pre-commit: run pyupgrade (#2264)

Set up pre-commit hook and run [pyupgrade](https://github.com/asottile/pyupgrade) (update type annotations, ...).

.pre-commit-config.yaml

@@ -27,4 +27,11 @@ repos:
         - --config
         - python/sdist/pyproject.toml
 
+-   repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+    -   id: pyupgrade
+        args: ["--py39-plus"]
+        additional_dependencies: [pyupgrade==3.15.0]
+
 exclude: '^(ThirdParty|models)/'

documentation/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #
@@ -15,7 +14,7 @@
 import amici
 import exhale.deploy
 import exhale_multiproject_monkeypatch
-import mock
+from unittest import mock
 import pandas as pd
 import sphinx
 import sympy as sp

documentation/recreate_reference_list.py

@@ -20,7 +20,7 @@
 def get_keys_by_year(bibfile):
     """Get bibtex entry keys as dict by year"""
 
-    with open(bibfile, "r") as f:
+    with open(bibfile) as f:
         db = biblib.bib.Parser().parse(f, log_fp=sys.stderr).get_entries()
         recoverer = biblib.messages.InputErrorRecoverer()
         by_year = {}

python/sdist/amici/conserved_quantities_demartino.py

@@ -2,7 +2,8 @@
 import math
 import random
 import sys
-from typing import List, MutableSequence, Optional, Sequence, Tuple, Union
+from typing import Optional, Union
+from collections.abc import MutableSequence, Sequence
 
 from .logging import get_logger
 
@@ -22,7 +23,7 @@ def compute_moiety_conservation_laws(
     max_num_monte_carlo: int = 20,
     rng_seed: Union[None, bool, int] = False,
     species_names: Optional[Sequence[str]] = None,
-) -> Tuple[List[List[int]], List[List[float]]]:
+) -> tuple[list[list[int]], list[list[float]]]:
     """Compute moiety conservation laws.
 
     According to the algorithm proposed by De Martino et al. (2014)
@@ -112,9 +113,9 @@ def compute_moiety_conservation_laws(
 def _output(
     int_kernel_dim: int,
     kernel_dim: int,
-    int_matched: List[int],
-    species_indices: List[List[int]],
-    species_coefficients: List[List[float]],
+    int_matched: list[int],
+    species_indices: list[list[int]],
+    species_coefficients: list[list[float]],
     species_names: Optional[Sequence[str]] = None,
     verbose: bool = False,
     log_level: int = logging.DEBUG,
@@ -203,7 +204,7 @@ def _qsort(
 
 def _kernel(
     stoichiometric_list: Sequence[float], num_species: int, num_reactions: int
-) -> Tuple[int, List[int], int, List[int], List[List[int]], List[List[float]]]:
+) -> tuple[int, list[int], int, list[int], list[list[int]], list[list[float]]]:
     """
     Kernel (left nullspace of :math:`S`) calculation by Gaussian elimination
 
@@ -227,8 +228,8 @@ def _kernel(
         kernel dimension, MCLs, integer kernel dimension, integer MCLs and
         indices to species and reactions in the preceding order as a tuple
     """
-    matrix: List[List[int]] = [[] for _ in range(num_species)]
-    matrix2: List[List[float]] = [[] for _ in range(num_species)]
+    matrix: list[list[int]] = [[] for _ in range(num_species)]
+    matrix2: list[list[float]] = [[] for _ in range(num_species)]
     i_reaction = 0
     i_species = 0
     for val in stoichiometric_list:
@@ -243,7 +244,7 @@ def _kernel(
         matrix[i].append(num_reactions + i)
         matrix2[i].append(1)
 
-    order: List[int] = list(range(num_species))
+    order: list[int] = list(range(num_species))
     pivots = [
         matrix[i][0] if len(matrix[i]) else _MAX for i in range(num_species)
     ]
@@ -283,7 +284,7 @@ def _kernel(
             if pivots[order[j + 1]] == pivots[order[j]] != _MAX:
                 k1 = order[j + 1]
                 k2 = order[j]
-                column: List[float] = [0] * (num_species + num_reactions)
+                column: list[float] = [0] * (num_species + num_reactions)
                 g = matrix2[k2][0] / matrix2[k1][0]
                 for i in range(1, len(matrix[k1])):
                     column[matrix[k1][i]] = matrix2[k1][i] * g
@@ -369,7 +370,7 @@ def _fill(
     stoichiometric_list: Sequence[float],
     matched: Sequence[int],
     num_species: int,
-) -> Tuple[List[List[int]], List[List[int]], List[int]]:
+) -> tuple[list[list[int]], list[list[int]], list[int]]:
     """Construct interaction matrix
 
     Construct the interaction matrix out of the given stoichiometric matrix
@@ -454,8 +455,8 @@ def _is_linearly_dependent(
         boolean indicating linear dependence (true) or not (false)
     """
     K = int_kernel_dim + 1
-    matrix: List[List[int]] = [[] for _ in range(K)]
-    matrix2: List[List[float]] = [[] for _ in range(K)]
+    matrix: list[list[int]] = [[] for _ in range(K)]
+    matrix2: list[list[float]] = [[] for _ in range(K)]
     # Populate matrices with species ids and coefficients for CLs
     for i in range(K - 1):
         for j in range(len(cls_species_idxs[i])):
@@ -508,7 +509,7 @@ def _is_linearly_dependent(
             if pivots[order[j + 1]] == pivots[order[j]] != _MAX:
                 k1 = order[j + 1]
                 k2 = order[j]
-                column: List[float] = [0] * num_species
+                column: list[float] = [0] * num_species
                 g = matrix2[k2][0] / matrix2[k1][0]
                 for i in range(1, len(matrix[k1])):
                     column[matrix[k1][i]] = matrix2[k1][i] * g
@@ -540,7 +541,7 @@ def _monte_carlo(
     initial_temperature: float = 1,
     cool_rate: float = 1e-3,
     max_iter: int = 10,
-) -> Tuple[bool, int, Sequence[int]]:
+) -> tuple[bool, int, Sequence[int]]:
     """MonteCarlo simulated annealing for finding integer MCLs
 
     Finding integer solutions for the MCLs by Monte Carlo, see step (b) in
@@ -712,8 +713,8 @@ def _relax(
         (``False``)
     """
     K = len(int_matched)
-    matrix: List[List[int]] = [[] for _ in range(K)]
-    matrix2: List[List[float]] = [[] for _ in range(K)]
+    matrix: list[list[int]] = [[] for _ in range(K)]
+    matrix2: list[list[float]] = [[] for _ in range(K)]
     i_reaction = 0
     i_species = 0
     for val in stoichiometric_list:
@@ -767,7 +768,7 @@ def _relax(
             if pivots[order[j + 1]] == pivots[order[j]] != _MAX:
                 k1 = order[j + 1]
                 k2 = order[j]
-                column: List[float] = [0] * num_reactions
+                column: list[float] = [0] * num_reactions
                 g = matrix2[k2][0] / matrix2[k1][0]
                 for i in range(1, len(matrix[k1])):
                     column[matrix[k1][i]] = matrix2[k1][i] * g
@@ -807,7 +808,7 @@ def _relax(
 
                 # subtract rows
                 # matrix2[k] = matrix2[k] - matrix2[j] * matrix2[k][i]
-                row_k: List[float] = [0] * num_reactions
+                row_k: list[float] = [0] * num_reactions
                 for a in range(len(matrix[k])):
                     row_k[matrix[k][a]] = matrix2[k][a]
                 for a in range(len(matrix[j])):
@@ -955,7 +956,7 @@ def _reduce(
             k1 = order[i]
             for j in range(i + 1, K):
                 k2 = order[j]
-                column: List[float] = [0] * num_species
+                column: list[float] = [0] * num_species
                 for species_idx, coefficient in zip(
                     cls_species_idxs[k1], cls_coefficients[k1]
                 ):

python/sdist/amici/conserved_quantities_rref.py

@@ -1,6 +1,6 @@
 """Find conserved quantities deterministically"""
 
-from typing import List, Literal, Optional, Union
+from typing import Literal, Optional, Union
 
 import numpy as np
 
@@ -67,7 +67,7 @@ def _round(mat):
     return mat
 
 
-def pivots(mat: np.array) -> List[int]:
+def pivots(mat: np.array) -> list[int]:
     """Get indices of pivot columns in ``mat``, assumed to be in reduced row
     echelon form"""
     pivot_cols = []

python/sdist/amici/cxxcodeprinter.py

@@ -2,7 +2,8 @@
 import itertools
 import os
 import re
-from typing import Dict, Iterable, List, Optional, Tuple
+from typing import Optional
+from collections.abc import Iterable
 
 import sympy as sp
 from sympy.codegen.rewriting import Optimization, optimize
@@ -73,7 +74,7 @@ def _print_min_max(self, expr, cpp_fun: str, sympy_fun):
         )
         if len(expr.args) == 1:
             return self._print(arg0)
-        return "%s%s(%s, %s)" % (
+        return "{}{}({}, {})".format(
             self._ns,
             cpp_fun,
             self._print(arg0),
@@ -92,7 +93,7 @@ def _print_Max(self, expr):
 
     def _get_sym_lines_array(
         self, equations: sp.Matrix, variable: str, indent_level: int
-    ) -> List[str]:
+    ) -> list[str]:
         """
         Generate C++ code for assigning symbolic terms in symbols to C++ array
         `variable`.
@@ -122,7 +123,7 @@ def _get_sym_lines_symbols(
         equations: sp.Matrix,
         variable: str,
         indent_level: int,
-    ) -> List[str]:
+    ) -> list[str]:
         """
         Generate C++ code for where array elements are directly replaced with
         their corresponding macro symbol
@@ -209,11 +210,11 @@ def format_line(symbol: sp.Symbol):
     def csc_matrix(
         self,
         matrix: sp.Matrix,
-        rownames: List[sp.Symbol],
-        colnames: List[sp.Symbol],
+        rownames: list[sp.Symbol],
+        colnames: list[sp.Symbol],
         identifier: Optional[int] = 0,
         pattern_only: Optional[bool] = False,
-    ) -> Tuple[List[int], List[int], sp.Matrix, List[str], sp.Matrix]:
+    ) -> tuple[list[int], list[int], sp.Matrix, list[str], sp.Matrix]:
         """
         Generates the sparse symbolic identifiers, symbolic identifiers,
         sparse matrix, column pointers and row values for a symbolic
@@ -298,7 +299,7 @@ def print_bool(expr) -> str:
 
 def get_switch_statement(
     condition: str,
-    cases: Dict[int, List[str]],
+    cases: dict[int, list[str]],
     indentation_level: Optional[int] = 0,
     indentation_step: Optional[str] = " " * 4,
 ):