Enable Flake8-bugbear (pybamm-team#3859)

* Enable flake8-bugbear

Fix unused-loop-control-variable (B007)

Fix function-uses-loop-variable (B023)

Fix raise-without-from-inside-except (B904)

Fix mutable-argument-default (B006)

Fix no-explicit-stacklevel (B028)

Fix get-attr-with-constant (B009)

Fix loop-variable-overrides-iterator (B020)

Fix unary-prefix-increment-decrement (B002)

Fix function-call-in-default-argument (B008)

Fix cached-instance-method (B019)

* Show exception chain (B904)

* Disable single lint check (B019)

* delay xarray.DataArray initialization

* revert example

* Bump the actions group with 1 update (pybamm-team#3861)

Bumps the actions group with 1 update: [awalsh128/cache-apt-pkgs-action](https://github.com/awalsh128/cache-apt-pkgs-action).


Updates `awalsh128/cache-apt-pkgs-action` from 1.4.1 to 1.4.2
- [Release notes](https://github.com/awalsh128/cache-apt-pkgs-action/releases)
- [Commits](awalsh128/cache-apt-pkgs-action@v1.4.1...v1.4.2)

---
updated-dependencies:
- dependency-name: awalsh128/cache-apt-pkgs-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Make `typing-extensions` and `sympy` required dependencies to fix PyBaMM import (pybamm-team#3848)

* import `typing_extensions` as optional_dependency

* Make `typing-extensions` a required dependency

* Try forward referencing for `sympy` in `IndependentVariable`

* Make `sympy` a required dependency

* Update docs for SymPy

* Import `sympy` without `have_optional_dependency`

* Import `sympy` without `TYPE_CHECKING`

* Changelog

* Update CHANGELOG.md

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* Rearrange position in changelog

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>

* Rename have_optional_dependency (pybamm-team#3866)

* Rename have_optional_dependency

* Change log

* Fix import

* style: pre-commit fixes

* Update pybamm/util.py

---------

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

* update changelog for pybamm-team#3862 (pybamm-team#3869)

* update changelog for pybamm-team#3862

* reword

* fix deprecation warning and check for electrode/particle diffusivity

* update test

* Edit naming for unused loop control variable (B007)

* pybamm-team#3883 updates to install from source (pybamm-team#3884)

* Disable benchmarks on PRs (pybamm-team#3876)

* Remove`[ latexify` extra (pybamm-team#3888)

* Improve Getting Started notebooks (pybamm-team#3750)

* improve tutorials 1 to 3

* use new syntax for plot_voltage_components

* style: pre-commit fixes

* simplify notebook by removing drive cycle

* add additional comment on dynamic_plot

* improve tutorial 5

* remove the use of solution in notebook 5, this is introduced in notebook 6

* fix minor typo

* minor text updates

* style: pre-commit fixes

* minor text updates plus extra links

* minor text updates!

* minor text updates

* remove tutorial 10 as very similar to tutorial 3 in creating models

* move and rename tutorial 11 to creating models section

* style: pre-commit fixes

* fix minor typo in current_with_time

* implement Rob & Eric's comments

* update docs links

* Valentin's comments

* style: pre-commit fixes

---------

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

* chore: update pre-commit hooks (pybamm-team#3890)

* chore: update pre-commit hooks

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.2](astral-sh/ruff-pre-commit@v0.2.2...v0.3.2)

* style: pre-commit fixes

* Update .git-blame-ignore-revs

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* style: pre-commit fixes

* Resolve conflicts (B904, B028, B020)

* Added a schedule on `needs-reply remove` workflow  (pybamm-team#3891)

* added schedule to need-reply workflow

* added schedule to need-reply workflow

---------

Co-authored-by: Arjun Verma <arjunverma.oc@gmail.com>

* style: pre-commit fixes

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Arjun Verma <arjunverma.oc@gmail.com>
Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Eric G. Kratz <kratman@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Martin Robinson <martinjrobins@gmail.com>
Co-authored-by: Ferran Brosa Planella <Ferran.Brosa-Planella@warwick.ac.uk>
Co-authored-by: Santhosh <52504160+santacodes@users.noreply.github.com>

benchmarks/work_precision_sets/time_vs_abstols.py

@@ -72,7 +72,7 @@
             solver.solve(model, t_eval=t_eval)
             time = 0
             runs = 20
-            for k in range(0, runs):
+            for _ in range(0, runs):
                 solution = solver.solve(model, t_eval=t_eval)
                 time += solution.solve_time.value
             time = time / runs

benchmarks/work_precision_sets/time_vs_dt_max.py

@@ -76,7 +76,7 @@
             solver.solve(model, t_eval=t_eval)
             time = 0
             runs = 20
-            for k in range(0, runs):
+            for _ in range(0, runs):
                 solution = solver.solve(model, t_eval=t_eval)
                 time += solution.solve_time.value
             time = time / runs

benchmarks/work_precision_sets/time_vs_mesh_size.py

@@ -54,7 +54,7 @@
 
             time = 0
             runs = 20
-            for k in range(0, runs):
+            for _ in range(0, runs):
                 solution = sim.solve([0, 3500])
                 time += solution.solve_time.value
             time = time / runs

benchmarks/work_precision_sets/time_vs_no_of_states.py

@@ -54,7 +54,7 @@
 
             time = 0
             runs = 20
-            for k in range(0, runs):
+            for _ in range(0, runs):
                 solution = sim.solve([0, 3500])
                 time += solution.solve_time.value
             time = time / runs

benchmarks/work_precision_sets/time_vs_reltols.py

@@ -78,7 +78,7 @@
             solver.solve(model, t_eval=t_eval)
             time = 0
             runs = 20
-            for k in range(0, runs):
+            for _ in range(0, runs):
                 solution = solver.solve(model, t_eval=t_eval)
                 time += solution.solve_time.value
             time = time / runs

docs/source/examples/notebooks/batch_study.ipynb

@@ -199,7 +199,7 @@
     "\n",
     "# changing the value of \"Current function [A]\" in all the parameter values present in the\n",
     "# parameter_values dictionary\n",
-    "for k, v, current_value in zip(\n",
+    "for _, v, current_value in zip(\n",
     "    parameter_values.keys(), parameter_values.values(), current_values\n",
     "):\n",
     "    v[\"Current function [A]\"] = current_value\n",
@@ -505,7 +505,7 @@
     "inner_sei_oc_v_values = [2.0e-4, 2.7e-4, 3.4e-4]\n",
     "\n",
     "# updating the value of \"Inner SEI open-circuit potential [V]\" in all the dictionary items\n",
-    "for k, v, inner_sei_oc_v in zip(\n",
+    "for _, v, inner_sei_oc_v in zip(\n",
     "    parameter_values.keys(), parameter_values.values(), inner_sei_oc_v_values\n",
     "):\n",
     "    v.update(\n",

pybamm/citations.py

@@ -92,7 +92,7 @@ def _add_citation(self, key, entry):
         # Warn if overwriting a previous citation
         new_citation = entry.to_string("bibtex")
         if key in self._all_citations and new_citation != self._all_citations[key]:
-            warnings.warn(f"Replacing citation for {key}")
+            warnings.warn(f"Replacing citation for {key}", stacklevel=2)
 
         # Add to database
         self._all_citations[key] = new_citation
@@ -165,9 +165,9 @@ def _parse_citation(self, key):
                 # Add to _papers_to_cite set
                 self._papers_to_cite.add(key)
                 return
-        except PybtexError:
+        except PybtexError as error:
             # Unable to parse / unknown key
-            raise KeyError(f"Not a bibtex citation or known citation: {key}")
+            raise KeyError(f"Not a bibtex citation or known citation: {key}") from error
 
     def _tag_citations(self):
         """Prints the citation tags for the citations that have been registered
@@ -226,6 +226,7 @@ def print(self, filename=None, output_format="text", verbose=False):
             warnings.warn(
                 message=f'\nCitation with key "{key}" is invalid. Please try again\n',
                 category=UserWarning,
+                stacklevel=2,
             )
             # delete the invalid citation from the set
             self._unknown_citations.remove(key)

pybamm/discretisations/discretisation.py

@@ -280,7 +280,7 @@ def set_variable_slices(self, variables):
                 sec_points = spatial_method._get_auxiliary_domain_repeats(
                     variable.domains
                 )
-                for i in range(sec_points):
+                for _ in range(sec_points):
                     for child, mesh in meshes.items():
                         for domain_mesh in mesh:
                             end += domain_mesh.npts_for_broadcast_to_nodes
@@ -886,14 +886,14 @@ def _process_symbol(self, symbol):
             # model.check_well_posedness, but won't be if debug_mode is False
             try:
                 y_slices = self.y_slices[symbol]
-            except KeyError:
+            except KeyError as error:
                 raise pybamm.ModelError(
                     f"""
                     No key set for variable '{symbol.name}'. Make sure it is included in either
                     model.rhs or model.algebraic in an unmodified form
                     (e.g. not Broadcasted)
                     """
-                )
+                ) from error
             # Add symbol's reference and multiply by the symbol's scale
             # so that the state vector is of order 1
             return symbol.reference + symbol.scale * pybamm.StateVector(

pybamm/experiment/step/_steps_util.py

@@ -287,8 +287,8 @@ def _convert_electric(value_string):
     }
     try:
         typ = units_to_type[unit]
-    except KeyError:
+    except KeyError as error:
         raise ValueError(
             f"units must be 'A', 'V', 'W', 'Ohm', or 'C'. For example: {_examples}"
-        )
+        ) from error
     return typ, value

pybamm/expression_tree/concatenations.py

@@ -337,7 +337,7 @@ def create_slices(self, node: pybamm.Symbol) -> defaultdict:
                 """Concatenation and children must have the same number of
                 points in secondary dimensions"""
             )
-        for i in range(second_pts):
+        for _ in range(second_pts):
             for dom in node.domain:
                 end += self.full_mesh[dom].npts
                 slices[dom].append(slice(start, end))

pybamm/expression_tree/input_parameter.py

@@ -102,8 +102,8 @@ def _base_evaluate(
         try:
             input_eval = inputs[self.name]
         # raise more informative error if can't find name in dict
-        except KeyError:
-            raise KeyError(f"Input parameter '{self.name}' not found")
+        except KeyError as error:
+            raise KeyError(f"Input parameter '{self.name}' not found") from error
 
         if isinstance(input_eval, numbers.Number):
             input_size = 1

pybamm/expression_tree/operations/jacobian.py

@@ -90,10 +90,10 @@ def _jac(self, symbol: pybamm.Symbol, variable: pybamm.Symbol):
         else:
             try:
                 jac = symbol._jac(variable)
-            except NotImplementedError:
+            except NotImplementedError as error:
                 raise NotImplementedError(
                     f"Cannot calculate Jacobian of symbol of type '{type(symbol)}'"
-                )
+                ) from error
 
         # Jacobian by default removes the domain(s)
         if self._clear_domain:

pybamm/expression_tree/operations/latexify.py

@@ -76,7 +76,7 @@ def _get_geometry_displays(self, var):
             rng_min = get_rng_min_max_name(rng, "min")
 
         # Take range maximum from the last domain
-        for var_name, rng in self.model.default_geometry[var.domain[-1]].items():
+        for _, rng in self.model.default_geometry[var.domain[-1]].items():
             rng_max = get_rng_min_max_name(rng, "max")
 
         geo_latex = f"\quad {rng_min} < {name} < {rng_max}"
@@ -303,7 +303,8 @@ def latexify(self, output_variables=None):
                 # When equations are too huge, set output resolution to default
                 except RuntimeError:  # pragma: no cover
                     warnings.warn(
-                        "RuntimeError - Setting the output resolution to default"
+                        "RuntimeError - Setting the output resolution to default",
+                        stacklevel=2,
                     )
                     return sympy.preview(
                         eqn_new_line,

pybamm/expression_tree/symbol.py

@@ -7,7 +7,7 @@
 import numpy as np
 import sympy
 from scipy.sparse import csr_matrix, issparse
-from functools import lru_cache, cached_property
+from functools import cached_property
 from typing import TYPE_CHECKING, Sequence, cast
 
 import pybamm
@@ -876,7 +876,7 @@ def evaluate_ignoring_errors(self, t: float | None = 0):
                 return None
             raise pybamm.ShapeError(
                 f"Cannot find shape (original error: {error})"
-            )  # pragma: no cover
+            ) from error  # pragma: no cover
         return result
 
     def evaluates_to_number(self):
@@ -895,7 +895,6 @@ def evaluates_to_number(self):
     def evaluates_to_constant_number(self):
         return self.evaluates_to_number() and self.is_constant()
 
-    @lru_cache
     def evaluates_on_edges(self, dimension: str) -> bool:
         """
         Returns True if a symbol evaluates on an edge, i.e. symbol contains a gradient
@@ -914,9 +913,12 @@ def evaluates_on_edges(self, dimension: str) -> bool:
             Whether the symbol evaluates on edges (in the finite volume discretisation
             sense)
         """
-        eval_on_edges = self._evaluates_on_edges(dimension)
-        self._saved_evaluates_on_edges[dimension] = eval_on_edges
-        return eval_on_edges
+        if dimension not in self._saved_evaluates_on_edges:
+            self._saved_evaluates_on_edges[dimension] = self._evaluates_on_edges(
+                dimension
+            )
+
+        return self._saved_evaluates_on_edges[dimension]
 
     def _evaluates_on_edges(self, dimension):
         # Default behaviour: return False
@@ -1039,7 +1041,7 @@ def test_shape(self):
         try:
             self.shape_for_testing
         except ValueError as e:
-            raise pybamm.ShapeError(f"Cannot find shape (original error: {e})")
+            raise pybamm.ShapeError(f"Cannot find shape (original error: {e})") from e
 
     @property
     def print_name(self):

pybamm/install_odes.py

@@ -47,8 +47,8 @@ def install_sundials(download_dir, install_dir):
 
     try:
         subprocess.run(["cmake", "--version"])
-    except OSError:
-        raise RuntimeError("CMake must be installed to build SUNDIALS.")
+    except OSError as error:
+        raise RuntimeError("CMake must be installed to build SUNDIALS.") from error
 
     url = f"https://github.com/LLNL/sundials/releases/download/v{SUNDIALS_VERSION}/sundials-{SUNDIALS_VERSION}.tar.gz"
     logger.info("Downloading sundials")

pybamm/meshes/meshes.py

@@ -85,8 +85,8 @@ def __init__(self, geometry, submesh_types, var_pts):
             for spatial_variable, spatial_limits in geometry[domain].items():
                 # process tab information if using 1 or 2D current collectors
                 if spatial_variable == "tabs":
-                    for tab, position_size in spatial_limits.items():
-                        for position_size, sym in position_size.items():
+                    for tab, position_info in spatial_limits.items():
+                        for position_size, sym in position_info.items():
                             if isinstance(sym, pybamm.Symbol):
                                 sym_eval = sym.evaluate()
                                 geometry[domain]["tabs"][tab][position_size] = sym_eval
@@ -102,7 +102,7 @@ def __init__(self, geometry, submesh_types, var_pts):
                                         "geometry. Make sure that something like "
                                         "`param.process_geometry(geometry)` has been "
                                         "run."
-                                    )
+                                    ) from error
                                 else:
                                     raise error
                         elif isinstance(sym, numbers.Number):

pybamm/models/base_model.py

@@ -590,7 +590,7 @@ def build_coupled_variables(self):
                                 f"Missing variable for submodel '{submodel_name}': {key}.\n"
                                 + "Check the selected "
                                 "submodels provide all of the required variables."
-                            )
+                            ) from key
                         else:
                             # try setting coupled variables on next loop through
                             pybamm.logger.debug(
@@ -677,7 +677,7 @@ def set_initial_conditions_from(self, solution, inplace=True, return_type="model
                         "model.initial_conditions must appear in the solution with "
                         "the same key as the variable name. In the solution provided, "
                         f"'{e.args[0]}' was not found."
-                    )
+                    ) from e
                 if isinstance(solution, pybamm.Solution):
                     final_state = final_state.data
                 if final_state.ndim == 0:
@@ -701,7 +701,7 @@ def set_initial_conditions_from(self, solution, inplace=True, return_type="model
                             "model.initial_conditions must appear in the solution with "
                             "the same key as the variable name. In the solution "
                             f"provided, {e.args[0]}"
-                        )
+                        ) from e
                     if isinstance(solution, pybamm.Solution):
                         final_state = final_state.data
                     if final_state.ndim == 2:
@@ -873,8 +873,8 @@ def check_well_determined(self, post_discretisation):
                 ]
             )
             all_vars_in_eqns.update(vars_in_eqns)
-        for var, side_eqn in self.boundary_conditions.items():
-            for side, (eqn, typ) in side_eqn.items():
+        for _, side_eqn in self.boundary_conditions.items():
+            for _, (eqn, _) in side_eqn.items():
                 vars_in_eqns = unpacker.unpack_symbol(eqn)
                 all_vars_in_eqns.update(vars_in_eqns)
 
@@ -1001,7 +1001,7 @@ def check_discretised_or_discretise_inplace_if_0D(self):
                 raise pybamm.DiscretisationError(
                     "Cannot automatically discretise model, model should be "
                     f"discretised before exporting casadi functions ({e})"
-                )
+                ) from e
 
     def export_casadi_objects(self, variable_names, input_parameter_order=None):
         """
@@ -1242,6 +1242,7 @@ def save_model(self, filename=None, mesh=None, variables=None):
                 Plotting may not be available.
                 """,
                 pybamm.ModelWarning,
+                stacklevel=2,
             )
 
         Serialise().save_model(self, filename=filename, mesh=mesh, variables=variables)

pybamm/models/full_battery_models/lithium_ion/electrode_soh_half_cell.py

@@ -129,17 +129,21 @@ def get_initial_stoichiometry_half_cell(
     return x
 
 
-def get_min_max_stoichiometries(
-    parameter_values, options={"working electrode": "positive"}
-):
+def get_min_max_stoichiometries(parameter_values, options=None):
     """
     Get the minimum and maximum stoichiometries from the parameter values
 
     Parameters
     ----------
     parameter_values : pybamm.ParameterValues
         The parameter values to use in the calculation
+    options : dict, optional
+        A dictionary of options to be passed to the parameters, see
+        :class:`pybamm.BatteryModelOptions`.
+        If None, the default is used: {"working electrode": "positive"}
     """
+    if options is None:
+        options = {"working electrode": "positive"}
     esoh_model = pybamm.lithium_ion.ElectrodeSOHHalfCell("ElectrodeSOH")
     param = pybamm.LithiumIonParameters(options)
     esoh_sim = pybamm.Simulation(esoh_model, parameter_values=parameter_values)

pybamm/models/submodels/thermal/base_thermal.py

@@ -117,7 +117,7 @@ def _get_standard_coupled_variables(self, variables):
         # Total Ohmic heating
         Q_ohm = Q_ohm_s + Q_ohm_e
 
-        num_phases = int(getattr(self.options, "positive")["particle phases"])
+        num_phases = int(self.options.positive["particle phases"])
         phase_names = [""]
         if num_phases > 1:
             phase_names = ["primary ", "secondary "]
@@ -135,7 +135,7 @@ def _get_standard_coupled_variables(self, variables):
             dUdT_p = variables[f"Positive electrode {phase}entropic change [V.K-1]"]
             Q_rev_p += a_j_p * T_p * dUdT_p
 
-        num_phases = int(getattr(self.options, "negative")["particle phases"])
+        num_phases = int(self.options.negative["particle phases"])
         phase_names = [""]
         if num_phases > 1:
             phase_names = ["primary", "secondary"]

pybamm/parameters/base_parameters.py

@@ -19,7 +19,9 @@ def __getattribute__(self, name):
             return super().__getattribute__(name)
         except AttributeError as e:
             if name == "cap_init":
-                warnings.warn("Parameter 'cap_init' has been renamed to 'Q_init'")
+                warnings.warn(
+                    "Parameter 'cap_init' has been renamed to 'Q_init'", stacklevel=2
+                )
                 return self.Q_init
             for domain in ["n", "s", "p"]:
                 if f"_{domain}_" in name or name.endswith(f"_{domain}"):
@@ -32,14 +34,14 @@ def __getattribute__(self, name):
                             raise AttributeError(
                                 f"param.{name} does not exist. It has been renamed to "
                                 f"param.{domain}.{name_without_domain}"
-                            )
+                            ) from e
                         elif hasattr(self_domain, "prim") and hasattr(
                             self_domain.prim, name_without_domain
                         ):
                             raise AttributeError(
                                 f"param.{name} does not exist. It has been renamed to "
                                 f"param.{domain}.prim.{name_without_domain}"
-                            )
+                            ) from e
                         else:
                             raise e
                     else: