Adds typing to expression tree

mypy.ini

@@ -0,0 +1,10 @@
+[mypy]
+ignore_missing_imports = True
+allow_redefinition = True
+disable_error_code = call-overload, operator
+
+[mypy-pybamm.models.base_model.*]
+disable_error_code = attr-defined
+
+[mypy-pybamm.models.full_battery_models.base_battery_model.*]
+disable_error_code = attr-defined

pybamm/citations.py

@@ -60,6 +60,7 @@ def _reset(self):
         self.register("Sulzer2021")
         self.register("Harris2020")
 
+    @staticmethod
     def _caller_name():
         """
         Returns the qualified name of classes that call :meth:`register` internally.

pybamm/experiment/experiment.py

@@ -73,7 +73,7 @@ def __init__(
         for cycle in operating_conditions:
             # Check types and convert to list
             if not isinstance(cycle, tuple):
-                cycle = (cycle,)
+                cycle = (cycle,)  # type: ignore[assignment]
             operating_conditions_cycles.append(cycle)
 
         self.operating_conditions_cycles = operating_conditions_cycles

pybamm/expression_tree/array.py

@@ -1,12 +1,17 @@
 #
 # NumpyArray class
 #
+from __future__ import annotations
 import numpy as np
 from scipy.sparse import csr_matrix, issparse
+from typing import TYPE_CHECKING
 
 import pybamm
 from pybamm.util import have_optional_dependency
 
+if TYPE_CHECKING:  # pragma: no cover
+    import sympy
+
 
 class Array(pybamm.Symbol):
     """
@@ -36,13 +41,13 @@ class Array(pybamm.Symbol):
 
     def __init__(
         self,
-        entries,
-        name=None,
-        domain=None,
-        auxiliary_domains=None,
-        domains=None,
-        entries_string=None,
-    ):
+        entries: np.ndarray | list[float] | csr_matrix,
+        name: str | None = None,
+        domain: list[str] | str | None = None,
+        auxiliary_domains: dict[str, str] | None = None,
+        domains: dict[str, list[str] | str] | None = None,
+        entries_string: str | None = None,
+    ) -> None:
         # if
         if isinstance(entries, list):
             entries = np.array(entries)
@@ -59,8 +64,6 @@ def __init__(
 
     @classmethod
     def _from_json(cls, snippet: dict):
-        instance = cls.__new__(cls)
-
         if isinstance(snippet["entries"], dict):
             matrix = csr_matrix(
                 (
@@ -73,14 +76,12 @@ def _from_json(cls, snippet: dict):
         else:
             matrix = snippet["entries"]
 
-        instance.__init__(
+        return cls(
             matrix,
             name=snippet["name"],
             domains=snippet["domains"],
         )
 
-        return instance
-
     @property
     def entries(self):
         return self._entries
@@ -100,7 +101,7 @@ def entries_string(self):
         return self._entries_string
 
     @entries_string.setter
-    def entries_string(self, value):
+    def entries_string(self, value: None | tuple):
         # We must include the entries in the hash, since different arrays can be
         # indistinguishable by class, name and domain alone
         # Slightly different syntax for sparse and non-sparse matrices
@@ -110,10 +111,10 @@ def entries_string(self, value):
             entries = self._entries
             if issparse(entries):
                 dct = entries.__dict__
-                self._entries_string = ["shape", str(dct["_shape"])]
+                entries_string = ["shape", str(dct["_shape"])]
                 for key in ["data", "indices", "indptr"]:
-                    self._entries_string += [key, dct[key].tobytes()]
-                self._entries_string = tuple(self._entries_string)
+                    entries_string += [key, dct[key].tobytes()]
+                self._entries_string = tuple(entries_string)
                 # self._entries_string = str(entries.__dict__)
             else:
                 self._entries_string = (entries.tobytes(),)
@@ -124,7 +125,7 @@ def set_id(self):
             (self.__class__, self.name, *self.entries_string, *tuple(self.domain))
         )
 
-    def _jac(self, variable):
+    def _jac(self, variable) -> pybamm.Matrix:
         """See :meth:`pybamm.Symbol._jac()`."""
         # Return zeros of correct size
         jac = csr_matrix((self.size, variable.evaluation_array.count(True)))
@@ -139,15 +140,15 @@ def create_copy(self):
             entries_string=self.entries_string,
         )
 
-    def _base_evaluate(self, t=None, y=None, y_dot=None, inputs=None):
+    def _base_evaluate(self, t, y, y_dot, inputs):
         """See :meth:`pybamm.Symbol._base_evaluate()`."""
         return self._entries
 
     def is_constant(self):
         """See :meth:`pybamm.Symbol.is_constant()`."""
         return True
 
-    def to_equation(self):
+    def to_equation(self) -> sympy.Array:
         """Returns the value returned by the node when evaluated."""
         sympy = have_optional_dependency("sympy")
         entries_list = self.entries.tolist()
@@ -178,7 +179,7 @@ def to_json(self):
         return json_dict
 
 
-def linspace(start, stop, num=50, **kwargs):
+def linspace(start: float, stop: float, num: int = 50, **kwargs) -> pybamm.Array:
     """
     Creates a linearly spaced array by calling `numpy.linspace` with keyword
     arguments 'kwargs'. For a list of 'kwargs' see the
@@ -187,7 +188,9 @@ def linspace(start, stop, num=50, **kwargs):
     return pybamm.Array(np.linspace(start, stop, num, **kwargs))
 
 
-def meshgrid(x, y, **kwargs):
+def meshgrid(
+    x: pybamm.Array, y: pybamm.Array, **kwargs
+) -> tuple[pybamm.Array, pybamm.Array]:
     """
     Return coordinate matrices as from coordinate vectors by calling
     `numpy.meshgrid` with keyword arguments 'kwargs'. For a list of 'kwargs'

pybamm/expression_tree/averages.py

@@ -1,6 +1,8 @@
 #
 # Classes and methods for averaging
 #
+from __future__ import annotations
+from typing import Callable
 import pybamm
 
 
@@ -14,13 +16,19 @@ class _BaseAverage(pybamm.Integral):
         The child node
     """
 
-    def __init__(self, child, name, integration_variable):
+    def __init__(
+        self,
+        child: pybamm.Symbol,
+        name: str,
+        integration_variable: list[pybamm.IndependentVariable]
+        | pybamm.IndependentVariable,
+    ) -> None:
         super().__init__(child, integration_variable)
         self.name = name
 
 
 class XAverage(_BaseAverage):
-    def __init__(self, child):
+    def __init__(self, child: pybamm.Symbol) -> None:
         if all(n in child.domain[0] for n in ["negative", "particle"]):
             x = pybamm.standard_spatial_vars.x_n
         elif all(n in child.domain[0] for n in ["positive", "particle"]):
@@ -30,56 +38,60 @@ def __init__(self, child):
         integration_variable = x
         super().__init__(child, "x-average", integration_variable)
 
-    def _unary_new_copy(self, child):
+    def _unary_new_copy(self, child: pybamm.Symbol):
         """See :meth:`UnaryOperator._unary_new_copy()`."""
         return x_average(child)
 
 
 class YZAverage(_BaseAverage):
-    def __init__(self, child):
+    def __init__(self, child: pybamm.Symbol) -> None:
         y = pybamm.standard_spatial_vars.y
         z = pybamm.standard_spatial_vars.z
-        integration_variable = [y, z]
+        integration_variable: list[pybamm.IndependentVariable] = [y, z]
         super().__init__(child, "yz-average", integration_variable)
 
-    def _unary_new_copy(self, child):
+    def _unary_new_copy(self, child: pybamm.Symbol):
         """See :meth:`UnaryOperator._unary_new_copy()`."""
         return yz_average(child)
 
 
 class ZAverage(_BaseAverage):
-    def __init__(self, child):
-        integration_variable = [pybamm.standard_spatial_vars.z]
+    def __init__(self, child: pybamm.Symbol) -> None:
+        integration_variable: list[pybamm.IndependentVariable] = [
+            pybamm.standard_spatial_vars.z
+        ]
         super().__init__(child, "z-average", integration_variable)
 
-    def _unary_new_copy(self, child):
+    def _unary_new_copy(self, child: pybamm.Symbol):
         """See :meth:`UnaryOperator._unary_new_copy()`."""
         return z_average(child)
 
 
 class RAverage(_BaseAverage):
-    def __init__(self, child):
-        integration_variable = [pybamm.SpatialVariable("r", child.domain)]
+    def __init__(self, child: pybamm.Symbol) -> None:
+        integration_variable: list[pybamm.IndependentVariable] = [
+            pybamm.SpatialVariable("r", child.domain)
+        ]
         super().__init__(child, "r-average", integration_variable)
 
-    def _unary_new_copy(self, child):
+    def _unary_new_copy(self, child: pybamm.Symbol):
         """See :meth:`UnaryOperator._unary_new_copy()`."""
         return r_average(child)
 
 
 class SizeAverage(_BaseAverage):
-    def __init__(self, child, f_a_dist):
+    def __init__(self, child: pybamm.Symbol, f_a_dist) -> None:
         R = pybamm.SpatialVariable("R", domains=child.domains, coord_sys="cartesian")
-        integration_variable = [R]
+        integration_variable: list[pybamm.IndependentVariable] = [R]
         super().__init__(child, "size-average", integration_variable)
         self.f_a_dist = f_a_dist
 
-    def _unary_new_copy(self, child):
+    def _unary_new_copy(self, child: pybamm.Symbol):
         """See :meth:`UnaryOperator._unary_new_copy()`."""
         return size_average(child, f_a_dist=self.f_a_dist)
 
 
-def x_average(symbol):
+def x_average(symbol: pybamm.Symbol) -> pybamm.Symbol:
     """
     Convenience function for creating an average in the x-direction.
 
@@ -168,7 +180,7 @@ def x_average(symbol):
         return XAverage(symbol)
 
 
-def z_average(symbol):
+def z_average(symbol: pybamm.Symbol) -> pybamm.Symbol:
     """
     Convenience function for creating an average in the z-direction.
 
@@ -205,7 +217,7 @@ def z_average(symbol):
         return ZAverage(symbol)
 
 
-def yz_average(symbol):
+def yz_average(symbol: pybamm.Symbol) -> pybamm.Symbol:
     """
     Convenience function for creating an average in the y-z-direction.
 
@@ -239,11 +251,11 @@ def yz_average(symbol):
         return YZAverage(symbol)
 
 
-def xyz_average(symbol):
+def xyz_average(symbol: pybamm.Symbol) -> pybamm.Symbol:
     return yz_average(x_average(symbol))
 
 
-def r_average(symbol):
+def r_average(symbol: pybamm.Symbol) -> pybamm.Symbol:
     """
     Convenience function for creating an average in the r-direction.
 
@@ -286,7 +298,9 @@ def r_average(symbol):
         return RAverage(symbol)
 
 
-def size_average(symbol, f_a_dist=None):
+def size_average(
+    symbol: pybamm.Symbol, f_a_dist: pybamm.Symbol | None = None
+) -> pybamm.Symbol:
     """Convenience function for averaging over particle size R using the area-weighted
     particle-size distribution.
 
@@ -339,7 +353,10 @@ def size_average(symbol, f_a_dist=None):
         return SizeAverage(symbol, f_a_dist)
 
 
-def _sum_of_averages(symbol, average_function):
+def _sum_of_averages(
+    symbol: pybamm.Addition | pybamm.Subtraction,
+    average_function: Callable[[pybamm.Symbol], pybamm.Symbol],
+):
     if isinstance(symbol, pybamm.Addition):
         return average_function(symbol.left) + average_function(symbol.right)
     elif isinstance(symbol, pybamm.Subtraction):