Merge pull request #71 from gdsfactory/pydantic2_final

port to pydantic 2

docs/_config.yml

@@ -60,7 +60,6 @@ sphinx:
     - "sphinx.ext.napoleon"
     - "sphinx.ext.viewcode"
     - "matplotlib.sphinxext.plot_directive"
-    - "sphinxcontrib.autodoc_pydantic"
     - "sphinxcontrib.bibtex"
   config:
     #autodoc_typehints: description

docs/notebooks/tidy3d_01_tidy3d_modes.py

@@ -47,14 +47,12 @@
 )  # get the index of a material with a given refractive index float
 
 # %%
-gt.materials.get_index(
-    "SiO2"
-)  # get the index of a material with a name string, for the case that the refractive index has only one variant
+# get the index of a material with a name string, for the case that the refractive index has only one variant
+gt.materials.get_index("AlxOy")
 
 # %%
-gt.materials.get_index(
-    ("cSi", "Li1993_293K")
-)  # get the index of a material with a name string, for the case that the refractive index has more than one variant
+# get the index of a material with a name string, for the case that the refractive index has more than one variant
+gt.materials.get_index(("cSi", "Li1993_293K"))
 
 # %% [markdown]
 # ## Waveguides

gplugins/devsim/doping.py

@@ -3,7 +3,7 @@
 import numpy as np
 from gdsfactory.generic_tech import LAYER
 from gdsfactory.typings import Layer
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class DopingLayerLevel(BaseModel):
@@ -20,13 +20,7 @@ class DopingLayerLevel(BaseModel):
     layer: Layer
     type: str
     z_profile: Callable
-    # xy_profile: Optional[Callable] = None # not implemented yet
-
-    class Config:
-        """pydantic config."""
-
-        frozen = True
-        extra = "forbid"
+    model_config = ConfigDict(frozen=True, extra="forbid")
 
 
 cm3_to_um3 = 1e-12

gplugins/devsim/get_simulation_xsection.py

@@ -20,7 +20,7 @@
 import pyvista as pv
 import tidy3d as td
 from devsim.python_packages import model_create, simple_physics
-from pydantic import BaseModel, Extra
+from pydantic import BaseModel, ConfigDict
 from scipy.interpolate import griddata
 
 from gplugins.tidy3d.materials import get_nk
@@ -171,11 +171,7 @@ class PINWaveguide(BaseModel):
     atol: float = 1e8
     rtol: float = 1e-8
     max_iter: int = 60
-
-    class Config:
-        """Enable adding new."""
-
-        extra = Extra.allow
+    model_config = ConfigDict(extra="allow")
 
     # @property
     # def t_sim(self):

gplugins/tidy3d/materials.py

@@ -115,5 +115,6 @@ def get_medium(spec: MaterialSpecTidy3d) -> td.Medium:
     # print(get_index(spec="si"))
     # print(get_index(spec=3.4))
     # m = get_medium("SiO2")
-    m = get_medium(("cSi", "Li1993_293K"))
+    # m = get_medium(("cSi", "Li1993_293K"))
     # m = td.Medium(permittivity=1.45 ** 2)
+    m = get_medium(td.material_library["cSi"]["Li1993_293K"])

gplugins/tidy3d/modes.py

@@ -18,12 +18,12 @@
 from typing import Any, Literal
 
 import numpy as np
-import pydantic
+import pydantic.v1 as pydantic
 import tidy3d as td
 import xarray
 from gdsfactory.config import PATH, logger
 from gdsfactory.typings import PathType
-from pydantic import BaseModel
+from pydantic.v1 import BaseModel, ConfigDict
 from tidy3d.plugins import waveguide
 from tqdm.auto import tqdm
 
@@ -58,7 +58,7 @@ def custom_serializer(data: str | float | BaseModel) -> str:
     raise ValueError(f"Unsupported data type: {type(data)}")
 
 
-class Waveguide(pydantic.BaseModel):
+class Waveguide(BaseModel):
     """Waveguide Model.
 
     All dimensions must be specified in μm (1e-6 m).
@@ -155,15 +155,11 @@ class Waveguide(pydantic.BaseModel):
 
     _cached_data = pydantic.PrivateAttr()
     _waveguide = pydantic.PrivateAttr()
-
-    class Config:
-        """pydantic config."""
-
-        extra = "forbid"
+    model_config = ConfigDict(extra="forbid")
 
     @pydantic.validator("wavelength")
-    def _fix_wavelength_type(cls, value):
-        return np.array(value, dtype=float)
+    def _fix_wavelength_type(cls, v):
+        return np.array(v, dtype=float)
 
     @property
     def filepath(self) -> pathlib.Path | None:
@@ -272,7 +268,7 @@ def _data(self):
 
             wg = self.waveguide
 
-            fields = wg.mode_solver.data._centered_fields
+            fields = wg.mode_solver.data.field_components
             self._cached_data = {
                 f + c: fields[f + c].squeeze(drop=True).values
                 for f in "EH"
@@ -377,13 +373,14 @@ def plot_grid(self) -> None:
         """Plot the waveguide grid."""
         self.waveguide.plot_grid(z=0)
 
-    def plot_index(self, **kwargs) -> None:
+    def plot_index(self, **kwargs):
         """Plot the waveguide index distribution.
 
         Keyword arguments are passed to xarray.DataArray.plot.
         """
         artist = self.index.real.plot(**kwargs)
         artist.axes.set_aspect("equal")
+        return artist
 
     def plot_field(
         self,
@@ -392,7 +389,7 @@ def plot_field(
         mode_index: int = 0,
         wavelength: float | None = None,
         **kwargs,
-    ) -> None:
+    ):
         """Plot the selected field distribution from a waveguide mode.
 
         Parameters:
@@ -445,6 +442,7 @@ def plot_field(
         data_array.name = field_name
         artist = data_array.plot(**kwargs)
         artist.axes.set_aspect("equal")
+        return artist
 
     def _ipython_display_(self) -> None:
         """Show index in matplotlib for Jupyter Notebooks."""
@@ -1006,23 +1004,22 @@ def sweep_coupling_length(
     #     overwrite=True
     # )
 
-    import matplotlib.pyplot as plt
-
     strip = Waveguide(
         wavelength=1.55,
         core_width=1.0,
         slab_thickness=0.0,
         # core_material="si",
-        core_material=td.material_library["cSi"]["Li1993_293K"],
+        # core_material=td.material_library["cSi"]["Li1993_293K"],
+        core_material=3.47,
         clad_material="sio2",
         core_thickness=220 * nm,
         num_modes=4,
     )
     # strip._data
     # strip.filepath
     # strip.plot_index()
-    strip.plot_field("Ex", mode_index=0, wavelength=1.55, value="dB")
-    plt.show()
+    # strip.plot_field("Ex", mode_index=0, wavelength=1.55, value="dB")
+    # plt.show()
     # w = np.linspace(400 * nm, 1000 * nm, 7)
     # n_eff = sweep_n_eff(strip, core_width=w)
     # fraction_te = sweep_fraction_te(strip, core_width=w)

gplugins/tidy3d/tests/test_materials.py

@@ -2,7 +2,7 @@
 
 import pytest
 import tidy3d as td
-from pydantic import ValidationError
+from pydantic.v1 import ValidationError
 
 import gplugins.tidy3d as gt
 
@@ -66,8 +66,8 @@ def test_material_library_many_variants() -> None:
 
 def test_material_library_single_variant() -> None:
     strip = gt.modes.Waveguide(
-        core_material="SiO2",
-        clad_material="sio2",
+        core_material="AlxOy",
+        clad_material="AlxOy",
         **settings,
     )
     strip._data
@@ -84,6 +84,7 @@ def test_material_library() -> None:
 
 if __name__ == "__main__":
     pytest.main([__file__])
+    # test_material_validation_error()
     # test_material_medium()
     # test_material_float()
     # test_material_library()

pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
   "Operating System :: OS Independent"
 ]
 dependencies = [
-  "gdsfactory[cad]>=7.3.2",
+  "gdsfactory[cad]>=7.4.0",
   "pint"
 ]
 description = "gdsfactory plugins"
@@ -26,12 +26,11 @@ requires-python = ">=3.10"
 version = "0.3.1"
 
 [project.optional-dependencies]
+dagster = ["dagster", "dagit"]
 database = [
   "sqlalchemy",
   "sqlalchemy-utils",
-  "dagster",
-  "dagit",
-  "sqlmodel",
+  # "sqlmodel>=0.0.8,<0.1",
   "boto3",
   "pymysql"
 ]
@@ -44,17 +43,16 @@ dev = [
   "mypy",
   "pyswarms",
   "autograd",
-  "ray[tune,air]",
-  "hyperopt"
+  "hyperopt",
+  "ray"
 ]
 devsim = [
   "devsim",
   "pyvista",
-  "tidy3d"
+  "tidy3d>=2.4.0rc2,<2.5.0"
 ]
 docs = [
   "jupytext",
-  "autodoc_pydantic",
   "matplotlib",
   "jupyter-book==0.15.1",
   "pyvista[jupyter]"
@@ -74,14 +72,14 @@ gmsh = [
   "meshwell>=0.0.9,<0.3.1"
 ]
 klayout = [
-  "kfactory[git,ipy]==0.7.5"
+  "kfactory[git,ipy]>=0.8.4,<0.9"
 ]
 meow = [
-  "meow-sim>=0.7.1,<0.8.0",
-  "tidy3d>=2.3.3,<2.4.0"
+  "meow-sim>=0.7.3,<0.8.0",
+  "tidy3d>=2.4.0rc2,<2.5.0"
 ]
 sax = [
-  "sax>=0.8.8,<0.9.0",
+  "sax>=0.9.2,<0.10.0",
   "jaxlib",
   "jax",
   "scikit-learn"
@@ -91,12 +89,12 @@ schematic = [
   "natsort"
 ]
 tidy3d = [
-  "tidy3d>=2.3.3,<2.4.0"
+  "tidy3d>=2.4.0rc2,<2.5.0"
 ]
 web = [
   "jinja2",
   "python-multipart",
-  "fastapi",
+  "fastapi>=0.102.0,<1",
   "uvicorn[standard]"
 ]
 
@@ -136,6 +134,8 @@ strict = true
 addopts = '--tb=short'
 norecursedirs = [
   "extra/*.py",
+  'gplugins/dagster',
+  'gplugins/database',
   'gplugins/devsim',
   'gplugins/sax/integrations',
   'gplugins/tidy3d/tests/tests_sparameters'