Fix mypy

.pre-commit-config.yaml

@@ -24,6 +24,16 @@ repos:
       - id: ruff-format
         files: ^gplugins/(femwell|gmsh|meow|sax|tidy3d|klayout|vlsir)/
 
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.15.0"
+    hooks:
+      - id: mypy
+        args: [--ignore-missing-imports, --strict, --config-file=pyproject.toml]
+        additional_dependencies:
+          - gdsfactory
+          - pytest
+        files: ^gplugins/(femwell|gmsh|meow|sax|tidy3d|klayout|vlsir)/
+
   # - repo: https://github.com/shellcheck-py/shellcheck-py
   #   rev: v0.9.0.5
   #   hooks:

Makefile

@@ -6,7 +6,7 @@ venv:
 
 install:
 	uv venv --python 3.11
-	uv pip install -e .[dev,docs,devsim,femwell,gmsh,klayout,meow,sax,schematic,tidy3d,vlsir]
+	uv pip install -e .[dev,docs,femwell,gmsh,meow,sax,tidy3d,klayout,vlsir]
 	uv run pre-commit install
 
 dev: test-data gmsh elmer install

gplugins/common/utils/get_component_with_net_layers.py

@@ -1,6 +1,7 @@
 import copy
 
 import gdsfactory as gf
+import klayout.db as kdb
 from gdsfactory import Component
 from gdsfactory.technology import LayerStack, LogicalLayer
 
@@ -35,8 +36,8 @@ def get_component_layer_stack(
 
 
 def get_component_with_net_layers(
-    component,
-    layer_stack,
+    component: Component,
+    layer_stack: LayerStack,
     port_names: list[str],
     delimiter: str = "#",
     new_layers_init: tuple[int, int] = (10010, 0),
@@ -74,7 +75,9 @@ def get_component_with_net_layers(
         net_component = net_component.remove_layers(layers=(port.layer,))
         for polygon in polygons:
             # If polygon belongs to port, create a unique new layer, and add the polygon to it
-            if polygon.sized(3 * gf.kcl.dbu).inside(port.center):
+            if polygon.sized(int(3 * gf.kcl.dbu)).inside(
+                kdb.Point(*port.to_itype().center)
+            ):
                 # if gdstk.inside(
                 #     [port.center],
                 #     gdstk.offset(gdstk.Polygon(polygon), gf.get_active_pdk().grid_size),
@@ -111,8 +114,3 @@ def get_component_with_net_layers(
 
     net_component.name = f"{component.name}_net_layers"
     return net_component
-
-
-if __name__ == "__main__":
-    c = get_component_with_net_layers()
-    c.show()

gplugins/common/utils/get_effective_indices.py

@@ -2,9 +2,10 @@
 
 from __future__ import annotations
 
-from typing import Literal
+from typing import Any, Literal, cast
 
 import numpy as np
+import numpy.typing as npt
 from scipy.optimize import fsolve
 
 
@@ -19,9 +20,9 @@ def get_effective_indices(
     """Returns the effective refractive indices for a 1D mode.
 
     Args:
-        epsilon_core: Relative permittivity of the film.
-        epsilon_substrate: Relative permittivity of the substrate.
-        epsilon_cladding: Relative permittivity of the cladding.
+        core_material: Refractive index of the core material.
+        nsubstrate: Refractive index of the substrate.
+        clad_materialding: Refractive index of the cladding.
         thickness: Thickness of the film in um.
         wavelength: Wavelength in um.
         polarization: Either "te" or "tm".
@@ -66,18 +67,20 @@ def get_effective_indices(
 
     k_0 = 2 * np.pi / wavelength
 
-    def k_f(e_eff):
+    def k_f(e_eff: npt.NDArray[np.floating[Any]]) -> npt.NDArray[np.floating[Any]]:
         return k_0 * np.sqrt(epsilon_core - e_eff) / (epsilon_core if tm else 1)
 
-    def k_s(e_eff):
+    def k_s(e_eff: npt.NDArray[np.floating[Any]]) -> npt.NDArray[np.floating[Any]]:
         return (
             k_0 * np.sqrt(e_eff - epsilon_substrate) / (epsilon_substrate if tm else 1)
         )
 
-    def k_c(e_eff):
+    def k_c(e_eff: npt.NDArray[np.floating[Any]]) -> npt.NDArray[np.floating[Any]]:
         return k_0 * np.sqrt(e_eff - epsilon_cladding) / (epsilon_cladding if tm else 1)
 
-    def objective(e_eff):
+    def objective(
+        e_eff: npt.NDArray[np.floating[Any]],
+    ) -> npt.NDArray[np.floating[Any]]:
         return 1 / np.tan(k_f(e_eff) * thickness) - (
             k_f(e_eff) ** 2 - k_s(e_eff) * k_c(e_eff)
         ) / (k_f(e_eff) * (k_s(e_eff) + k_c(e_eff)))
@@ -92,14 +95,14 @@ def objective(e_eff):
         return []
 
     # and then use fsolve to get exact indices
-    indices_temp = fsolve(objective, indices_temp)
+    indices_temp = cast(npt.NDArray[np.floating[Any]], fsolve(objective, indices_temp))
 
-    indices = []
+    indices: list[float] = []
     for index in indices_temp:
         if not any(np.isclose(index, i, atol=1e-5) for i in indices):
             indices.append(index)
 
-    return np.sqrt(indices).tolist()
+    return cast(list[float], np.sqrt(indices).tolist())
 
 
 def test_effective_index() -> None:

gplugins/common/utils/parse_layer_stack.py

@@ -26,7 +26,7 @@ def list_unique_layer_stack_z(
 def map_unique_layer_stack_z(
     layer_stack: LayerStack,
     include_zmax: bool = True,
-):
+) -> dict[str, set[float]]:
     """Map unique LayerStack z coordinates to various layers.
 
     Args:
@@ -57,7 +57,7 @@ def map_unique_layer_stack_z(
 def get_layer_overlaps_z(
     layer_stack: LayerStack,
     include_zmax: bool = True,
-):
+) -> dict[float, set[str]]:
     """Maps layers to unique LayerStack z coordinates.
 
     Args:
@@ -67,7 +67,7 @@ def get_layer_overlaps_z(
     """
     z_grid = list_unique_layer_stack_z(layer_stack)
     unique_z_dict = map_unique_layer_stack_z(layer_stack, include_zmax)
-    intersection_z_dict = {}
+    intersection_z_dict: dict[float, set[str]] = {}
     for z in z_grid:
         current_layers = {
             layername for layername, layer_zs in unique_z_dict.items() if z in layer_zs
@@ -77,11 +77,12 @@ def get_layer_overlaps_z(
     return intersection_z_dict
 
 
-def get_layers_at_z(layer_stack: LayerStack, z: float):
+def get_layers_at_z(layer_stack: LayerStack, z: float) -> list[str]:
     """Returns layers present at a given z-position.
 
     Args:
         layer_stack: LayerStack
+        z: float
     Returns:
         List of layers
     """
@@ -93,11 +94,11 @@ def get_layers_at_z(layer_stack: LayerStack, z: float):
         raise ValueError("Requested z-value is above the minimum layer_stack z")
     for z_unique in intersection_z_dict.keys():
         if z <= z_unique:
-            return intersection_z_dict[z_unique]
+            return list(intersection_z_dict[z_unique])
     raise AssertionError("Could not find z-value in layer_stack z-range.")
 
 
-def order_layer_stack(layer_stack: LayerStack):
+def order_layer_stack(layer_stack: LayerStack) -> list[str]:
     """Orders layer_stack according to mesh_order.
 
     Args:

gplugins/common/utils/plot.py

@@ -4,21 +4,25 @@
 from collections.abc import Sequence
 from functools import partial
 from itertools import combinations
+from typing import Any
 
-import gdsfactory as gf
 import matplotlib.pyplot as plt
 import numpy as np
+import numpy.typing as npt
+from matplotlib.axes import Axes
 
 
-def _check_ports(sp: dict[str, np.ndarray], ports: Sequence[str]) -> None:
+def _check_ports(
+    sp: dict[str, npt.NDArray[np.floating[Any]]], ports: Sequence[str]
+) -> None:
     """Ensure ports exist in Sparameters."""
     for port in ports:
         if port not in sp:
             raise ValueError(f"Did not find port {port!r} in {list(sp.keys())}")
 
 
 def plot_sparameters(
-    sp: dict[str, np.ndarray],
+    sp: dict[str, npt.NDArray[np.floating[Any]]],
     logscale: bool = True,
     plot_phase: bool = False,
     keys: tuple[str, ...] | None = None,
@@ -39,7 +43,7 @@ def plot_sparameters(
 
     """
     w = sp["wavelengths"] * units
-    keys = keys or [key for key in sp if not key.lower().startswith("wav")]
+    keys = keys or tuple(key for key in sp if not key.lower().startswith("wav"))
 
     for key in keys:
         if with_simpler_input_keys:
@@ -74,9 +78,12 @@ def plot_sparameters(
 
 
 def plot_imbalance(
-    sp: dict[str, np.ndarray], ports: Sequence[str], ax: plt.Axes | None = None
+    sp: dict[str, npt.NDArray[np.floating[Any]]],
+    ports: Sequence[str],
+    ax: Axes | None = None,
 ) -> None:
     """Plots imbalance in dB for coupler.
+
     The imbalance is always defined between two ports, so this function plots the
     imbalance between all unique port combinations.
 
@@ -107,7 +114,9 @@ def plot_imbalance(
 
 
 def plot_loss(
-    sp: dict[str, np.ndarray], ports: Sequence[str], ax: plt.Axes | None = None
+    sp: dict[str, npt.NDArray[np.floating[Any]]],
+    ports: Sequence[str],
+    ax: Axes | None = None,
 ) -> None:
     """Plots loss dB for coupler.
 
@@ -137,7 +146,9 @@ def plot_loss(
 
 
 def plot_reflection(
-    sp: dict[str, np.ndarray], ports: Sequence[str], ax: plt.Axes | None = None
+    sp: dict[str, npt.NDArray[np.floating[Any]]],
+    ports: Sequence[str],
+    ax: Axes | None = None,
 ) -> None:
     """Plots reflection in dB for coupler.
 
@@ -172,11 +183,3 @@ def plot_reflection(
 plot_imbalance2x2 = partial(plot_imbalance, ports=["o1@0,o3@0", "o1@0,o4@0"])
 plot_reflection1x2 = partial(plot_reflection, ports=["o1@0,o1@0"])
 plot_reflection2x2 = partial(plot_reflection, ports=["o1@0,o1@0", "o2@0,o1@0"])
-
-if __name__ == "__main__":
-    import gplugins as sim
-
-    sp = sim.get_sparameters_data_tidy3d(component=gf.components.mmi1x2)
-    # plot_sparameters(sp, logscale=False, keys=["o1@0,o2@0"])
-    # plot_sparameters(sp, logscale=False, keys=["S21"])
-    # plt.show()

gplugins/gmsh/define_polysurfaces.py

@@ -6,16 +6,16 @@
 
 
 def define_polysurfaces(
-    polygons_dict: dict,
+    polygons_dict: dict[str, Any],
     layer_stack: LayerStack,
-    layer_physical_map: dict,
-    layer_meshbool_map: dict,
+    layer_physical_map: dict[str, Any],
+    layer_meshbool_map: dict[str, Any],
     model: Any,
-    resolutions: dict,
+    resolutions: dict[str, Any] | None = None,
     scale_factor: float = 1,
-):
+) -> list[PolySurface]:
     """Define meshwell polysurfaces dimtags from gdsfactory information."""
-    polysurfaces_list = []
+    polysurfaces_list: list[PolySurface] = []
 
     if resolutions is None:
         resolutions = {}
@@ -24,6 +24,11 @@ def define_polysurfaces(
         if polygons_dict[layername].is_empty:
             continue
 
+        layer_stack_ = layer_stack.layers.get(layername)
+
+        if layer_stack_ is None:
+            continue
+
         polysurfaces_list.append(
             PolySurface(
                 polygons=scale(
@@ -33,7 +38,7 @@ def define_polysurfaces(
                 ),
                 model=model,
                 resolution=resolutions.get(layername, None),
-                mesh_order=layer_stack.layers.get(layername).mesh_order,
+                mesh_order=layer_stack_.mesh_order,
                 physical_name=layer_physical_map[layername]
                 if layername in layer_physical_map
                 else layername,

gplugins/gmsh/uz_xsection_mesh.py

@@ -1,7 +1,7 @@
-# type: ignore
 from __future__ import annotations
 
 from collections.abc import Sequence
+from typing import Any
 
 import gdsfactory as gf
 import numpy as np
@@ -206,12 +206,12 @@ def uz_xsection_mesh(
     component: ComponentOrReference,
     xsection_bounds: tuple[tuple[float, float], tuple[float, float]],
     layer_stack: LayerStack,
-    layer_physical_map: dict,
-    layer_meshbool_map: dict,
-    resolutions: dict | None = None,
+    layer_physical_map: dict[str, Any],
+    layer_meshbool_map: dict[str, Any],
+    resolutions: dict[str, Any] | None = None,
     default_characteristic_length: float = 0.5,
     background_tag: str | None = None,
-    background_padding: Sequence[float, float, float, float, float, float] = (2.0,) * 6,
+    background_padding: Sequence[float] = (2.0,) * 6,
     background_mesh_order: int | float = 2**63 - 1,
     global_scaling: float = 1,
     global_scaling_premesh: float = 1,
@@ -225,9 +225,9 @@ def uz_xsection_mesh(
     n_threads: int = get_number_of_cores(),
     gmsh_version: float | None = None,
     interface_delimiter: str = "___",
-    background_remeshing_file=None,
+    background_remeshing_file: str | None = None,
     optimization_flags: tuple[tuple[str, int]] | None = None,
-    **kwargs,
+    **kwargs: Any,
 ):
     """Mesh uz cross-section of component along line u = [[x1,y1] , [x2,y2]].