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chore(deps): bump the python group across 1 directory with 18 updates #3353

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chore(deps): bump the python group across 1 directory with 18 updates #3353

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70 changes: 35 additions & 35 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,28 +18,28 @@ classifiers = [
dependencies = [
"pyroots>=0.5.0,<0.6.0",
"xarray>=2023.08,<2026.0.0",
"importlib-metadata>=6.0.0,<9.0.0",
"h5netcdf==1.0.2",
"importlib-metadata>=6.0.0,<10.0.0",
"h5netcdf==1.8.1",
"h5py>=3.0.0,<3.15; python_version < '3.14'",
"h5py>=3.16.0,<3.17; python_version >= '3.14'",
"rich>=13.0,<14.0",
"rich>=13.0,<15.0",
"numpy>=2.2.6,<2.5.0",
"matplotlib>=3.10.0,<4.0.0",
"shapely>=2.0,<3.0",
"pandas>=2.2,<3.0",
"pydantic>=2.10.3,<3",
"pydantic-settings>=2.10.0,<3.0.0",
"PyYAML>=6.0.3,<7.0.0",
"dask>=2025.12.0,<2026.0.0",
"dask>=2025.12.0,<2027.0.0",
"toml>=0.10.2,<0.11.0",
"tomlkit>=0.13.2,<0.14.0",
"tomlkit>=0.13.2,<0.15.0",
"autograd>=1.7.0,<2.0.0",
"scipy>=1.14,<2.0",
"boto3>=1.28.0,<2.0.0",
"requests>=2.31.0,<3.0.0",
"pyjwt>=2.10.1,<3.0.0",
"click>=8.1.0,<9.0.0",
"responses>=0.25.8,<0.26.0",
"responses>=0.25.8,<0.27.0",
"joblib>=1.5.3,<2.0.0",
"typing-extensions>=4.15.0,<5.0.0",
"filelock>=3.20.1,<4.0.0",
Expand All @@ -53,10 +53,10 @@ Documentation = "https://docs.flexcompute.com/projects/tidy3d/en/latest/"

[project.optional-dependencies]
dev = [
"bayesian-optimization<2",
"bayesian-optimization<4",
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@cursor cursor bot Mar 31, 2026

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Version bump allows incompatible bayesian-optimization API versions

High Severity

The bayesian-optimization constraint changed from <2 to <4, but the codebase uses UtilityFunction (removed in v2.0.0) and the old suggest(utility) API pattern. In tidy3d/plugins/design/method.py, from bayes_opt import BayesianOptimization, UtilityFunction will raise ImportError with v2.0+, caught misleadingly as "module not found." The entire Bayesian optimization design plugin becomes non-functional when v2.x or v3.x is resolved.

Additional Locations (1)
Fix in Cursor Fix in Web

"coverage>=7.13.1,<8.0.0",
"dill>=0.4.0,<0.5.0",
"gdstk>=0.9.49,<0.10.0",
"gdstk>=0.9.49,<1.1.0",
"grcwa>=0.1.2,<0.2.0",
"ipython>=8.38.0,<9.0.0",
"torch>=2.2.0,<3.0.0; sys_platform == 'darwin'",
Expand All @@ -65,28 +65,28 @@ dev = [
"jupyter>=1.1.1,<2.0.0",
"myst-parser>=4.0.1,<5.0.0",
"memory_profiler>=0.61.0,<0.62.0",
"mypy==1.13.0",
"mypy==1.20.0",
"nbconvert>=7.17.0,<8.0.0",
"nbdime>=4.0.2,<5.0.0",
"nbsphinx>=0.8.7,<0.10.0",
"networkx>=2.6.3,<3.0.0",
"networkx>=2.6.3,<4.0.0",
"optax>=0.2.2,<0.3.0",
"orbax-checkpoint<0.11.33",
"orbax-checkpoint<0.11.34",
"psutil>=7.2.1,<8.0.0",
"pre-commit>=4,<5",
"pydata-sphinx-theme>=0.13.3,<0.16.0",
"pygad==3.3.1",
"pydata-sphinx-theme>=0.13.3,<0.17.0",
"pygad==3.5.0",
"pylint>=4.0.4,<5.0.0",
"pyswarms>=1.3.0,<2.0.0",
"pytest>=8.1,<10.0.0",
"pytest-timeout>=2.4.0,<3.0.0",
"pytest-xdist>=3.6.1,<4.0.0",
"pytest-cov>=6.0.0,<7.0.0",
"pytest-cov>=6.0.0,<8.0.0",
"pytest-env>=1.1.5,<2.0.0",
"pytest-testmon>=2.1.3,<3.0.0",
"rtree==1.2.0",
"ruff==0.11.11",
"sax>=0.11,<0.12",
"rtree==1.4.1",
"ruff==0.15.8",
"sax>=0.11,<0.15",
"signac>=2.3.0,<3.0.0",
"sphinx>=6,<9.0.0",
"sphinx-book-theme>=1.0.1,<2.0.0",
Expand All @@ -106,30 +106,30 @@ dev = [
"pyvista>=0.45,<0.48.0",
"trame>=3.0.0,<4.0.0",
"trame-vtk>=2.0.0,<3.0.0",
"trame-vuetify>=2.0.0,<3.0.0",
"trame-vuetify>=2.0.0,<4.0.0",
"cma>=4.4.1,<5.0.0",
"diff-cover>=10.1.0,<11.0.0",
"openpyxl>=3.1.5,<4.0.0",
"zizmor>=1.20.0,<2.0.0",
"libcst>=1.5.0,<2.0.0",
]
tests = [
"orbax-checkpoint<0.11.33",
"orbax-checkpoint<0.11.34",
"psutil>=7.2.1,<8.0.0",
"pre-commit>=4,<5",
"pylint>=4.0.4,<5.0.0",
"pytest>=8.1,<10.0.0",
"pytest-timeout>=2.4.0,<3.0.0",
"pytest-xdist>=3.6.1,<4.0.0",
"pytest-env>=1.1.5,<2.0.0",
"pytest-cov>=6.0.0,<7.0.0",
"pytest-cov>=6.0.0,<8.0.0",
"pytest-testmon>=2.1.3,<3.0.0",
"trimesh>=4.6,<5.0.0",
"networkx>=2.6.3,<3.0.0",
"rtree==1.2.0",
"networkx>=2.6.3,<4.0.0",
"rtree==1.4.1",
]
docs = [
"orbax-checkpoint<0.11.33",
"orbax-checkpoint<0.11.34",
"jupyter>=1.1.1,<2.0.0",
"jinja2>=3.1.2,<4.0.0",
"nbconvert>=7.17.0,<8.0.0",
Expand All @@ -140,52 +140,52 @@ docs = [
"sphinx-copybutton>=0.5.2,<0.6.0",
"sphinx-favicon>=1.0.1,<2.0.0",
"sphinx-book-theme>=1.0.1,<2.0.0",
"pydata-sphinx-theme>=0.13.3,<0.16.0",
"pydata-sphinx-theme>=0.13.3,<0.17.0",
"tmm>=0.2.0,<0.3.0",
"gdstk>=0.9.49,<0.10.0",
"gdstk>=0.9.49,<1.1.0",
"grcwa>=0.1.2,<0.2.0",
"sphinx-sitemap>=2.5.1,<3.0.0",
"sphinx-notfound-page>=1.1.0,<2.0.0",
"nbdime>=4.0.2,<5.0.0",
"optax>=0.2.2,<0.3.0",
"signac>=2.3.0,<3.0.0",
"sax>=0.11,<0.12",
"sax>=0.11,<0.15",
"pylint>=4.0.4,<5.0.0",
"sphinx-tabs>=3.4.7,<4.0.0",
"sphinxemoji>=0.3.2,<0.4.0",
"myst-parser>=4.0.1,<5.0.0",
"cma>=4.4.1,<5.0.0",
"openpyxl>=3.1.5,<4.0.0",
]
gdstk = ["gdstk>=0.9.49,<0.10.0"]
gdstk = ["gdstk>=0.9.49,<1.1.0"]
scikit-rf = ["scikit-rf>=1.9.0,<2.0.0"]
trimesh = [
"trimesh>=4.6,<5.0.0",
"networkx>=2.6.3,<3.0.0",
"rtree==1.2.0",
"networkx>=2.6.3,<4.0.0",
"rtree==1.4.1",
]
vtk = ["vtk>=9.6.0,<10.0.0"]
pyvista = [
"pyvista>=0.45,<0.48.0",
"vtk>=9.6.0,<10.0.0",
"trame>=3.0.0,<4.0.0",
"trame-vtk>=2.0.0,<3.0.0",
"trame-vuetify>=2.0.0,<3.0.0",
"trame-vuetify>=2.0.0,<4.0.0",
]
ruff = ["ruff==0.11.11"]
ruff = ["ruff==0.15.8"]
heatcharge = [
"trimesh>=4.6,<5.0.0",
"networkx>=2.6.3,<3.0.0",
"rtree==1.2.0",
"networkx>=2.6.3,<4.0.0",
"rtree==1.4.1",
"vtk>=9.6.0,<10.0.0",
]
pytorch = [
"torch>=2.2.0,<3.0.0; sys_platform == 'darwin'",
"torch>=2.2.0,<3.0.0; sys_platform != 'darwin'",
]
design = [
"bayesian-optimization<2",
"pygad==3.3.1",
"bayesian-optimization<4",
"pygad==3.5.0",
"pyswarms>=1.3.0,<2.0.0",
]
extras = ["tidy3d-extras==2.11.0"]
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