pyupgrade, pre-commit autoupdate (#2411)

* Run pyupgrade for python>=3.10
* Update configuration for recent ruff 


manual changes:
* .pre-commit-config.yam
* pyproject.toml

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: check-added-large-files
   - id: check-merge-conflict
@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.11
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,10 +28,9 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
     -   id: pyupgrade
-        args: ["--py39-plus"]
-        additional_dependencies: [pyupgrade==3.15.0]
+        args: ["--py310-plus"]
 
 exclude: '^(ThirdParty|models)/'

python/sdist/amici/__init__.py

@@ -13,7 +13,8 @@
 import sys
 from pathlib import Path
 from types import ModuleType as ModelModule
-from typing import Any, Callable, Union
+from typing import Any
+from collections.abc import Callable
 
 
 def _get_amici_path():
@@ -138,7 +139,7 @@ def get_model(self) -> amici.Model:
 class add_path:
     """Context manager for temporarily changing PYTHONPATH"""
 
-    def __init__(self, path: Union[str, Path]):
+    def __init__(self, path: str | Path):
         self.path: str = str(path)
 
     def __enter__(self):
@@ -151,7 +152,7 @@ def __exit__(self, exc_type, exc_value, traceback):
 
 
 def import_model_module(
-    module_name: str, module_path: Union[Path, str]
+    module_name: str, module_path: Path | str
 ) -> ModelModule:
     """
     Import Python module of an AMICI model

python/sdist/amici/_codegen/cxx_functions.py

@@ -1,4 +1,5 @@
 """Info about C++ functions in the generated model code."""
+
 from __future__ import annotations
 
 from dataclasses import dataclass

python/sdist/amici/_codegen/model_class.py

@@ -1,4 +1,5 @@
 """Function for generating the ``amici::Model`` subclass for an amici model."""
+
 from __future__ import annotations
 
 from .cxx_functions import functions, multiobs_functions

python/sdist/amici/_codegen/template.py

@@ -1,7 +1,7 @@
 """Functions to apply template substitution to files."""
+
 from pathlib import Path
 from string import Template
-from typing import Union
 
 
 class TemplateAmici(Template):
@@ -17,8 +17,8 @@ class TemplateAmici(Template):
 
 
 def apply_template(
-    source_file: Union[str, Path],
-    target_file: Union[str, Path],
+    source_file: str | Path,
+    target_file: str | Path,
     template_data: dict[str, str],
 ) -> None:
     """

python/sdist/amici/antimony_import.py

@@ -3,11 +3,11 @@
 https://antimony.sourceforge.net/
 https://tellurium.readthedocs.io/en/latest/antimony.html
 """
+
 from pathlib import Path
-from typing import Union
 
 
-def antimony2sbml(ant_model: Union[str, Path]) -> str:
+def antimony2sbml(ant_model: str | Path) -> str:
     """Convert Antimony model to SBML.
 
     :param ant_model: Antimony model as string or path to file
@@ -46,7 +46,7 @@ def antimony2sbml(ant_model: Union[str, Path]) -> str:
     return sbml_str
 
 
-def antimony2amici(ant_model: Union[str, Path], *args, **kwargs):
+def antimony2amici(ant_model: str | Path, *args, **kwargs):
     """Convert Antimony model to AMICI model.
 
     Converts the Antimony model provided as string of file to SBML and then imports it into AMICI.

python/sdist/amici/bngl_import.py

@@ -5,7 +5,6 @@
 in the :term:`BNGL` format.
 """
 
-
 from pysb.importers.bngl import model_from_bngl
 
 from .pysb_import import pysb2amici

python/sdist/amici/compile.py

@@ -2,18 +2,18 @@
 Functionality for building the C++ extensions of an amici-created model
 package.
 """
+
 import subprocess
 import sys
-from typing import Optional, Union
 from pathlib import Path
 import os
 
 
 def build_model_extension(
-    package_dir: Union[str, Path],
-    verbose: Optional[Union[bool, int]] = False,
-    compiler: Optional[str] = None,
-    extra_msg: Optional[str] = None,
+    package_dir: str | Path,
+    verbose: bool | int | None = False,
+    compiler: str | None = None,
+    extra_msg: str | None = None,
 ) -> None:
     """
     Compile the model extension of an amici-created model package.

python/sdist/amici/conserved_quantities_demartino.py

@@ -2,7 +2,6 @@
 import math
 import random
 import sys
-from typing import Optional, Union
 from collections.abc import MutableSequence, Sequence
 
 from .logging import get_logger
@@ -21,8 +20,8 @@ def compute_moiety_conservation_laws(
     num_species: int,
     num_reactions: int,
     max_num_monte_carlo: int = 20,
-    rng_seed: Union[None, bool, int] = False,
-    species_names: Optional[Sequence[str]] = None,
+    rng_seed: None | bool | int = False,
+    species_names: Sequence[str] | None = None,
 ) -> tuple[list[list[int]], list[list[float]]]:
     """Compute moiety conservation laws.
 
@@ -116,7 +115,7 @@ def _output(
     int_matched: list[int],
     species_indices: list[list[int]],
     species_coefficients: list[list[float]],
-    species_names: Optional[Sequence[str]] = None,
+    species_names: Sequence[str] | None = None,
     verbose: bool = False,
     log_level: int = logging.DEBUG,
 ):

python/sdist/amici/conserved_quantities_rref.py

@@ -1,12 +1,12 @@
 """Find conserved quantities deterministically"""
 
-from typing import Literal, Optional, Union
+from typing import Literal
 
 import numpy as np
 
 
 def rref(
-    mat: np.array, round_ndigits: Optional[Union[Literal[False], int]] = None
+    mat: np.array, round_ndigits: Literal[False] | int | None = None
 ) -> np.array:
     """
     Bring matrix ``mat`` to reduced row echelon form

python/sdist/amici/cxxcodeprinter.py

@@ -1,8 +1,8 @@
 """C++ code generation"""
+
 import itertools
 import os
 import re
-from typing import Optional
 from collections.abc import Sequence
 from collections.abc import Iterable
 
@@ -49,7 +49,7 @@ def __init__(self):
         else:
             self._fpoptimizer = None
 
-    def doprint(self, expr: sp.Expr, assign_to: Optional[str] = None) -> str:
+    def doprint(self, expr: sp.Expr, assign_to: str | None = None) -> str:
         if self._fpoptimizer:
             if isinstance(expr, list):
                 expr = list(map(self._fpoptimizer, expr))
@@ -124,7 +124,7 @@ def _get_sym_lines_symbols(
         equations: sp.Matrix,
         variable: str,
         indent_level: int,
-        indices: Optional[Sequence[int]] = None,
+        indices: Sequence[int] | None = None,
     ) -> list[str]:
         """
         Generate C++ code for where array elements are directly replaced with
@@ -230,8 +230,8 @@ def print_bool(expr) -> str:
 def get_switch_statement(
     condition: str,
     cases: dict[int, list[str]],
-    indentation_level: Optional[int] = 0,
-    indentation_step: Optional[str] = " " * 4,
+    indentation_level: int | None = 0,
+    indentation_step: str | None = " " * 4,
 ):
     """
     Generate code for a C++ switch statement.
@@ -296,8 +296,8 @@ def csc_matrix(
     matrix: sp.Matrix,
     rownames: list[sp.Symbol],
     colnames: list[sp.Symbol],
-    identifier: Optional[int] = 0,
-    pattern_only: Optional[bool] = False,
+    identifier: int | None = 0,
+    pattern_only: bool | None = False,
 ) -> tuple[list[int], list[int], sp.Matrix, list[str], sp.Matrix]:
     """
     Generates the sparse symbolic identifiers, symbolic identifiers,

python/sdist/amici/de_export.py

@@ -9,6 +9,7 @@
 :py:func:`amici.sbml_import.SbmlImporter.sbml2amici` and
 :py:func:`amici.petab_import.import_model`.
 """
+
 from __future__ import annotations
 import copy
 import logging
@@ -1140,36 +1141,36 @@ def _write_model_header_cpp(self) -> None:
                         ] = impl
                 continue
 
-            tpl_data[
-                f"{func_name.upper()}_DEF"
-            ] = get_function_extern_declaration(
-                func_name, self.model_name, self.model.is_ode()
+            tpl_data[f"{func_name.upper()}_DEF"] = (
+                get_function_extern_declaration(
+                    func_name, self.model_name, self.model.is_ode()
+                )
             )
-            tpl_data[
-                f"{func_name.upper()}_IMPL"
-            ] = get_model_override_implementation(
-                func_name, self.model_name, self.model.is_ode()
+            tpl_data[f"{func_name.upper()}_IMPL"] = (
+                get_model_override_implementation(
+                    func_name, self.model_name, self.model.is_ode()
+                )
             )
             if func_name in sparse_functions:
-                tpl_data[
-                    f"{func_name.upper()}_COLPTRS_DEF"
-                ] = get_sunindex_extern_declaration(
-                    func_name, self.model_name, "colptrs"
+                tpl_data[f"{func_name.upper()}_COLPTRS_DEF"] = (
+                    get_sunindex_extern_declaration(
+                        func_name, self.model_name, "colptrs"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_COLPTRS_IMPL"
-                ] = get_sunindex_override_implementation(
-                    func_name, self.model_name, "colptrs"
+                tpl_data[f"{func_name.upper()}_COLPTRS_IMPL"] = (
+                    get_sunindex_override_implementation(
+                        func_name, self.model_name, "colptrs"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_ROWVALS_DEF"
-                ] = get_sunindex_extern_declaration(
-                    func_name, self.model_name, "rowvals"
+                tpl_data[f"{func_name.upper()}_ROWVALS_DEF"] = (
+                    get_sunindex_extern_declaration(
+                        func_name, self.model_name, "rowvals"
+                    )
                 )
-                tpl_data[
-                    f"{func_name.upper()}_ROWVALS_IMPL"
-                ] = get_sunindex_override_implementation(
-                    func_name, self.model_name, "rowvals"
+                tpl_data[f"{func_name.upper()}_ROWVALS_IMPL"] = (
+                    get_sunindex_override_implementation(
+                        func_name, self.model_name, "rowvals"
+                    )
                 )
 
         if self.model.num_states_solver() == self.model.num_states_rdata():

python/sdist/amici/de_model.py

@@ -1,12 +1,14 @@
 """Symbolic differential equation model."""
+
 from __future__ import annotations
 
 import contextlib
 import copy
 import itertools
 import re
 from itertools import chain
-from typing import Callable, TYPE_CHECKING
+from typing import TYPE_CHECKING
+from collections.abc import Callable
 from collections.abc import Sequence
 
 import numpy as np