chore: update pre-commit hooks (#4752)

* chore: update pre-commit hooks

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.6 → v0.9.1](astral-sh/ruff-pre-commit@v0.8.6...v0.9.1)

* style: pre-commit fixes

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.8.6"
+    rev: "v0.9.1"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

docs/source/examples/notebooks/initialize-model-with-solution.ipynb

@@ -83,7 +83,7 @@
     "# import drive cycle from file\n",
     "data_loader = pybamm.DataLoader()\n",
     "drive_cycle = pd.read_csv(\n",
-    "    f\"{data_loader.get_data(\"US06.csv\")}\", comment=\"#\", header=None\n",
+    "    f\"{data_loader.get_data('US06.csv')}\", comment=\"#\", header=None\n",
     ").to_numpy()\n",
     "# create interpolant\n",
     "param = model.default_parameter_values\n",

docs/source/examples/notebooks/models/compare-ecker-data.ipynb

@@ -59,10 +59,10 @@
     "data_loader = pybamm.DataLoader()\n",
     "\n",
     "voltage_data_1C = pd.read_csv(\n",
-    "    f\"{data_loader.get_data(\"Ecker_1C.csv\")}\", header=None\n",
+    "    f\"{data_loader.get_data('Ecker_1C.csv')}\", header=None\n",
     ").to_numpy()\n",
     "voltage_data_5C = pd.read_csv(\n",
-    "    f\"{data_loader.get_data(\"Ecker_5C.csv\")}\", header=None\n",
+    "    f\"{data_loader.get_data('Ecker_5C.csv')}\", header=None\n",
     ").to_numpy()"
    ]
   },

docs/source/examples/notebooks/models/pouch-cell-model.ipynb

@@ -193,7 +193,7 @@
    "source": [
     "data_loader = pybamm.DataLoader()\n",
     "comsol_results_path = pybamm.get_parameters_filepath(\n",
-    "    f\"{data_loader.get_data(\"comsol_1plus1D_3C.json\")}\"\n",
+    "    f\"{data_loader.get_data('comsol_1plus1D_3C.json')}\"\n",
     ")\n",
     "comsol_variables = json.load(open(comsol_results_path))"
    ]

docs/source/examples/notebooks/parameterization/change-input-current.ipynb

@@ -194,7 +194,7 @@
     "# import drive cycle from file\n",
     "data_loader = pybamm.DataLoader()\n",
     "drive_cycle = pd.read_csv(\n",
-    "    f\"{data_loader.get_data(\"US06.csv\")}\", comment=\"#\", header=None\n",
+    "    f\"{data_loader.get_data('US06.csv')}\", comment=\"#\", header=None\n",
     ").to_numpy()\n",
     "\n",
     "# load parameter values\n",

docs/source/examples/notebooks/solvers/idaklu-jax-interface.ipynb

@@ -307,13 +307,13 @@
     "# Calculate the Jacobian matrix (via forward autodiff)\n",
     "t_start = time.time()\n",
     "out = jax.jacfwd(f, argnums=1)(t_eval, inputs)\n",
-    "print(f\"Jacobian forward method ran in {time.time()-t_start:0.3} secs\")\n",
+    "print(f\"Jacobian forward method ran in {time.time() - t_start:0.3} secs\")\n",
     "print(out)\n",
     "\n",
     "# Calculate Jacobian matrix (via backward autodiff)\n",
     "t_start = time.time()\n",
     "out = jax.jacrev(f, argnums=1)(t_eval, inputs)\n",
-    "print(f\"\\nJacobian reverse method ran in {time.time()-t_start:0.3} secs\")\n",
+    "print(f\"\\nJacobian reverse method ran in {time.time() - t_start:0.3} secs\")\n",
     "print(out)"
    ]
   },
@@ -382,7 +382,7 @@
     "    ),\n",
     "    in_axes=(0, None),  # map time over the 0th dimension and do not map inputs\n",
     ")(t_eval, inputs)\n",
-    "print(f\"Gradient method ran in {time.time()-t_start:0.3} secs\")\n",
+    "print(f\"Gradient method ran in {time.time() - t_start:0.3} secs\")\n",
     "print(data)"
    ]
   },
@@ -436,7 +436,7 @@
     "# Get the value and gradient of the SSE function\n",
     "t_start = time.time()\n",
     "value, gradient = jax.value_and_grad(sse, argnums=1)(t_eval, inputs_pred)\n",
-    "print(f\"Value and gradient computed in {time.time()-t_start:0.3} secs\")\n",
+    "print(f\"Value and gradient computed in {time.time() - t_start:0.3} secs\")\n",
     "print(\"SSE value: \", value)\n",
     "print(\"SSE gradient (wrt each input): \", gradient)"
    ]

docs/source/examples/notebooks/solvers/speed-up-solver.ipynb

@@ -806,23 +806,23 @@
     "y = pybamm.Variable(\"y\")\n",
     "\n",
     "# Normal maximum\n",
-    "print(f\"Exact maximum: {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Exact maximum: {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# Softplus\n",
     "print(\"Softplus (k=10): \", pybamm.softplus(x, y, 10))\n",
     "\n",
     "# Changing the setting to call softplus automatically\n",
     "pybamm.settings.min_max_mode = \"soft\"\n",
     "pybamm.settings.min_max_smoothing = 20\n",
-    "print(f\"Softplus (k=20): {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Softplus (k=20): {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# All smoothing parameters can be changed at once\n",
     "pybamm.settings.set_smoothing_parameters(30)\n",
-    "print(f\"Softplus (k=30): {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Softplus (k=30): {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# Change back\n",
     "pybamm.settings.set_smoothing_parameters(\"exact\")\n",
-    "print(f\"Exact maximum: {pybamm.maximum(x,y)}\")"
+    "print(f\"Exact maximum: {pybamm.maximum(x, y)}\")"
    ]
   },
   {
@@ -1025,23 +1025,23 @@
     "y = pybamm.Variable(\"y\")\n",
     "\n",
     "# Normal maximum\n",
-    "print(f\"Exact maximum: {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Exact maximum: {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# Smooth plus can be called explicitly\n",
     "print(\"Smooth plus (k=100): \", pybamm.smooth_max(x, y, 100))\n",
     "\n",
     "# Smooth plus and smooth minus will be used when the mode is set to \"smooth\"\n",
     "pybamm.settings.min_max_mode = \"smooth\"\n",
     "pybamm.settings.min_max_smoothing = 200\n",
-    "print(f\"Smooth plus (k=200): {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Smooth plus (k=200): {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# Setting the smoothing parameters with set_smoothing_parameters() defaults to softplus\n",
     "pybamm.settings.set_smoothing_parameters(10)\n",
-    "print(f\"Softplus (k=10): {pybamm.maximum(x,y)}\")\n",
+    "print(f\"Softplus (k=10): {pybamm.maximum(x, y)}\")\n",
     "\n",
     "# Change back\n",
     "pybamm.settings.set_smoothing_parameters(\"exact\")\n",
-    "print(f\"Exact maximum: {pybamm.maximum(x,y)}\")"
+    "print(f\"Exact maximum: {pybamm.maximum(x, y)}\")"
    ]
   },
   {
@@ -1206,11 +1206,11 @@
    ],
    "source": [
     "pybamm.settings.set_smoothing_parameters(10)\n",
-    "print(f\"Soft minimum (softminus):\\t {pybamm.minimum(x,y)!s}\")\n",
+    "print(f\"Soft minimum (softminus):\\t {pybamm.minimum(x, y)!s}\")\n",
     "print(f\"Smooth heaviside (sigmoid):\\t {x < y!s}\")\n",
     "print(f\"Smooth absolute value: \\t\\t {abs(x)!s}\")\n",
     "pybamm.settings.min_max_mode = \"smooth\"\n",
-    "print(f\"Smooth minimum:\\t\\t\\t {pybamm.minimum(x,y)!s}\")\n",
+    "print(f\"Smooth minimum:\\t\\t\\t {pybamm.minimum(x, y)!s}\")\n",
     "pybamm.settings.set_smoothing_parameters(\"exact\")"
    ]
   },

docs/source/examples/notebooks/spatial_methods/finite-volumes.ipynb

@@ -492,7 +492,7 @@
     "macro_mesh = mesh.combine_submeshes(*macroscale)\n",
     "print(\"gradient matrix is:\\n\")\n",
     "print(\n",
-    "    f\"1/dx *\\n{macro_mesh.d_nodes[:,np.newaxis] * grad_u_disc.children[0].entries.toarray()}\"\n",
+    "    f\"1/dx *\\n{macro_mesh.d_nodes[:, np.newaxis] * grad_u_disc.children[0].entries.toarray()}\"\n",
     ")"
    ]
   },
@@ -610,7 +610,7 @@
     "micro_mesh = mesh[\"negative particle\"]\n",
     "print(\"\\n gradient matrix is:\\n\")\n",
     "print(\n",
-    "    f\"1/dr *\\n{micro_mesh.d_nodes[:,np.newaxis] * grad_v_disc.children[0].entries.toarray()}\"\n",
+    "    f\"1/dr *\\n{micro_mesh.d_nodes[:, np.newaxis] * grad_v_disc.children[0].entries.toarray()}\"\n",
     ")\n",
     "\n",
     "r_edge = micro_mesh.edges[1:-1]  # note that grad_u_disc is evaluated on the node edges\n",
@@ -677,8 +677,8 @@
     "(grad_u_disc.render())\n",
     "u_eval = grad_u_disc.evaluate(y=y)\n",
     "dx = np.diff(macro_mesh.nodes)[-1]\n",
-    "print(f\"The value of u on the left-hand boundary is {y[0] - dx*u_eval[0]/2}\")\n",
-    "print(f\"The value of u on the right-hand boundary is {y[1] + dx*u_eval[-1]/2}\")"
+    "print(f\"The value of u on the left-hand boundary is {y[0] - dx * u_eval[0] / 2}\")\n",
+    "print(f\"The value of u on the right-hand boundary is {y[1] + dx * u_eval[-1] / 2}\")"
    ]
   },
   {
@@ -765,7 +765,7 @@
     "(grad_u_disc.render())\n",
     "grad_u_eval = grad_u_disc.evaluate(y=y)\n",
     "u_eval = grad_u_disc.children[1].evaluate(y=y)\n",
-    "print(f\"The value of u on the left-hand boundary is {(u_eval[0] + u_eval[1])/2}\")\n",
+    "print(f\"The value of u on the left-hand boundary is {(u_eval[0] + u_eval[1]) / 2}\")\n",
     "print(f\"The gradient on the right-hand boundary is {grad_u_eval[-1]}\")"
    ]
   },
@@ -914,7 +914,7 @@
    "source": [
     "int_u = pybamm.Integral(u, x_var)\n",
     "int_u_disc = disc.process_symbol(int_u)\n",
-    "print(f\"int(u) = {int_u_disc.evaluate(y=y)} is approximately equal to 1/12, {1/12}\")\n",
+    "print(f\"int(u) = {int_u_disc.evaluate(y=y)} is approximately equal to 1/12, {1 / 12}\")\n",
     "\n",
     "# We divide v by r to evaluate the integral more easily\n",
     "int_v_over_r2 = pybamm.Integral(v / r_var**2, r_var)\n",

examples/scripts/thermal_lithium_ion.py

@@ -25,10 +25,8 @@
 full_params = parameter_values.copy()
 full_params.update(
     {
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 5,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 5,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 5,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 5,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 0,
         "Edge heat transfer coefficient [W.m-2.K-1]": 0,

src/pybamm/expression_tree/operations/evaluate_python.py

@@ -266,8 +266,7 @@ def find_symbols(
                 and scipy.sparse.issparse(dummy_eval_right)
             ):
                 raise NotImplementedError(
-                    "sparse mat-mat multiplication not supported "
-                    "for output_jax == True"
+                    "sparse mat-mat multiplication not supported for output_jax == True"
                 )
             else:
                 symbol_str = (
@@ -451,7 +450,7 @@ def __init__(self, symbol: pybamm.Symbol):
 
         # add function def to first line
         python_str = (
-            "def evaluate(constants, t=None, y=None, " "inputs=None):\n" + python_str
+            "def evaluate(constants, t=None, y=None, inputs=None):\n" + python_str
         )
 
         # calculate the final variable that will output the result of calling `evaluate`

src/pybamm/expression_tree/symbol.py

@@ -583,7 +583,7 @@ def __str__(self):
 
     def __repr__(self):
         """returns the string `__class__(id, name, children, domain)`"""
-        return f"{self.__class__.__name__!s}({hex(self.id)}, {self._name!s}, children={[str(child) for child in self.children]!s}, domains={({k: v for k, v in self.domains.items() if v != []})!s})"
+        return f"{self.__class__.__name__!s}({hex(self.id)}, {self._name!s}, children={[str(child) for child in self.children]!s}, domains={ ({k: v for k, v in self.domains.items() if v != []})!s})"
 
     def __add__(self, other: ChildSymbol) -> pybamm.Addition:
         """return an :class:`Addition` object."""

src/pybamm/input/parameters/lead_acid/Sulzer2019.py

@@ -289,8 +289,7 @@ def get_parameter_values():
         "Positive electrode oxygen exchange-current density [A.m-2]"
         "": oxygen_exchange_current_density_Sulzer2019,
         "Positive electrode Butler-Volmer transfer coefficient": 0.5,
-        "Positive electrode reference exchange-current density (hydrogen) [A.m-2]"
-        "": 0.0,
+        "Positive electrode reference exchange-current density (hydrogen) [A.m-2]": 0.0,
         "Positive electrode double-layer capacity [F.m-2]": 0.2,
         "Positive electrode density [kg.m-3]": 9375.0,
         "Positive electrode specific heat capacity [J.kg-1.K-1]": 256.0,
@@ -328,10 +327,8 @@ def get_parameter_values():
         "Reference temperature [K]": 294.85,
         "Maximum temperature [K]": 333.15,
         "Ambient temperature [K]": 294.85,
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Total heat transfer coefficient [W.m-2.K-1]": 10.0,

src/pybamm/input/parameters/lithium_ion/Marquis2019.py

@@ -450,10 +450,8 @@ def get_parameter_values():
         # experiment
         "Reference temperature [K]": 298.15,
         "Ambient temperature [K]": 298.15,
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Edge heat transfer coefficient [W.m-2.K-1]": 0.3,

src/pybamm/input/parameters/lithium_ion/Mohtat2020.py

@@ -423,8 +423,7 @@ def get_parameter_values():
         "Positive electrode density [kg.m-3]": 3100.0,
         "Positive electrode specific heat capacity [J.kg-1.K-1]": 1100.0,
         "Positive electrode thermal conductivity [W.m-1.K-1]": 2.1,
-        "Positive electrode OCP entropic change [V.K-1]"
-        "": NMC_entropic_change_PeymanMPM,
+        "Positive electrode OCP entropic change [V.K-1]": NMC_entropic_change_PeymanMPM,
         # separator
         "Separator porosity": 0.4,
         "Separator Bruggeman coefficient (electrolyte)": 1.5,
@@ -441,10 +440,8 @@ def get_parameter_values():
         "Electrolyte conductivity [S.m-1]": electrolyte_conductivity_PeymanMPM,
         # experiment
         "Reference temperature [K]": 298.15,
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Edge heat transfer coefficient [W.m-2.K-1]": 5.0,

src/pybamm/input/parameters/lithium_ion/NCA_Kim2011.py

@@ -404,10 +404,8 @@ def get_parameter_values():
         "Electrolyte conductivity [S.m-1]": electrolyte_conductivity_Kim2011,
         # experiment
         "Reference temperature [K]": 298.15,
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 25.0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 25.0,
         "Edge heat transfer coefficient [W.m-2.K-1]": 0.3,

src/pybamm/input/parameters/lithium_ion/OKane2022.py

@@ -636,8 +636,7 @@ def get_parameter_values():
         "Initial concentration in electrolyte [mol.m-3]": 1000.0,
         "Cation transference number": 0.2594,
         "Thermodynamic factor": 1.0,
-        "Electrolyte diffusivity [m2.s-1]"
-        "": electrolyte_diffusivity_Nyman2008_arrhenius,
+        "Electrolyte diffusivity [m2.s-1]": electrolyte_diffusivity_Nyman2008_arrhenius,
         "Electrolyte conductivity [S.m-1]"
         "": electrolyte_conductivity_Nyman2008_arrhenius,
         # experiment

src/pybamm/input/parameters/lithium_ion/OKane2022_graphite_SiOx_halfcell.py

@@ -492,8 +492,7 @@ def get_parameter_values():
         "Initial concentration in electrolyte [mol.m-3]": 1000.0,
         "Cation transference number": 0.2594,
         "Thermodynamic factor": 1.0,
-        "Electrolyte diffusivity [m2.s-1]"
-        "": electrolyte_diffusivity_Nyman2008_arrhenius,
+        "Electrolyte diffusivity [m2.s-1]": electrolyte_diffusivity_Nyman2008_arrhenius,
         "Electrolyte conductivity [S.m-1]"
         "": electrolyte_conductivity_Nyman2008_arrhenius,
         # experiment

src/pybamm/input/parameters/lithium_ion/ORegan2022.py

@@ -953,8 +953,7 @@ def get_parameter_values():
         # negative electrode
         "Negative electrode conductivity [S.m-1]": 215.0,
         "Maximum concentration in negative electrode [mol.m-3]": 29583.0,
-        "Negative particle diffusivity [m2.s-1]"
-        "": graphite_LGM50_diffusivity_ORegan2022,
+        "Negative particle diffusivity [m2.s-1]": graphite_LGM50_diffusivity_ORegan2022,
         "Negative electrode OCP [V]": graphite_LGM50_ocp_Chen2020,
         "Negative electrode porosity": 0.25,
         "Negative electrode active material volume fraction": 0.75,

src/pybamm/input/parameters/lithium_ion/Ramadass2004.py

@@ -459,10 +459,8 @@ def get_parameter_values():
         # experiment
         "Reference temperature [K]": 298.15,
         "Ambient temperature [K]": 298.15,
-        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
-        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]"
-        "": 0.0,
+        "Negative current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
+        "Positive current collector surface heat transfer coefficient [W.m-2.K-1]": 0.0,
         "Negative tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Positive tab heat transfer coefficient [W.m-2.K-1]": 10.0,
         "Edge heat transfer coefficient [W.m-2.K-1]": 0.3,

src/pybamm/models/full_battery_models/lithium_ion/basic_dfn_composite.py

@@ -356,8 +356,7 @@ def __init__(self, name="Composite graphite/silicon Doyle-Fuller-Newman model"):
             "[mol.m-3]": c_s_rav_n_p1,
             "R-averaged negative secondary particle concentration "
             "[mol.m-3]": c_s_rav_n_p2,
-            "Average negative primary particle concentration "
-            "[mol.m-3]": c_s_xrav_n_p1,
+            "Average negative primary particle concentration [mol.m-3]": c_s_xrav_n_p1,
             "Average negative secondary particle concentration "
             "[mol.m-3]": c_s_xrav_n_p2,
             "Positive particle concentration [mol.m-3]": c_s_p,

src/pybamm/models/full_battery_models/lithium_ion/electrode_soh_half_cell.py

@@ -131,8 +131,7 @@ def get_initial_stoichiometry_half_cell(
 
     else:
         raise ValueError(
-            "Initial value must be a float between 0 and 1, "
-            "or a string ending in 'V'"
+            "Initial value must be a float between 0 and 1, or a string ending in 'V'"
         )
 
     x = x_0 + initial_soc * (x_100 - x_0)

src/pybamm/models/submodels/interface/base_interface.py

@@ -239,8 +239,7 @@ def _get_standard_interfacial_current_variables(self, j):
             j = pybamm.PrimaryBroadcast(j, f"{domain} electrode")
 
         variables = {
-            f"{Domain} electrode {reaction_name}"
-            "interfacial current density [A.m-2]": j,
+            f"{Domain} electrode {reaction_name}interfacial current density [A.m-2]": j,
             f"X-averaged {domain} electrode {reaction_name}"
             "interfacial current density [A.m-2]": j_av,
         }
@@ -296,8 +295,7 @@ def _get_standard_exchange_current_variables(self, j0):
             j0 = pybamm.PrimaryBroadcast(j0, f"{domain} electrode")
 
         variables = {
-            f"{Domain} electrode {reaction_name}"
-            "exchange current density [A.m-2]": j0,
+            f"{Domain} electrode {reaction_name}exchange current density [A.m-2]": j0,
             f"X-averaged {domain} electrode {reaction_name}"
             "exchange current density [A.m-2]": j0_av,
         }