Fixed mypy sp check guidelines

docs/conf.py

@@ -107,7 +107,7 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".ipynb_checkpoints"]
 
 # Suppress warnings generated by Sphinx and/or by Sphinx extensions
-suppress_warnings = []
+suppress_warnings = []  # type: list[str]
 
 # -- Options for HTML output -------------------------------------------------
 
@@ -174,7 +174,7 @@
 html_title = f"{project} v{version} Manual"
 html_last_updated_fmt = "%Y-%m-%d"
 html_css_files = ["pybamm.css"]
-html_context = {"default_mode": "light"}
+html_context = {"default_mode": "light"}  # type: dict[str, str | bool | None | ParameterSets]
 html_use_modindex = True
 html_copy_source = False
 html_domain_indices = False
@@ -195,7 +195,7 @@
 )
 
 # Set canonical URL from the Read the Docs Domain
-html_baseurl = os.getenv("READTHEDOCS_CANONICAL_URL", "")
+html_baseurl = os.getenv("READTHEDOCS_CANONICAL_URL", "")  # type: str
 
 # Tell Jinja2 templates the build is running on Read the Docs
 if os.getenv("READTHEDOCS") == "True":
@@ -231,7 +231,7 @@
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
-}
+}  # type: dict[str, str]
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
@@ -321,7 +321,7 @@
 # made to a notebook, if any.
 # On local builds, the version is not set, so we use "latest".
 
-notebooks_version = version
+notebooks_version = version  # type: str | None
 append_to_url = f"blob/v{notebooks_version}"
 
 if (os.environ.get("READTHEDOCS_VERSION") == "latest") or (

examples/scripts/SPM_compare_particle_grid.py

@@ -48,7 +48,7 @@
     disc.process_model(model)
 
 # solve model
-solutions = [None] * len(models)
+solutions = [None] * len(models)  # type: Any
 t_eval = np.linspace(0, 3600, 100)
 for i, model in enumerate(models):
     solutions[i] = model.default_solver.solve(model, t_eval)

examples/scripts/SPMe_step.py

@@ -43,13 +43,14 @@
     time += dt
 
 # plot
-time_in_seconds = solution["Time [s]"].entries
-step_time_in_seconds = step_solution["Time [s]"].entries
-voltage = solution["Voltage [V]"].entries
-step_voltage = step_solution["Voltage [V]"].entries
-plt.plot(time_in_seconds, voltage, "b-", label="SPMe (continuous solve)")
-plt.plot(step_time_in_seconds, step_voltage, "ro", label="SPMe (stepped solve)")
-plt.xlabel(r"$t$")
-plt.ylabel("Voltage [V]")
-plt.legend()
-plt.show()
+if step_solution is not None:
+    time_in_seconds = solution["Time [s]"].entries
+    step_time_in_seconds = step_solution["Time [s]"].entries
+    voltage = solution["Voltage [V]"].entries
+    step_voltage = step_solution["Voltage [V]"].entries
+    plt.plot(time_in_seconds, voltage, "b-", label="SPMe (continuous solve)")
+    plt.plot(step_time_in_seconds, step_voltage, "ro", label="SPMe (stepped solve)")
+    plt.xlabel(r"$t$")
+    plt.ylabel("Voltage [V]")
+    plt.legend()
+    plt.show()

examples/scripts/heat_equation.py

@@ -106,7 +106,7 @@ def T_exact(x, t):
 # Plot ------------------------------------------------------------------------
 x_nodes = mesh["rod"].nodes  # numerical gridpoints
 xx = np.linspace(0, 2, 101)  # fine mesh to plot exact solution
-plot_times = np.linspace(0, 1, 5)
+plot_times = np.linspace(0, 1, 5)  # type: np.ndarray
 
 plt.figure(figsize=(15, 8))
 cmap = plt.get_cmap("inferno")

examples/scripts/minimal_example_of_lookup_tables.py

@@ -34,12 +34,12 @@ def process_2D(name, data):
 D_s_n_data = process_2D("Negative particle diffusivity [m2.s-1]", df)
 
 
-def D_s_n(sto, T):
+def D_s_n_func(sto, T):
     name, (x, y) = D_s_n_data
     return pybamm.Interpolant(x, y, [T, sto], name)
 
 
-parameter_values["Negative particle diffusivity [m2.s-1]"] = D_s_n
+parameter_values["Negative particle diffusivity [m2.s-1]"] = D_s_n_func
 
 k_n = parameter_values["Negative electrode exchange-current density [A.m-2]"]
 

pyproject.toml

@@ -252,6 +252,10 @@ concurrency = ["multiprocessing"]
 ignore_missing_imports = true
 allow_redefinition = true
 disable_error_code = ["call-overload", "operator"]
+strict = false
+warn_unreachable = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+exclude = 'build/'
 
 [[tool.mypy.overrides]]
 module = [

src/pybamm/experiment/experiment.py

@@ -40,7 +40,9 @@ class Experiment:
 
     def __init__(
         self,
-        operating_conditions: list[str | tuple[str] | BaseStep],
+        operating_conditions: list[
+            str | tuple[str, ...] | tuple[str | BaseStep] | BaseStep
+        ],
         period: str | None = None,
         temperature: float | None = None,
         termination: list[str] | None = None,

src/pybamm/experiment/step/base_step.py

@@ -140,7 +140,7 @@ def __init__(
             self.value = pybamm.Interpolant(
                 t,
                 y,
-                pybamm.t - pybamm.InputParameter("start time"),
+                pybamm.t - pybamm.InputParameter("start time"),  # type: ignore[arg-type]
                 name="Drive Cycle",
             )
             self.period = np.diff(t).min()

src/pybamm/expression_tree/binary_operators.py

@@ -2,7 +2,6 @@
 # Binary operator classes
 #
 from __future__ import annotations
-import numbers
 
 import numpy as np
 import sympy
@@ -33,8 +32,8 @@ def _preprocess_binary(
             raise ValueError("right must be a 1D array")
         right = pybamm.Vector(right)
 
-    # Check both left and right are pybamm Symbols
-    if not (isinstance(left, pybamm.Symbol) and isinstance(right, pybamm.Symbol)):
+    # Check right is pybamm Symbol
+    if not isinstance(right, pybamm.Symbol):
         raise NotImplementedError(
             f"BinaryOperator not implemented for symbols of type {type(left)} and {type(right)}"
         )
@@ -127,7 +126,7 @@ def create_copy(
         children = self._children_for_copying(new_children)
 
         if not perform_simplifications:
-            out = self.__class__(children[0], children[1])
+            out = self.__class__(*children)
         else:
             # creates a new instance using the overloaded binary operator to perform
             # additional simplifications, rather than just calling the constructor
@@ -1538,7 +1537,7 @@ def source(
         corresponding to a source term in the bulk.
     """
     # Broadcast if left is number
-    if isinstance(left, numbers.Number):
+    if isinstance(left, (int, float)):
         left = pybamm.PrimaryBroadcast(left, "current collector")
 
     # force type cast for mypy

src/pybamm/expression_tree/broadcasts.py

@@ -463,7 +463,7 @@ def __init__(
         self,
         child_input: Numeric | pybamm.Symbol,
         broadcast_domain: DomainType = None,
-        auxiliary_domains: AuxiliaryDomainType = None,
+        auxiliary_domains: AuxiliaryDomainType | str = None,
         broadcast_domains: DomainsType = None,
         name: str | None = None,
     ):

src/pybamm/expression_tree/concatenations.py

@@ -473,7 +473,7 @@ def __init__(self, *children, name: Optional[str] = None):
         if name is None:
             # Name is the intersection of the children names (should usually make sense
             # if the children have been named consistently)
-            name = intersect(children[0].name, children[1].name)
+            name = intersect(children[0].name, children[1].name) or ""
             for child in children[2:]:
                 name = intersect(name, child.name)
             if len(name) == 0:

src/pybamm/expression_tree/operations/serialise.py

@@ -20,7 +20,7 @@ def __init__(self):
     class _SymbolEncoder(json.JSONEncoder):
         """Converts PyBaMM symbols into a JSON-serialisable format"""
 
-        def default(self, node: dict):
+        def default(self, node: dict | pybamm.Symbol):
             node_dict = {"py/object": str(type(node))[8:-2], "py/id": id(node)}
             if isinstance(node, pybamm.Symbol):
                 node_dict.update(node.to_json())  # this doesn't include children
@@ -46,7 +46,7 @@ def default(self, node: dict):
     class _MeshEncoder(json.JSONEncoder):
         """Converts PyBaMM meshes into a JSON-serialisable format"""
 
-        def default(self, node: pybamm.Mesh):
+        def default(self, node: pybamm.Mesh | pybamm.SubMesh):
             node_dict = {"py/object": str(type(node))[8:-2], "py/id": id(node)}
             if isinstance(node, pybamm.Mesh):
                 node_dict.update(node.to_json())
@@ -64,9 +64,6 @@ def default(self, node: pybamm.Mesh):
                 node_dict.update(node.to_json())
                 return node_dict
 
-            node_dict["json"] = json.JSONEncoder.default(self, node)  # pragma: no cover
-            return node_dict  # pragma: no cover
-
     class _Empty:
         """A dummy class to aid deserialisation"""
 

src/pybamm/expression_tree/symbol.py

@@ -66,7 +66,9 @@ def create_object_of_size(size: int, typ="vector"):
         return np.nan * np.ones((size, size))
 
 
-def evaluate_for_shape_using_domain(domains: dict[str, list[str] | str], typ="vector"):
+def evaluate_for_shape_using_domain(
+    domains: dict[str, list[str] | str] | list[str], typ="vector"
+):
     """
     Return a vector of the appropriate shape, based on the domains.
     Domain 'sizes' can clash, but are unlikely to, and won't cause failures if they do.
@@ -964,7 +966,9 @@ def to_casadi(
         """
         return pybamm.CasadiConverter(casadi_symbols).convert(self, t, y, y_dot, inputs)
 
-    def _children_for_copying(self, children: list[Symbol] | None = None) -> Symbol:
+    def _children_for_copying(
+        self, children: list[Symbol] | None = None
+    ) -> list[Symbol]:
         """
         Gets existing children for a symbol being copied if they aren't provided.
         """

src/pybamm/expression_tree/unary_operators.py

@@ -8,7 +8,7 @@
 import sympy
 import pybamm
 from pybamm.util import import_optional_dependency
-from pybamm.type_definitions import DomainsType
+from pybamm.type_definitions import DomainsType, Numeric
 
 
 class UnaryOperator(pybamm.Symbol):
@@ -31,7 +31,7 @@ class UnaryOperator(pybamm.Symbol):
     def __init__(
         self,
         name: str,
-        child: pybamm.Symbol,
+        child: pybamm.Symbol | Numeric,
         domains: DomainsType = None,
     ):
         if isinstance(child, (float, int, np.number)):

src/pybamm/expression_tree/variable.py

@@ -61,12 +61,12 @@ def __init__(
         domains: DomainsType = None,
         bounds: tuple[pybamm.Symbol] | None = None,
         print_name: str | None = None,
-        scale: float | pybamm.Symbol | None = 1,
-        reference: float | pybamm.Symbol | None = 0,
+        scale: float | int | pybamm.Symbol | None = 1,
+        reference: float | int | pybamm.Symbol | None = 0,
     ):
-        if isinstance(scale, numbers.Number):
+        if isinstance(scale, (float, int)):
             scale = pybamm.Scalar(scale)
-        if isinstance(reference, numbers.Number):
+        if isinstance(reference, (float, int)):
             reference = pybamm.Scalar(reference)
         self._scale = scale
         self._reference = reference
@@ -88,7 +88,7 @@ def bounds(self):
         return self._bounds
 
     @bounds.setter
-    def bounds(self, values: tuple[Numeric, Numeric]):
+    def bounds(self, values: tuple[Numeric, Numeric] | None):
         if values is None:
             values = (-np.inf, np.inf)
         else:

src/pybamm/models/base_model.py

@@ -77,6 +77,8 @@ def __init__(self, name="Unnamed model"):
         self.use_jacobian = True
         self.convert_to_format = "casadi"
 
+        self.calculate_sensitivities = []
+
         # Model is not initially discretised
         self.is_discretised = False
         self.y_slices = None

src/pybamm/plotting/quick_plot.py

@@ -126,7 +126,7 @@ def __init__(
         # Set colors, linestyles, figsize, axis limits
         # call LoopList to make sure list index never runs out
         if colors is None:
-            self.colors = LoopList(colors or ["r", "b", "k", "g", "m", "c"])
+            self.colors = LoopList(["r", "b", "k", "g", "m", "c"])
         else:
             self.colors = LoopList(colors)
         self.linestyles = LoopList(linestyles or ["-", ":", "--", "-."])

src/pybamm/solvers/base_solver.py

@@ -94,8 +94,8 @@ def supports_parallel_solve(self):
     def requires_explicit_sensitivities(self):
         return True
 
-    @root_method.setter
-    def root_method(self, method):
+    @root_method.setter  # type: ignore[attr-defined, no-redef]
+    def root_method(self, method) -> None:
         if method == "casadi":
             method = pybamm.CasadiAlgebraicSolver(self.root_tol)
         elif isinstance(method, str):
@@ -1122,7 +1122,7 @@ def _set_sens_initial_conditions_from(
         """
 
         ninputs = len(model.calculate_sensitivities)
-        initial_conditions = tuple([] for _ in range(ninputs))
+        initial_conditions = tuple([] for _ in range(ninputs))  # type: tuple
         solution = solution.last_state
         for var in model.initial_conditions:
             final_state = solution[var.name]
@@ -1143,10 +1143,10 @@ def _set_sens_initial_conditions_from(
         slices = [y_slices[symbol][0] for symbol in model.initial_conditions.keys()]
 
         # sort equations according to slices
-        concatenated_initial_conditions = [
+        concatenated_initial_conditions = tuple(
             casadi.vertcat(*[eq for _, eq in sorted(zip(slices, init))])
             for init in initial_conditions
-        ]
+        )
         return concatenated_initial_conditions
 
     def process_t_interp(self, t_interp):

src/pybamm/solvers/solution.py

@@ -160,7 +160,7 @@ def __init__(
     def has_sensitivities(self) -> bool:
         if isinstance(self._all_sensitivities, bool):
             return self._all_sensitivities
-        elif isinstance(self._all_sensitivities, dict):
+        else:
             return len(self._all_sensitivities) > 0
 
     def extract_explicit_sensitivities(self):