⚡️ Preliminary support for Pyrefly

.github/workflows/ci.yml

@@ -77,6 +77,9 @@ jobs:
       - name: install dependencies
         run: uv pip install --exact --group type numpy==${{ matrix.np }}.* .
 
+      - name: pyrefly check scipy-stubs
+        run: pyrefly check scipy-stubs
+
       - name: basedpyright scipy-stubs
         run: basedpyright scipy-stubs
 
@@ -115,6 +118,9 @@ jobs:
       - name: install dependencies
         run: uv pip install --exact --group type numpy==${{ matrix.np }}.* .
 
+      - name: pyrefly check tests
+        run: pyrefly check tests
+
       - name: basedpyright tests
         run: basedpyright tests
 

CONTRIBUTING.md

@@ -24,7 +24,7 @@ Ensure you have [`uv`](https://docs.astral.sh/uv/getting-started/installation/)
 installed. Now you can install the project with the dev dependencies:
 
 ```shell
-uv sync --python 3.11
+uv sync --exact --python 3.11
 ```
 
 Installing the lowest supported Python version (3.11 in this example) prevents
@@ -76,18 +76,22 @@ uvx tox p
 <summary>Output:</summary>
 
 ```plaintext
-lint: OK ✔ in 0.6 seconds
-pyright: OK ✔ in 11.97 seconds
-mypy: OK ✔ in 16.69 seconds
-3.11: OK ✔ in 18.05 seconds
-3.12: OK ✔ in 22.94 seconds
-  lint: OK (0.60=setup[0.30]+cmd[0.16,0.11,0.04] seconds)
-  pyright: OK (11.97=setup[0.30]+cmd[11.67] seconds)
-  mypy: OK (16.69=setup[0.30]+cmd[16.39] seconds)
-  3.13: OK (25.80=setup[0.30]+cmd[25.51] seconds)
-  3.12: OK (22.94=setup[0.29]+cmd[22.64] seconds)
-  3.11: OK (18.05=setup[0.30]+cmd[17.75] seconds)
-  congratulations :) (25.84 seconds)
+lint: OK ✔ in 0.79 seconds
+pyrefly: OK ✔ in 1.19 seconds
+mypy: OK ✔ in 15.16 seconds
+pyright: OK ✔ in 17.69 seconds
+3.14: OK ✔ in 17.97 seconds
+3.13: OK ✔ in 18.37 seconds
+3.12: OK ✔ in 18.61 seconds
+  lint: OK (0.79=setup[0.11]+cmd[0.43,0.06,0.14,0.04] seconds)
+  pyrefly: OK (1.19=setup[0.18]+cmd[1.01] seconds)
+  pyright: OK (17.69=setup[0.13]+cmd[17.56] seconds)
+  mypy: OK (15.16=setup[0.29]+cmd[14.86] seconds)
+  3.11: OK (18.72=setup[0.20]+cmd[18.52] seconds)
+  3.12: OK (18.61=setup[0.26]+cmd[18.35] seconds)
+  3.13: OK (18.37=setup[0.37]+cmd[18.00] seconds)
+  3.14: OK (17.97=setup[0.17]+cmd[17.80] seconds)
+  congratulations :) (18.74 seconds)
 ```
 
 </details>

README.md

@@ -93,45 +93,39 @@ conda install conda-forge::scipy-typed
 
 ## Frequently Asked Questions
 
+### Q: What static type-checkers are supported?
+
+**A:** `scipy-stubs` is tested against the most recent stable versions of
+
+- [Mypy](https://github.com/python/mypy),
+- [Pyright](https://github.com/microsoft/pyright) (a.k.a. Pylance),
+- [BasedPyright](https://github.com/detachhead/basedpyright), and
+- [Pyrefly](https://github.com/facebook/pyrefly) (currently in alpha, so it may not always work as expected).
+
 ### Q: Do I need to change my existing code?
 
 **A:** No! `scipy-stubs` works with your existing code without any modifications.
 Just install it and your type checker and IDE will automatically use the type information.
 
-### Q: Will this slow down my code?
-
-**A:** Not at all. Type stubs are only used during development and type checking.
-They have zero runtime overhead since they're not imported when your code runs.
-
-### Q: What if I don't use type hints in my code?
+### Q: How much of SciPy is covered?
 
-**A:** You'll still benefit! Your IDE will provide better autocompletion and error detection
-even without explicit type annotations in your code.
+**A:** All of it! If you find any missing or incorrect type annotations, please open an issue on
+[GitHub](https://github.com/scipy/scipy-stubs/issues).
 
 ### Q: Can I use this with Jupyter notebooks?
 
-**A:** Yes! Most modern Jupyter environments (JupyterLab, VS Code notebooks) support
+**A:** Yes! Most modern Jupyter environments (JupyterLab, VSCode notebooks) support
 type checking and will benefit from `scipy-stubs`.
 
-### Q: What's the difference between this and the built-in scipy typing?
+### Q: What if I don't use type hints in my code?
 
-**A:** SciPy itself has limited type annotations. `scipy-stubs` provides comprehensive,
-precise type information for the entire SciPy API, including shape-typing and advanced type features.
+**A:** You'll still benefit! Your IDE will provide better autocompletion and error detection
+even without explicit type annotations in your code.
 
 ### Q: How do I know if it's working?
 
 **A:** You should see improved autocompletion in your IDE and more precise type information.
-You can also run `pyright` or another type checker on your code to see type checking in action.
-
-### Q: How much of SciPy is covered?
-
-**A:** All of it! If you find any missing or incorrect type annotations, please open an issue on [GitHub](https://github.com/scipy/scipy-stubs/issues).
-
-### Q: What static type-checkers are supported?
-
-**A:** `scipy-stubs` is compatible with [`pyright`](https://pyright.readthedocs.io/en/latest/index.html) (a.k.a. pylance),
-[`basedpyright`](https://github.com/DetachHead/basedpyright), and [`mypy`](https://github.com/python/mypy).
-We only support the latest versions of these type-checkers, so make sure to keep them up to date.
+You can also run `mypy`, `pyright` or another type checker on your code to see type checking in action.
 
 ## Versioning and requirements
 

lefthook.yml

@@ -8,6 +8,7 @@ pre-commit:
       glob: "*.{json,jsonc,md,toml,yaml,yml}"
       stage_fixed: true
       run: uv {run} dprint fmt --incremental=false
+
     - name: ruff
       glob: "*.{py,pyi}"
       stage_fixed: true
@@ -18,9 +19,15 @@ pre-commit:
             run: uv {run} ruff check --fix {staged_files}
           - name: format
             run: uv {run} ruff format {staged_files}
+
     - name: basedpyright
       glob: "*.{py,pyi}"
       run: uv {run} basedpyright --threads=3 {staged_files}
+
+    - name: pyrefly
+      glob: "*.{py,pyi}"
+      run: uv {run} pyrefly check {staged_files}
+
     - name: check-version-literals
       run: uv {run} scripts/check_version_literals.py
 

pyproject.toml

@@ -62,6 +62,7 @@ type = [
   "array-api-compat==1.12.0", # bundled as `scipy._lib.array_api_compat`
   "basedpyright==1.31.5",
   "mypy[faster-cache]==1.18.2",
+  "pyrefly==0.35.0",
 ]
 dev = [
   { include-group = "lint" },
@@ -106,6 +107,25 @@ warn_unreachable = false
 local_partial_types = true
 allow_redefinition_new = true
 
+[tool.pyrefly]
+project-includes = ["scipy-stubs", "scripts", "tests"]
+
+[[tool.pyrefly.sub-config]]
+matches = "scipy-stubs/*/__init__.pyi"
+errors = { deprecated = "ignore" }
+
+[[tool.pyrefly.sub-config]]
+matches = "scipy-stubs/special/_ufuncs.pyi"
+errors = { bad-override = "ignore" }
+
+[[tool.pyrefly.sub-config]]
+matches = "scipy-stubs/special/orthogonal.pyi"
+errors = { deprecated = "ignore" }
+
+[[tool.pyrefly.sub-config]]
+matches = "scipy-stubs/stats/_distn_infrastructure.pyi"
+errors = { bad-override = "ignore" }
+
 [tool.pyright]
 exclude = [
   "**/__pycache__",
@@ -205,7 +225,7 @@ split-on-trailing-comma = false
 [tool.tox]
 min_version = "4"
 requires = ["tox-uv>=1"]
-env_list = ["lint", "pyright", "mypy", "3.11", "3.12", "3.13", "3.14"]
+env_list = ["lint", "pyrefly", "pyright", "mypy", "3.11", "3.12", "3.13", "3.14"]
 
 [tool.tox.env_run_base]
 description = "stubtest with {base_python}"
@@ -232,11 +252,17 @@ commands = [
   ["ruff", "format", "--check"],
 ]
 
+[tool.tox.env.pyrefly]
+description = "pyrefly"
+runner = "uv-venv-lock-runner"
+dependency_groups = ["type"]
+commands = [["pyrefly", "check", { replace = "posargs", default = [], extend = true }]]
+
 [tool.tox.env.pyright]
 description = "basedpyright"
 runner = "uv-venv-lock-runner"
 dependency_groups = ["type"]
-commands = [["basedpyright"]]
+commands = [["basedpyright", { replace = "posargs", default = [], extend = true }]]
 
 [tool.tox.env.mypy]
 description = "mypy"
@@ -245,8 +271,6 @@ dependency_groups = ["type"]
 commands = [
   [
     "mypy",
-    "--hide-error-context",
-    "--hide-error-code-links",
     "--no-incremental",
     { replace = "posargs", default = ["."], extend = true },
   ],

scipy-stubs/fft/_backend.pyi

@@ -26,5 +26,5 @@ _named_backends: Final[dict[str, type[_Backend[Any]]]] = ...
 def _backend_from_arg(backend: _ToBackend[_T]) -> type[_Backend[_T]]: ...  # undocumented
 def set_global_backend(backend: _ToBackend, coerce: bool = False, only: bool = False, try_last: bool = False) -> None: ...
 def register_backend(backend: _ToBackend) -> None: ...
-def set_backend(backend: _ToBackend, coerce: bool = False, only: bool = False) -> op.CanWith[None]: ...
-def skip_backend(backend: _ToBackend) -> op.CanWith[None]: ...
+def set_backend(backend: _ToBackend, coerce: bool = False, only: bool = False) -> op.CanWith[None, None]: ...
+def skip_backend(backend: _ToBackend) -> op.CanWith[None, None]: ...

scipy-stubs/optimize/_nonlin.pyi

@@ -157,9 +157,9 @@ class GenericBroyden(Jacobian[_InexactT_co], Generic[_InexactT_co], metaclass=ab
     last_f: float
 
     @override
-    def setup(self, /, x0: _InexactND, f0: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def setup(self, /, x0: _InexactND, f0: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def update(self, /, x: _InexactND, f: _InexactND) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def update(self, /, x: _InexactND, f: _InexactND) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
 
 class LowRankMatrix(Generic[_InexactT_co]):
     dtype: np.dtype[_InexactT_co]
@@ -189,9 +189,9 @@ class BroydenFirst(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
         self, /, alpha: float | None = None, reduction_method: _ReductionMethod = "restart", max_rank: int | None = None
     ) -> None: ...
     @override
-    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.ArrayND[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.ArrayND[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     def rsolve(self, /, f: _InexactND, tol: float = 0) -> onp.ArrayND[_InexactT_co]: ...
     def matvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
     def rmatvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
@@ -208,17 +208,17 @@ class Anderson(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
 
     def __init__(self, /, alpha: float | None = None, w0: float = 0.01, M: float = 5) -> None: ...
     @override
-    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     def matvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
 
 class DiagBroyden(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
     d: onp.Array1D[_InexactT_co]
 
     def __init__(self, /, alpha: float | None = None) -> None: ...
     @override
-    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     def rsolve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...
     def matvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
     def rmatvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
@@ -227,7 +227,7 @@ class DiagBroyden(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
 class LinearMixing(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
     def __init__(self, /, alpha: float | None = None) -> None: ...
     @override
-    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     def rsolve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...
     def matvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
     def rmatvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
@@ -239,9 +239,9 @@ class ExcitingMixing(GenericBroyden[_InexactT_co], Generic[_InexactT_co]):
 
     def __init__(self, /, alpha: float | None = None, alphamax: float = 1.0) -> None: ...
     @override
-    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def setup(self, /, x: _InexactND, F: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     def rsolve(self, /, f: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...
     def matvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
     def rmatvec(self, /, f: _InexactND) -> onp.Array1D[_InexactT_co]: ...
@@ -268,11 +268,11 @@ class KrylovJacobian(Jacobian[_InexactT_co], Generic[_InexactT_co]):
     ) -> None: ...
     def matvec(self, /, v: _InexactND) -> onp.Array2D[_InexactT_co]: ...
     @override
-    def solve(self, /, rhs: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def solve(self, /, rhs: _InexactND, tol: float = 0) -> onp.Array2D[_InexactT_co]: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def update(self, /, x: _InexactND, f: _InexactND) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def update(self, /, x: _InexactND, f: _InexactND) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
     @override
-    def setup(self, /, x: _InexactND, f: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]
+    def setup(self, /, x: _InexactND, f: _InexactND, func: _ResidFunc) -> None: ...  # pyright: ignore[reportIncompatibleMethodOverride]  # pyrefly: ignore[bad-param-name-override]
 
 # undocumented
 @overload

scipy-stubs/optimize/_trustregion_exact.pyi

@@ -59,4 +59,5 @@ class IterativeSubproblem(BaseQuadraticSubproblem):
         k_hard: onp.ToFloat = 0.2,
     ) -> None: ...
     @override
+    # pyrefly: ignore[bad-param-name-override]
     def solve(self, /, tr_radius: onp.ToFloat) -> tuple[onp.ArrayND[np.float64], bool]: ...  # pyright: ignore[reportIncompatibleMethodOverride]

scipy-stubs/signal/bsplines.pyi

@@ -1,7 +1,7 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 from typing_extensions import deprecated
 
-from .spline import sepfir2d
+from .spline import sepfir2d  # pyrefly: ignore[deprecated]
 
 __all__ = ["cspline1d", "cspline1d_eval", "cspline2d", "gauss_spline", "qspline1d", "qspline1d_eval", "sepfir2d", "spline_filter"]
 

scipy-stubs/signal/filter_design.pyi

@@ -79,7 +79,7 @@ def group_delay(system: object, w: object = ..., whole: object = ..., fs: object
 @deprecated("will be removed in SciPy v2.0.0")
 def freqz_sos(sos: object, worN: object = ..., whole: object = ..., fs: object = ...) -> object: ...
 
-sosfreqz = freqz_sos  # pyright: ignore[reportDeprecated]
+sosfreqz = freqz_sos  # pyright: ignore[reportDeprecated]  # pyrefly: ignore[deprecated]
 
 @deprecated("will be removed in SciPy v2.0.0")
 def tf2zpk(b: object, a: object) -> object: ...

scipy-stubs/signal/lti_conversion.pyi

@@ -1,7 +1,7 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 from typing_extensions import deprecated
 
-from .filter_design import normalize, tf2zpk, zpk2tf
+from .filter_design import normalize, tf2zpk, zpk2tf  # pyrefly: ignore[deprecated]
 
 __all__ = ["abcd_normalize", "cont2discrete", "normalize", "ss2tf", "ss2zpk", "tf2ss", "tf2zpk", "zpk2ss", "zpk2tf"]
 

scipy-stubs/signal/ltisys.pyi

@@ -2,8 +2,8 @@
 from typing import Self
 from typing_extensions import deprecated
 
-from .filter_design import freqs, freqs_zpk, freqz, freqz_zpk, normalize, tf2zpk, zpk2tf
-from .lti_conversion import abcd_normalize, cont2discrete, ss2tf, ss2zpk, tf2ss, zpk2ss
+from .filter_design import freqs, freqs_zpk, freqz, freqz_zpk, normalize, tf2zpk, zpk2tf  # pyrefly: ignore[deprecated]
+from .lti_conversion import abcd_normalize, cont2discrete, ss2tf, ss2zpk, tf2ss, zpk2ss  # pyrefly: ignore[deprecated]
 
 __all__ = [
     "StateSpace",

scipy-stubs/signal/signaltools.pyi

@@ -1,10 +1,10 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 from typing_extensions import deprecated
 
-from .filter_design import cheby1
-from .fir_filter_design import firwin
-from .ltisys import dlti
-from .windows.windows import get_window
+from .filter_design import cheby1  # pyrefly: ignore[deprecated]
+from .fir_filter_design import firwin  # pyrefly: ignore[deprecated]
+from .ltisys import dlti  # pyrefly: ignore[deprecated]
+from .windows.windows import get_window  # pyrefly: ignore[deprecated]
 
 __all__ = [
     "cheby1",

scipy-stubs/signal/spectral.pyi

@@ -1,7 +1,7 @@
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
 from typing_extensions import deprecated
 
-from .windows.windows import get_window
+from .windows.windows import get_window  # pyrefly: ignore[deprecated]
 
 __all__ = [
     "check_COLA",

scipy-stubs/sparse/_base.pyi

@@ -126,9 +126,11 @@ _SpArrayOut: TypeAlias = bsr_array[_ScalarT] | csc_array[_ScalarT] | csr_array[_
 _ToCSRArray: TypeAlias = coo_array[_ScalarT] | csr_array[_ScalarT] | dia_array[_ScalarT] | dok_array[_ScalarT]
 _ToCSRMatrix: TypeAlias = coo_matrix[_ScalarT] | csr_matrix[_ScalarT] | dia_matrix[_ScalarT] | dok_matrix[_ScalarT]
 
-_SparseLike: TypeAlias = _T | _ScalarT | _spbase[_ScalarT]
-_To2D: TypeAlias = Sequence[Sequence[_T | _ScalarT] | onp.CanArrayND[_ScalarT]] | onp.CanArrayND[_ScalarT]
-_To2DLike: TypeAlias = Sequence[_T | _ScalarT] | _To2D[_T, _ScalarT]
+_SparseLike = TypeAliasType("_SparseLike", _T | _ScalarT | _spbase[_ScalarT], type_params=(_T, _ScalarT))
+_To2D = TypeAliasType(
+    "_To2D", Sequence[Sequence[_T | _ScalarT] | onp.CanArrayND[_ScalarT]] | onp.CanArrayND[_ScalarT], type_params=(_T, _ScalarT)
+)
+_To2DLike = TypeAliasType("_To2DLike", Sequence[_T | _ScalarT] | _To2D[_T, _ScalarT], type_params=(_T, _ScalarT))
 
 _BinOp: TypeAlias = Callable[[object, object], Any]