     """
+
     output_dim: int
     initializer_fun: Optional[Initializer] = nn.initializers.zeros
 

fortuna/model/scalar_hyper.py

@@ -16,6 +16,7 @@ class ScalarHyperparameterModel(nn.Module):
     value: float
         Scalar value of the hyperparameter.
     """
+
     output_dim: int
     value: float
 

fortuna/model/utils/spectral_norm.py

@@ -1,6 +1,7 @@
 """
 The code has been taken from https://github.com/google/edward2/blob/main/edward2/jax/nn/normalization.py
 """
+
 import dataclasses
 from typing import (
     Any,

fortuna/model/wideresnet.py

@@ -2,6 +2,7 @@
 Wide ResNet model
 (adapted from https://github.com/google/flax/blob/v0.2/examples/cifar10/models/wideresnet.py)
 """
+
 from functools import partial
 from typing import (
     Any,

fortuna/ood_detection/ddu.py

@@ -1,6 +1,7 @@
 """
 Adapted from https://github.com/omegafragger/DDU/blob/main/utils/gmm_utils.py
 """
+
 import logging
 from typing import (
     Callable,

fortuna/output_calib_model/classification.py

@@ -102,9 +102,11 @@ def calibrate(
         if val_outputs is not None:
             self._check_output_dim(val_outputs, val_targets)
         return super()._calibrate(
-            uncertainty_fn=config.monitor.uncertainty_fn
-            if config.monitor.uncertainty_fn is not None
-            else self.prob_output_layer.mean,
+            uncertainty_fn=(
+                config.monitor.uncertainty_fn
+                if config.monitor.uncertainty_fn is not None
+                else self.prob_output_layer.mean
+            ),
             calib_outputs=calib_outputs,
             calib_targets=calib_targets,
             val_outputs=val_outputs,

fortuna/output_calib_model/regression.py

@@ -99,9 +99,11 @@ def calibrate(
         if val_outputs is not None:
             self._check_output_dim(val_outputs, val_targets)
         return super()._calibrate(
-            uncertainty_fn=config.monitor.uncertainty_fn
-            if config.monitor.uncertainty_fn is not None
-            else self.prob_output_layer.variance,
+            uncertainty_fn=(
+                config.monitor.uncertainty_fn
+                if config.monitor.uncertainty_fn is not None
+                else self.prob_output_layer.variance
+            ),
             calib_outputs=calib_outputs,
             calib_targets=calib_targets,
             val_outputs=val_outputs,

fortuna/output_calib_model/state.py

@@ -52,11 +52,11 @@ def init(
         return cls(
             apply_fn=None,
             params=params,
-            opt_state=kwargs["opt_state"]
-            if optimizer is None and "opt_state" in kwargs
-            else None
-            if optimizer is None
-            else optimizer.init(params),
+            opt_state=(
+                kwargs["opt_state"]
+                if optimizer is None and "opt_state" in kwargs
+                else None if optimizer is None else optimizer.init(params)
+            ),
             mutable=mutable,
             step=kwargs.get("step", 0),
             tx=optimizer,

fortuna/plot.py

@@ -167,9 +167,11 @@ def plot_2d_classification_predictions_and_uncertainty(
             inputs[:, 0],
             inputs[:, 1],
             s=marker_size,
-            c=[preds_color[0] if i == 1 else preds_color[1] for i in preds]
-            if preds is not None
-            else base_inputs_color,
+            c=(
+                [preds_color[0] if i == 1 else preds_color[1] for i in preds]
+                if preds is not None
+                else base_inputs_color
+            ),
         )
     if colorbar:
         plt.colorbar(im, ax=ax.ravel().tolist() if hasattr(ax, "ravel") else ax)

fortuna/prob_model/classification.py

@@ -287,9 +287,11 @@ def calibrate(
         if val_data_loader is not None:
             self._check_output_dim(val_data_loader)
         return super()._calibrate(
-            uncertainty_fn=calib_config.monitor.uncertainty_fn
-            if calib_config.monitor.uncertainty_fn is not None
-            else self.prob_output_layer.mean,
+            uncertainty_fn=(
+                calib_config.monitor.uncertainty_fn
+                if calib_config.monitor.uncertainty_fn is not None
+                else self.prob_output_layer.mean
+            ),
             calib_data_loader=calib_data_loader,
             val_data_loader=val_data_loader,
             calib_config=calib_config,

fortuna/prob_model/posterior/deep_ensemble/deep_ensemble_posterior.py

@@ -172,9 +172,11 @@ def _fit(i):
         else:
             self.state = PosteriorMultiStateRepository(
                 size=self.posterior_approximator.ensemble_size,
-                checkpoint_dir=fit_config.checkpointer.save_checkpoint_dir
-                if fit_config.checkpointer.dump_state is True
-                else None,
+                checkpoint_dir=(
+                    fit_config.checkpointer.save_checkpoint_dir
+                    if fit_config.checkpointer.dump_state is True
+                    else None
+                ),
             )
 
         status = []

fortuna/prob_model/posterior/laplace/laplace_posterior.py

@@ -161,12 +161,16 @@ def apply_calib_model_manager(_params, _batch_inputs):
                 _params, _batch_inputs, mutable=mutable, train=False
             )
             outputs = self.joint.likelihood.output_calib_manager.apply(
-                params=calib_params["output_calibrator"]
-                if calib_params is not None
-                else None,
-                mutable=calib_mutable["output_calibrator"]
-                if calib_mutable is not None
-                else None,
+                params=(
+                    calib_params["output_calibrator"]
+                    if calib_params is not None
+                    else None
+                ),
+                mutable=(
+                    calib_mutable["output_calibrator"]
+                    if calib_mutable is not None
+                    else None
+                ),
                 outputs=outputs,
             )
             return outputs

fortuna/prob_model/posterior/map/map_posterior.py

@@ -101,9 +101,9 @@ def fit(
             n_epochs=fit_config.optimizer.n_epochs,
             metrics=fit_config.monitor.metrics,
             validation_dataloader=val_data_loader,
-            validation_dataset_size=val_data_loader.size
-            if val_data_loader is not None
-            else None,
+            validation_dataset_size=(
+                val_data_loader.size if val_data_loader is not None else None
+            ),
             verbose=fit_config.monitor.verbose,
             callbacks=fit_config.callbacks,
             max_grad_norm=fit_config.hyperparameters.max_grad_norm,

fortuna/prob_model/posterior/normalizing_flow/advi/advi_posterior.py

@@ -178,9 +178,9 @@ def fit(
             n_epochs=fit_config.optimizer.n_epochs,
             metrics=fit_config.monitor.metrics,
             validation_dataloader=val_data_loader,
-            validation_dataset_size=val_data_loader.size
-            if val_data_loader is not None
-            else None,
+            validation_dataset_size=(
+                val_data_loader.size if val_data_loader is not None else None
+            ),
             verbose=fit_config.monitor.verbose,
             unravel=self._unravel,
             n_samples=self.posterior_approximator.n_loss_samples,

fortuna/prob_model/posterior/posterior_multi_state_repository.py

@@ -21,9 +21,9 @@ def __init__(self, size: int, checkpoint_dir: Optional[Path] = None):
         self.size = size
         self.state = [
             PosteriorStateRepository(
-                checkpoint_dir=os.path.join(checkpoint_dir, str(i))
-                if checkpoint_dir
-                else None
+                checkpoint_dir=(
+                    os.path.join(checkpoint_dir, str(i)) if checkpoint_dir else None
+                )
             )
             for i in range(size)
         ]