Attempt at automatic typing for basix (#526)

* Not tested

* mypy passes on basix module

* Add __version__ to pyi file

* types should no longer be needed in wrapper docs

* remove types from template

* mypy checks

* remove pip install ffcx

* |

* mypy checks

* types

Co-authored-by: Matthew Scroggs <[email protected]>

Author: jhale

.github/workflows/dolfin-tests.yml

@@ -61,10 +61,6 @@ jobs:
           python3 -m pip install git+https://github.com/FEniCS/ufl.git@${{ github.event.inputs.ufl_branch }}
           python3 -m pip install git+https://github.com/FEniCS/ffcx.git@${{ github.event.inputs.ffcx_branch }}
 
-      - name: Run cpp demos
-        run: |
-          python3 -m pytest demo/cpp/test.py
-
       - name: Get DOLFINx
         if: github.event_name != 'workflow_dispatch'
         uses: actions/checkout@v3
@@ -78,14 +74,16 @@ jobs:
           path: ./dolfinx
           repository: FEniCS/dolfinx
           ref: ${{ github.event.inputs.dolfinx_branch }}
-
       - name: Install DOLFINx
         run: |
           cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build -S dolfinx/cpp/
           cmake --build build
           cmake --install build
           python3 -m pip -v install --global-option build --global-option --debug dolfinx/python/
 
+      - name: Run mypy checks
+        run: python3 -m mypy dolfinx/python/dolfinx
+
       - name: Build DOLFINx C++ unit tests
         run: |
           cmake -G Ninja -DCMAKE_BUILD_TYPE=Developer -B build/test/ -S build/test/

.github/workflows/ffcx-tests.yml

@@ -56,6 +56,11 @@ jobs:
           repository: FEniCS/ffcx
           ref: ${{ github.event.inputs.ffcx_branch }}
 
+      - name: Run mypy checks
+        run: |
+          python -m pip install mypy types-setuptools
+          python -m mypy ffcx/ffcx
+
       - name: Install FFCx
         run: pip install ./ffcx[ci]
       - name: Run FFCx tests

cpp/docs.template

@@ -113,7 +113,6 @@ def get_docstring(matches):
         return "\n".join(doclines)
 
     if info_type == "param":
-        assert typename is not None
         params = {}
         for i in doc.split("@param")[1:]:
             i = i.split("@return")[0]
@@ -127,16 +126,15 @@ def get_docstring(matches):
                 p = i
                 pdoc = "TODO: document this"
             params[p] = "\n        ".join(pdoc.split("\n"))
-        return f"{info} ({typename}): {params[info]}"
+        return f"{info}: {params[info]}"
 
     if info_type == "return":
-        assert typename is not None
         returns = [i.split("@param")[0].strip() for i in doc.split("@return")[1:]]
         if len(returns) == 0:
             returns.append("TODO: document this")
         assert len(returns) == 1
         returns = "\n    ".join(returns[0].split("\n"))
-        return f"{typename}: {returns}"
+        return f"{returns}"
 
 
 def generate_docs():

cpp/generate_docs.py

@@ -0,0 +1,331 @@
+from typing import Any, ClassVar, List, Tuple
+
+from typing import overload
+import numpy
+
+import numpy.typing as npt
+
+__version__: str = ...
+
+class CellType:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    hexahedron: ClassVar[CellType] = ...
+    interval: ClassVar[CellType] = ...
+    point: ClassVar[CellType] = ...
+    prism: ClassVar[CellType] = ...
+    pyramid: ClassVar[CellType] = ...
+    quadrilateral: ClassVar[CellType] = ...
+    tetrahedron: ClassVar[CellType] = ...
+    triangle: ClassVar[CellType] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class DPCVariant:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    diagonal_equispaced: ClassVar[DPCVariant] = ...
+    diagonal_gll: ClassVar[DPCVariant] = ...
+    horizontal_equispaced: ClassVar[DPCVariant] = ...
+    horizontal_gll: ClassVar[DPCVariant] = ...
+    legendre: ClassVar[DPCVariant] = ...
+    simplex_equispaced: ClassVar[DPCVariant] = ...
+    simplex_gll: ClassVar[DPCVariant] = ...
+    unset: ClassVar[DPCVariant] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class ElementFamily:
+    __members__: ClassVar[dict] = ...  # read-only
+    BDM: ClassVar[ElementFamily] = ...
+    CR: ClassVar[ElementFamily] = ...
+    DPC: ClassVar[ElementFamily] = ...
+    HHJ: ClassVar[ElementFamily] = ...
+    Hermite: ClassVar[ElementFamily] = ...
+    N1E: ClassVar[ElementFamily] = ...
+    N2E: ClassVar[ElementFamily] = ...
+    P: ClassVar[ElementFamily] = ...
+    RT: ClassVar[ElementFamily] = ...
+    Regge: ClassVar[ElementFamily] = ...
+    __entries: ClassVar[dict] = ...
+    bubble: ClassVar[ElementFamily] = ...
+    custom: ClassVar[ElementFamily] = ...
+    serendipity: ClassVar[ElementFamily] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class FiniteElement:
+    def __hash__(self, object, int): ClassVar[None] = ...
+    def __init__(self, *args, **kwargs) -> None: ...
+    def apply_dof_transformation(self, arg0: npt.NDArray[numpy.float64], arg1: int, arg2: int) -> npt.NDArray[numpy.float64]: ...
+    def apply_dof_transformation_to_transpose(self, arg0: npt.NDArray[numpy.float64], arg1: int, arg2: int) -> npt.NDArray[numpy.float64]: ...
+    def apply_inverse_transpose_dof_transformation(self, arg0: npt.NDArray[numpy.float64], arg1: int, arg2: int) -> npt.NDArray[numpy.float64]: ...
+    def base_transformations(self) -> npt.NDArray[numpy.float64]: ...
+    def entity_transformations(self) -> dict: ...
+    def get_tensor_product_representation(self) -> List[Tuple[List[FiniteElement],List[int]]]: ...
+    def pull_back(self, arg0: npt.NDArray[numpy.float64], arg1: npt.NDArray[numpy.float64], arg2: npt.NDArray[numpy.float64], arg3: npt.NDArray[numpy.float64]) -> npt.NDArray[numpy.float64]: ...
+    def push_forward(self, arg0: npt.NDArray[numpy.float64], arg1: npt.NDArray[numpy.float64], arg2: npt.NDArray[numpy.float64], arg3: npt.NDArray[numpy.float64]) -> npt.NDArray[numpy.float64]: ...
+    def tabulate(self, arg0: int, arg1: npt.NDArray[numpy.float64]) -> npt.NDArray[numpy.float64]: ...
+    def __eq__(self, arg0: object) -> bool: ...
+    @property
+    def M(self) -> List[List[npt.NDArray[numpy.float64]]]: ...
+    @property
+    def cell_type(self) -> CellType: ...
+    @property
+    def coefficient_matrix(self) -> npt.NDArray[numpy.float64]: ...
+    @property
+    def degree(self) -> int: ...
+    @property
+    def dim(self) -> int: ...
+    @property
+    def discontinuous(self) -> bool: ...
+    @property
+    def dof_transformations_are_identity(self) -> bool: ...
+    @property
+    def dof_transformations_are_permutations(self) -> bool: ...
+    @property
+    def dpc_variant(self) -> Any: ...
+    @property
+    def dual_matrix(self) -> npt.NDArray[numpy.float64]: ...
+    @property
+    def entity_closure_dofs(self) -> List[List[List[int]]]: ...
+    @property
+    def entity_dofs(self) -> List[List[List[int]]]: ...
+    @property
+    def family(self) -> ElementFamily: ...
+    @property
+    def has_tensor_product_factorisation(self) -> bool: ...
+    @property
+    def highest_complete_degree(self) -> int: ...
+    @property
+    def highest_degree(self) -> int: ...
+    @property
+    def interpolation_is_identity(self) -> bool: ...
+    @property
+    def interpolation_matrix(self) -> npt.NDArray[numpy.float64]: ...
+    @property
+    def interpolation_nderivs(self) -> int: ...
+    @property
+    def lagrange_variant(self) -> Any: ...
+    @property
+    def map_type(self) -> MapType: ...
+    @property
+    def num_entity_closure_dofs(self) -> List[List[int]]: ...
+    @property
+    def num_entity_dofs(self) -> List[List[int]]: ...
+    @property
+    def points(self) -> npt.NDArray[numpy.float64]: ...
+    @property
+    def value_shape(self) -> List[int]: ...
+    @property
+    def value_size(self) -> int: ...
+    @property
+    def wcoeffs(self) -> npt.NDArray[numpy.float64]: ...
+    @property
+    def x(self) -> List[List[npt.NDArray[numpy.float64]]]: ...
+
+class LagrangeVariant:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    chebyshev_centroid: ClassVar[LagrangeVariant] = ...
+    chebyshev_isaac: ClassVar[LagrangeVariant] = ...
+    chebyshev_warped: ClassVar[LagrangeVariant] = ...
+    equispaced: ClassVar[LagrangeVariant] = ...
+    gl_centroid: ClassVar[LagrangeVariant] = ...
+    gl_isaac: ClassVar[LagrangeVariant] = ...
+    gl_warped: ClassVar[LagrangeVariant] = ...
+    gll_centroid: ClassVar[LagrangeVariant] = ...
+    gll_isaac: ClassVar[LagrangeVariant] = ...
+    gll_warped: ClassVar[LagrangeVariant] = ...
+    legendre: ClassVar[LagrangeVariant] = ...
+    unset: ClassVar[LagrangeVariant] = ...
+    vtk: ClassVar[LagrangeVariant] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class LatticeSimplexMethod:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    centroid: ClassVar[LatticeSimplexMethod] = ...
+    isaac: ClassVar[LatticeSimplexMethod] = ...
+    none: ClassVar[LatticeSimplexMethod] = ...
+    warp: ClassVar[LatticeSimplexMethod] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class LatticeType:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    chebyshev: ClassVar[LatticeType] = ...
+    equispaced: ClassVar[LatticeType] = ...
+    gl: ClassVar[LatticeType] = ...
+    gll: ClassVar[LatticeType] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class MapType:
+    __members__: ClassVar[dict] = ...  # read-only
+    L2Piola: ClassVar[MapType] = ...
+    __entries: ClassVar[dict] = ...
+    contravariantPiola: ClassVar[MapType] = ...
+    covariantPiola: ClassVar[MapType] = ...
+    doubleContravariantPiola: ClassVar[MapType] = ...
+    doubleCovariantPiola: ClassVar[MapType] = ...
+    identity: ClassVar[MapType] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class PolynomialType:
+    __members__: ClassVar[dict] = ...  # read-only
+    __entries: ClassVar[dict] = ...
+    legendre: ClassVar[PolynomialType] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+class QuadratureType:
+    __members__: ClassVar[dict] = ...  # read-only
+    Default: ClassVar[QuadratureType] = ...
+    __entries: ClassVar[dict] = ...
+    gauss_jacobi: ClassVar[QuadratureType] = ...
+    gll: ClassVar[QuadratureType] = ...
+    xiao_gimbutas: ClassVar[QuadratureType] = ...
+    def __init__(self, value: int) -> None: ...
+    def __eq__(self, other: object) -> bool: ...
+    def __getstate__(self) -> int: ...
+    def __hash__(self) -> int: ...
+    def __index__(self) -> int: ...
+    def __int__(self) -> int: ...
+    def __ne__(self, other: object) -> bool: ...
+    def __setstate__(self, state: int) -> None: ...
+    @property
+    def name(self) -> str: ...
+    @property
+    def value(self) -> int: ...
+
+def cell_facet_jacobians(arg0: CellType) -> npt.NDArray[numpy.float64]: ...
+def cell_facet_normals(arg0: CellType) -> npt.NDArray[numpy.float64]: ...
+def cell_facet_orientations(arg0: CellType) -> List[bool]: ...
+def cell_facet_outward_normals(arg0: CellType) -> npt.NDArray[numpy.float64]: ...
+def cell_facet_reference_volumes(arg0: CellType) -> npt.NDArray[numpy.float64]: ...
+def cell_volume(arg0: CellType) -> float: ...
+def compute_interpolation_operator(arg0: FiniteElement, arg1: FiniteElement) -> npt.NDArray[numpy.float64]: ...
+def create_custom_element(arg0: CellType, arg1: List[int], arg2: npt.NDArray[numpy.float64], arg3: List[List[npt.NDArray[numpy.float64]]], arg4: List[List[npt.NDArray[numpy.float64]]], arg5: int, arg6: MapType, arg7: bool, arg8: int, arg9: int) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: bool) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: LagrangeVariant, arg4: bool) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: DPCVariant, arg4: bool) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: LagrangeVariant, arg4: DPCVariant, arg5: bool) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: LagrangeVariant) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: DPCVariant) -> FiniteElement: ...
+@overload
+def create_element(arg0: ElementFamily, arg1: CellType, arg2: int, arg3: LagrangeVariant, arg4: DPCVariant) -> FiniteElement: ...
+@overload
+def create_lattice(arg0, arg1: int, arg2: LatticeType, arg3: bool) -> npt.NDArray[numpy.float64]: ...
+@overload
+def create_lattice(arg0, arg1: int, arg2: LatticeType, arg3: bool, arg4: LatticeSimplexMethod) -> npt.NDArray[numpy.float64]: ...
+def geometry(arg0) -> npt.NDArray[numpy.float64]: ...
+@overload
+def index(arg0: int) -> int: ...
+@overload
+def index(arg0: int, arg1: int) -> int: ...
+@overload
+def index(arg0: int, arg1: int, arg2: int) -> int: ...
+@overload
+def make_quadrature(arg0: QuadratureType, arg1: CellType, arg2: int) -> Tuple[npt.NDArray[numpy.float64],npt.NDArray[numpy.float64]]: ...
+@overload
+def make_quadrature(arg0: CellType, arg1: int) -> Tuple[npt.NDArray[numpy.float64],npt.NDArray[numpy.float64]]: ...
+def sub_entity_connectivity(arg0) -> List[List[List[List[int]]]]: ...
+def sub_entity_geometry(arg0, arg1: int, arg2: int) -> npt.NDArray[numpy.float64]: ...
+def tabulate_polynomial_set(arg0: CellType, arg1: int, arg2: int, arg3: npt.NDArray[numpy.float64]) -> npt.NDArray[numpy.float64]: ...
+def tabulate_polynomials(arg0: PolynomialType, arg1, arg2: int, arg3: npt.NDArray[numpy.float64]) -> npt.NDArray[numpy.float64]: ...
+@overload
+def topology(arg0) -> List[List[List[int]]]: ...
+@overload
+def topology(vertexindices) -> Any: ...