pre-commit: pyupgrade (#1352)

Stop using deprecated type annotations and imports. Include ruff pyupgrade rules in pre-commit.

doc/conf.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 #
 # pyPESTO documentation build configuration file, created by
 # sphinx-quickstart on Mon Jul 30 08:30:38 2018.

pypesto/C.py

@@ -5,7 +5,7 @@
 """
 
 from enum import Enum
-from typing import Literal, Tuple, Union
+from typing import Literal, Union
 
 ###############################################################################
 # ENSEMBLE
@@ -307,8 +307,8 @@ class InnerParameterType(str, Enum):
 
 LEN_RGB = 3  # number of elements in an RGB color
 LEN_RGBA = 4  # number of elements in an RGBA color
-RGB = Tuple[(float,) * LEN_RGB]  # typing of an RGB color
-RGBA = Tuple[(float,) * LEN_RGBA]  # typing of an RGBA color
+RGB = tuple[(float,) * LEN_RGB]  # typing of an RGB color
+RGBA = tuple[(float,) * LEN_RGBA]  # typing of an RGBA color
 RGB_RGBA = Union[RGB, RGBA]  # typing of an RGB or RGBA color
 RGBA_MIN = 0  # min value for an RGBA element
 RGBA_MAX = 1  # max value for an RGBA element

pypesto/ensemble/covariance_analysis.py

@@ -1,4 +1,4 @@
-from typing import Tuple, Union
+from typing import Union
 
 import numpy as np
 
@@ -60,7 +60,7 @@ def get_spectral_decomposition_parameters(
     only_identifiable_directions: bool = False,
     cutoff_absolute_identifiable: float = 1e-16,
     cutoff_relative_identifiable: float = 1e-16,
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Compute the spectral decomposition of ensemble parameters.
 
@@ -128,7 +128,7 @@ def get_spectral_decomposition_predictions(
     only_identifiable_directions: bool = False,
     cutoff_absolute_identifiable: float = 1e-16,
     cutoff_relative_identifiable: float = 1e-16,
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Compute the spectral decomposition of ensemble predictions.
 
@@ -191,7 +191,7 @@ def get_spectral_decomposition_lowlevel(
     only_identifiable_directions: bool = False,
     cutoff_absolute_identifiable: float = 1e-16,
     cutoff_relative_identifiable: float = 1e-16,
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Compute the spectral decomposition of ensemble parameters or predictions.
 

pypesto/ensemble/dimension_reduction.py

@@ -1,4 +1,4 @@
-from typing import Callable, Tuple, Union
+from typing import Callable, Union
 
 import numpy as np
 
@@ -11,7 +11,7 @@ def get_umap_representation_parameters(
     n_components: int = 2,
     normalize_data: bool = False,
     **kwargs,
-) -> Tuple:
+) -> tuple:
     """
     UMAP of parameter ensemble.
 
@@ -51,7 +51,7 @@ def get_umap_representation_predictions(
     n_components: int = 2,
     normalize_data: bool = False,
     **kwargs,
-) -> Tuple:
+) -> tuple:
     """
     UMAP of ensemble prediction.
 
@@ -97,7 +97,7 @@ def get_pca_representation_parameters(
     n_components: int = 2,
     rescale_data: bool = True,
     rescaler: Union[Callable, None] = None,
-) -> Tuple:
+) -> tuple:
     """
     PCA of parameter ensemble.
 
@@ -139,7 +139,7 @@ def get_pca_representation_predictions(
     n_components: int = 2,
     rescale_data: bool = True,
     rescaler: Union[Callable, None] = None,
-) -> Tuple:
+) -> tuple:
     """
     PCA of ensemble prediction.
 
@@ -188,7 +188,7 @@ def _get_umap_representation_lowlevel(
     n_components: int = 2,
     normalize_data: bool = False,
     **kwargs,
-) -> Tuple:
+) -> tuple:
     """
     Low level UMAP of parameter ensemble.
 
@@ -239,7 +239,7 @@ def _get_pca_representation_lowlevel(
     n_components: int = 2,
     rescale_data: bool = True,
     rescaler: Union[Callable, None] = None,
-) -> Tuple:
+) -> tuple:
     """
     Low level PCA of parameter ensemble.
 

pypesto/ensemble/ensemble.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
 import logging
+from collections.abc import Sequence
 from functools import partial
-from typing import TYPE_CHECKING, Any, Callable, Optional, Sequence, Union
+from typing import TYPE_CHECKING, Any, Callable
 
 import numpy as np
 import pandas as pd
@@ -67,7 +68,7 @@ class EnsemblePrediction:
 
     def __init__(
         self,
-        predictor: Optional[Callable[[Sequence], PredictionResult]] = None,
+        predictor: Callable[[Sequence], PredictionResult] | None = None,
         prediction_id: str = None,
         prediction_results: Sequence[PredictionResult] = None,
         lower_bound: Sequence[np.ndarray] = None,
@@ -272,7 +273,7 @@ def _stack_outputs_sensi(ic: int) -> np.array:
             # stack into one numpy array
             return np.stack(output_sensi_list, axis=-1)
 
-        def _stack_weights(ic: int) -> Union[np.ndarray, None]:
+        def _stack_weights(ic: int) -> np.ndarray | None:
             """
             Stack weights.
 
@@ -845,7 +846,7 @@ def _map_parameters_by_objective(
         self,
         predictor: Callable,
         default_value: float = None,
-    ) -> list[Union[int, float]]:
+    ) -> list[int | float]:
         """
         Create mapping for parameters from ensemble to predictor.
 
@@ -1079,7 +1080,7 @@ def check_identifiability(self) -> pd.DataFrame:
 
 
 def entries_per_start(
-    fval_traces: list["np.ndarray"],
+    fval_traces: list[np.ndarray],
     cutoff: float,
     max_size: int,
     max_per_start: int,
@@ -1168,7 +1169,7 @@ def get_vector_indices(
         return sorted(candidates, key=lambda i: trace_start[i])[:n_vectors]
 
 
-def get_percentile_label(percentile: Union[float, int, str]) -> str:
+def get_percentile_label(percentile: float | int | str) -> str:
     """Convert a percentile to a label.
 
     Labels for percentiles are used at different locations (e.g. ensemble

pypesto/ensemble/task.py

@@ -1,5 +1,5 @@
 import logging
-from typing import Any, Callable, List
+from typing import Any, Callable
 
 import numpy as np
 
@@ -32,7 +32,7 @@ def __init__(
         self.vectors = vectors
         self.id = id
 
-    def execute(self) -> List[Any]:
+    def execute(self) -> list[Any]:
         """Execute the task."""
         logger.debug(f"Executing task {self.id}.")
         results = []

pypesto/ensemble/util.py

@@ -1,8 +1,9 @@
 """Ensemble utilities."""
 
 import os
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Callable, Literal, Sequence, Union
+from typing import Callable, Literal, Union
 
 import h5py
 import numpy as np

pypesto/hierarchical/inner_calculator_collector.py

@@ -7,7 +7,8 @@
 from __future__ import annotations
 
 import copy
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import numpy as np
 
@@ -89,9 +90,9 @@ class InnerCalculatorCollector(AmiciCalculator):
     def __init__(
         self,
         data_types: set[str],
-        petab_problem: "petab.Problem",
+        petab_problem: petab.Problem,
         model: AmiciModel,
-        edatas: list["amici.ExpData"],
+        edatas: list[amici.ExpData],
         inner_options: dict,
     ):
         super().__init__()
@@ -117,9 +118,9 @@ def initialize(self):
 
     def construct_inner_calculators(
         self,
-        petab_problem: "petab.Problem",
+        petab_problem: petab.Problem,
         model: AmiciModel,
-        edatas: list["amici.ExpData"],
+        edatas: list[amici.ExpData],
         inner_options: dict,
     ):
         """Construct inner calculators for each data type."""
@@ -217,7 +218,7 @@ def validate_options(self, inner_options: dict):
 
     def _get_quantitative_data_mask(
         self,
-        edatas: list["amici.ExpData"],
+        edatas: list[amici.ExpData],
     ) -> list[np.ndarray]:
         # transform experimental data
         edatas = [

pypesto/hierarchical/ordinal/calculator.py

@@ -1,7 +1,7 @@
 """Definition of an optimal scaling calculator class."""
 
 import copy
-from typing import Sequence
+from collections.abc import Sequence
 
 import numpy as np
 

pypesto/hierarchical/relative/calculator.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import copy
-from typing import Optional, Sequence
+from collections.abc import Sequence
 
 import numpy as np
 
@@ -46,7 +46,7 @@ class RelativeAmiciCalculator(AmiciCalculator):
     def __init__(
         self,
         inner_problem: AmiciInnerProblem,
-        inner_solver: Optional[InnerSolver] = None,
+        inner_solver: InnerSolver | None = None,
     ):
         """Initialize the calculator from the given problem.
 
@@ -83,7 +83,7 @@ def __call__(
         x_ids: Sequence[str],
         parameter_mapping: ParameterMapping,
         fim_for_hess: bool,
-        rdatas: list["amici.ReturnData"] = None,
+        rdatas: list[amici.ReturnData] = None,
     ):
         """Perform the actual AMICI call, with hierarchical optimization.
 
@@ -269,7 +269,7 @@ def calculate_directly(
         x_ids: Sequence[str],
         parameter_mapping: ParameterMapping,
         fim_for_hess: bool,
-        rdatas: list["amici.ReturnData"] = None,
+        rdatas: list[amici.ReturnData] = None,
     ):
         """Calculate directly via solver calculate methods.
 

pypesto/hierarchical/semiquantitative/calculator.py

@@ -1,5 +1,5 @@
 import copy
-from typing import Sequence
+from collections.abc import Sequence
 
 import numpy as np
 

pypesto/history/amici.py

@@ -1,5 +1,6 @@
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Sequence, Union
+from typing import Union
 
 import numpy as np
 

pypesto/history/base.py

@@ -3,7 +3,8 @@
 import numbers
 import time
 from abc import ABC, abstractmethod
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import numpy as np
 

pypesto/history/csv.py

@@ -3,7 +3,8 @@
 import copy
 import os
 import time
-from typing import Sequence, Union
+from collections.abc import Sequence
+from typing import Union
 
 import numpy as np
 import pandas as pd

pypesto/history/generate.py

@@ -1,7 +1,7 @@
 """Generate a history from options and inputs."""
 
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Sequence
 
 from ..C import SUFFIXES_CSV, SUFFIXES_HDF5
 from .base import CountHistory, HistoryBase

pypesto/history/hdf5.py

@@ -2,9 +2,10 @@
 
 import contextlib
 import time
+from collections.abc import Sequence
 from functools import wraps
 from pathlib import Path
-from typing import Sequence, Union
+from typing import Union
 
 import h5py
 import numpy as np

pypesto/history/memory.py

@@ -1,7 +1,8 @@
 """In-memory history."""
 
 import time
-from typing import Any, Sequence, Union
+from collections.abc import Sequence
+from typing import Any, Union
 
 import numpy as np
 

pypesto/history/util.py

@@ -1,8 +1,9 @@
 """History utility functions."""
 
 import numbers
+from collections.abc import Sequence
 from functools import wraps
-from typing import Sequence, Union
+from typing import Union
 
 import numpy as np