pre-commit updates (#2813)

* pre-commit updates

Update pre-commit hooks and re-run.

* Update python/sdist/amici/numpy.py

---------

Co-authored-by: Fabian Fröhlich <[email protected]>

Author: dweindl

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   - id: trailing-whitespace
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.6
+  rev: v0.12.0
   hooks:
     # Run the linter.
     - id: ruff
@@ -28,7 +28,7 @@ repos:
         - python/sdist/pyproject.toml
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.1
+    rev: v3.20.0
     hooks:
     -   id: pyupgrade
         args: ["--py310-plus"]

doc/conf.py

@@ -349,7 +349,7 @@ def install_doxygen():
             [
                 "INPUT = ../matlab",
                 "EXTENSION_MAPPING = .m=C++",
-                "FILTER_PATTERNS = " f"*.m={mtocpp_filter}",
+                f"FILTER_PATTERNS = *.m={mtocpp_filter}",
                 "EXCLUDE += ../matlab/examples",
                 "EXCLUDE += ../matlab/mtoc",
                 "EXCLUDE += ../matlab/SBMLimporter",
@@ -509,7 +509,7 @@ def process_docstring(app, what, name, obj, options, lines):
         cname = name.split(".")[2]
         lines.append(
             f"Swig-Generated class that implements smart pointers to "
-            f'{cname.replace("Ptr", "")} as objects.'
+            f"{cname.replace('Ptr', '')} as objects."
         )
         return
 

doc/examples/example_errors.ipynb

@@ -985,7 +985,7 @@
    "source": [
     "# Increase relative steady state tolerance\n",
     "for log10_relaxation_factor in range(1, 10):\n",
-    "    print(f\"Relaxing tolerances by factor {10 ** log10_relaxation_factor}\")\n",
+    "    print(f\"Relaxing tolerances by factor {10**log10_relaxation_factor}\")\n",
     "    amici_solver = amici_model.getSolver()\n",
     "    amici_solver.setRelativeToleranceSteadyState(\n",
     "        amici_solver.getRelativeToleranceSteadyState()\n",

doc/examples/example_large_models/example_performance_optimization.ipynb

@@ -127,7 +127,7 @@
     ")\n",
     "plt.show()\n",
     "\n",
-    "print(f\"speedup: {873.54/697.85:.2f}x\")"
+    "print(f\"speedup: {873.54 / 697.85:.2f}x\")"
    ]
   },
   {

doc/recreate_reference_list.py

@@ -42,10 +42,7 @@ def get_sub_bibliography(year, by_year, bibfile):
 
     entries = ",".join(["@" + x for x in by_year[year]])
     stdin_input = (
-        "---\n"
-        f"bibliography: {bibfile}\n"
-        f'nocite: "{entries}"\n...\n'
-        f"# {year}"
+        f'---\nbibliography: {bibfile}\nnocite: "{entries}"\n...\n# {year}'
     )
 
     out = subprocess.run(

python/sdist/amici/_codegen/cxx_functions.py

@@ -291,8 +291,7 @@ def var_in_signature(self, varname: str, ode: bool = True) -> bool:
         assume_pow_positivity=True,
     ),
     "x0": _FunctionInfo(
-        "realtype *x0, const realtype t, const realtype *p, "
-        "const realtype *k"
+        "realtype *x0, const realtype t, const realtype *p, const realtype *k"
     ),
     "x0_fixedParameters": _FunctionInfo(
         "realtype *x0_fixedParameters, const realtype t, "

python/sdist/amici/compile.py

@@ -49,7 +49,7 @@ def build_model_extension(
             # length of intermediate build files, that may easily become
             # problematic on Windows, due to its ridiculous 255-character path
             # length limit.
-            f'--build-temp={package_dir / "build"}',
+            f"--build-temp={package_dir / 'build'}",
         ]
     )
 

python/sdist/amici/cxxcodeprinter.py

@@ -130,8 +130,7 @@ def _get_sym_lines_array(
             C++ code as list of lines
         """
         return [
-            " " * indent_level + f"{variable}[{index}] = "
-            f"{self.doprint(math)};"
+            " " * indent_level + f"{variable}[{index}] = {self.doprint(math)};"
             for index, math in enumerate(equations)
             if math not in [0, 0.0]
         ]
@@ -366,7 +365,7 @@ def csc_matrix(
 
             symbol_row_vals.append(row)
             idx += 1
-            symbol_name = f"d{rownames[row].name}" f"_d{colnames[col].name}"
+            symbol_name = f"d{rownames[row].name}_d{colnames[col].name}"
             if identifier:
                 symbol_name += f"_{identifier}"
             symbol_list.append(symbol_name)

python/sdist/amici/de_export.py

@@ -648,7 +648,7 @@ def _generate_function_index(
 
         lines.extend(
             [
-                "}" "",
+                "}",
                 f"}} // namespace model_{self.model_name}",
                 "} // namespace amici\n",
             ]

python/sdist/amici/de_model.py

@@ -634,8 +634,7 @@ def add_conservation_law(
             )[0]
         except StopIteration:
             raise ValueError(
-                f"Specified state {state} was not found in the "
-                f"model states."
+                f"Specified state {state} was not found in the model states."
             )
 
         state_id = self._differential_states[ix].get_id()
@@ -1236,7 +1235,7 @@ def _generate_symbol(self, name: str) -> None:
             length = len(self.eq(name))
         self._syms[name] = sp.Matrix(
             [
-                sp.Symbol(f'{name}{0 if name == "stau" else i}', real=True)
+                sp.Symbol(f"{name}{0 if name == 'stau' else i}", real=True)
                 for i in range(length)
             ]
         )