Add type hints

.github/workflows/lint.yml

@@ -16,10 +16,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.8
+      - name: Set up Python 3.9
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Lint
         run: |

.pre-commit-config.yaml

@@ -72,3 +72,10 @@ repos:
       args:
         - --convention=numpy
         - --add-select=D417
+
+- repo: https://github.com/pre-commit/mirrors-mypy
+  rev: v0.982
+  hooks:
+  - id: mypy
+    additional_dependencies: [types-all]
+    exclude: conf.py$

news/66.misc

@@ -0,0 +1 @@
+Added type hints to the entire code base and a *mypy* hook to the *pre-commit* linters to identify potential typing issues.

pyproject.toml

@@ -111,6 +111,9 @@ force_grid_wrap = 0
 combine_as_imports = true
 line_length = 88
 
+[tool.mypy]
+ignore_missing_imports = true
+
 [tool.towncrier]
 directory = "news"
 package = "sequence"

sequence/_grid.py

@@ -1,12 +1,13 @@
 """Define the grid used for creating *Sequence* models."""
 import os
+import sys
 
 import numpy as np
 from landlab import RasterModelGrid
 
-try:
+if sys.version_info >= (3, 11):
     import tomllib
-except ModuleNotFoundError:
+else:
     import tomli as tomllib
 
 
@@ -41,7 +42,7 @@ def __init__(self, n_cols: int, spacing: float = 100.0):
         self.at_grid["sea_level__elevation"] = 0.0
 
     @classmethod
-    def from_toml(cls, filepath: os.PathLike[str]):
+    def from_toml(cls, filepath: os.PathLike[str]) -> "SequenceModelGrid":
         """Load a :class:`~SequenceModelGrid` from a *toml*-formatted file.
 
         Parameters
@@ -53,7 +54,7 @@ def from_toml(cls, filepath: os.PathLike[str]):
             return SequenceModelGrid.from_dict(tomllib.load(fp)["sequence"]["grid"])
 
     @classmethod
-    def from_dict(cls, params: dict):
+    def from_dict(cls, params: dict) -> "SequenceModelGrid":
         """Create a :class:`~SequenceModelGrid` from a `dict`.
 
         If possible, this alternate constructor simply passes

sequence/bathymetry.py

@@ -3,10 +3,16 @@
 This module contains *Landlab* components to read bathymetry into a
 `SequenceModelGrid`.
 """
+from os import PathLike
+from typing import Union
+
 import numpy as np
 from landlab import Component
+from numpy.typing import NDArray
 from scipy import interpolate
 
+from ._grid import SequenceModelGrid
+
 
 class BathymetryReader(Component):
     """Landlab component that reads bathymetry from a file."""
@@ -26,7 +32,12 @@ class BathymetryReader(Component):
         }
     }
 
-    def __init__(self, grid, filepath=None, kind="linear", **kwds):
+    def __init__(
+        self,
+        grid: SequenceModelGrid,
+        filepath: Union[str, PathLike[str]],
+        kind: str = "linear",
+    ):
         """Generate a bathymetric profile from a file.
 
         Parameters
@@ -40,7 +51,7 @@ def __init__(self, grid, filepath=None, kind="linear", **kwds):
             'nearest', 'zero', 'slinear', 'quadratic', 'cubic').
             Default is 'linear'.
         """
-        super().__init__(grid, **kwds)
+        super().__init__(grid)
 
         data = np.loadtxt(filepath, delimiter=",", comments="#")
         self._bathymetry = interpolate.interp1d(
@@ -56,18 +67,18 @@ def __init__(self, grid, filepath=None, kind="linear", **kwds):
             self.grid.add_zeros("topographic__elevation", at="node")
 
     @property
-    def x(self):
+    def x(self) -> NDArray[np.floating]:
         """Return the x-coordinates of the grid."""
         return self.grid.x_of_node[self.grid.nodes_at_bottom_edge]
 
     @property
-    def z(self):
+    def z(self) -> NDArray[np.floating]:
         """Return the elevations along the grid."""
         return self.grid.at_node["topographic__elevation"][
             self.grid.nodes_at_bottom_edge
         ]
 
-    def run_one_step(self, dt=None):
+    def run_one_step(self, dt: float = None) -> None:
         """Update the grid's bathymetry.
 
         Parameters
@@ -81,14 +92,14 @@ def run_one_step(self, dt=None):
 
 
 def _create_initial_profile(
-    x,
-    sl_plain=0.0008,
-    init_shore=19750.0,
-    hgt=15.0,
-    alpha=1 / 2000.0,
-    sl_sh=0.001,
-    wavebase=60.0,
-):
+    x: NDArray[np.floating],
+    sl_plain: float = 0.0008,
+    init_shore: float = 19750.0,
+    hgt: float = 15.0,
+    alpha: float = 1 / 2000.0,
+    sl_sh: float = 0.001,
+    wavebase: float = 60.0,
+) -> NDArray[np.floating]:
 
     # check shoreline is in array, else put in center of array
     if x[-1] < init_shore: