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Merged
jorgensd merged 1 commit into from
Aug 18, 2026
Merged

Various typing fixes #71

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34 changes: 17 additions & 17 deletions src/io4dolfinx/backends/__init__.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def get_default_backend_args(self, arguments: dict[str, Any] | None) -> dict[str
def write_attributes(
self,
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
attributes: dict[str, np.ndarray],
backend_args: dict[str, Any] | None,
Expand All @@ -93,7 +93,7 @@ def write_attributes(
def read_attributes(
self,
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
backend_args: dict[str, Any] | None,
) -> dict[str, Any]:
Expand All @@ -112,7 +112,7 @@ def read_attributes(
def read_timestamps(
self,
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
function_name: str,
backend_args: dict[str, Any] | None,
) -> npt.NDArray[np.float64 | str]: # type: ignore[type-var]
Expand All @@ -131,7 +131,7 @@ def read_timestamps(
def write_mesh(
self,
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
mesh: MeshData,
backend_args: dict[str, Any] | None,
mode: FileMode,
Expand All @@ -152,7 +152,7 @@ def write_mesh(
def write_meshtags(
self,
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
data: MeshTagsData,
backend_args: dict[str, Any] | None,
):
Expand All @@ -168,7 +168,7 @@ def write_meshtags(
def read_mesh_data(
self,
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
read_from_partition: bool,
backend_args: dict[str, Any] | None,
Expand All @@ -189,7 +189,7 @@ def read_mesh_data(
def read_meshtags_data(
self,
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
backend_args: dict[str, Any] | None,
) -> MeshTagsData:
Expand All @@ -208,7 +208,7 @@ def read_meshtags_data(
def read_dofmap(
self,
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
backend_args: dict[str, Any] | None,
) -> dolfinx.graph.AdjacencyList:
Expand All @@ -227,7 +227,7 @@ def read_dofmap(
def read_dofs(
self,
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
time: float,
backend_args: dict[str, Any] | None,
Expand All @@ -248,7 +248,7 @@ def read_dofs(
"""

def read_cell_perms(
self, comm: MPI.Intracomm, filename: Path | str, backend_args: dict[str, Any] | None
self, comm: MPI.Comm, filename: Path | str, backend_args: dict[str, Any] | None
) -> npt.NDArray[np.uint32]:
"""
Read cell permutation from file with given communicator,
Expand All @@ -267,7 +267,7 @@ def read_cell_perms(
def write_function(
self,
filename: Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
u: FunctionData,
time: float,
mode: FileMode,
Expand All @@ -285,7 +285,7 @@ def write_function(
"""

def read_legacy_mesh(
self, filename: Path | str, comm: MPI.Intracomm, group: str
self, filename: Path | str, comm: MPI.Comm, group: str
) -> tuple[npt.NDArray[np.int64], npt.NDArray[np.floating], str | None]:
"""Read in the mesh topology, geometry and (optionally) cell type from a
legacy DOLFIN HDF5-file.
Expand Down Expand Up @@ -320,7 +320,7 @@ def snapshot_checkpoint(

def read_hdf5_array(
self,
comm: MPI.Intracomm,
comm: MPI.Comm,
filename: Path | str,
group: str,
backend_args: dict[str, Any] | None,
Expand All @@ -344,7 +344,7 @@ def read_point_data(
self,
filename: Path | str,
name: str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
backend_args: dict[str, Any] | None,
) -> tuple[np.ndarray, int]:
Expand All @@ -362,7 +362,7 @@ def read_point_data(
...

def read_function_names(
self, filename: Path | str, comm: MPI.Intracomm, backend_args: dict[str, Any] | None
self, filename: Path | str, comm: MPI.Comm, backend_args: dict[str, Any] | None
) -> list[str]:
"""Read all function names from a file.

Expand All @@ -380,7 +380,7 @@ def read_cell_data(
self,
filename: Path | str,
name: str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
backend_args: dict[str, Any] | None,
) -> tuple[npt.NDArray[np.int64], np.ndarray]:
Expand All @@ -403,7 +403,7 @@ def write_data(
self,
filename: Path | str,
array_data: ArrayData,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
mode: FileMode,
backend_args: dict[str, Any] | None,
Expand Down
34 changes: 17 additions & 17 deletions src/io4dolfinx/backends/adios2/backend.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ def convert_file_mode(mode: FileMode) -> adios2.Mode: # type: ignore[override]

def write_attributes(
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
attributes: dict[str, np.ndarray],
backend_args: dict[str, Any] | None = None,
Expand Down Expand Up @@ -86,7 +86,7 @@ def write_attributes(

def read_attributes(
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
backend_args: dict[str, Any] | None = None,
) -> dict[str, np.ndarray]:
Expand Down Expand Up @@ -122,7 +122,7 @@ def read_attributes(

def read_timestamps(
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
function_name: str,
backend_args: dict[str, Any] | None = None,
) -> npt.NDArray[np.float64 | str]: # type: ignore[type-var]
Expand Down Expand Up @@ -169,7 +169,7 @@ def read_timestamps(

def write_mesh(
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
mesh: MeshData,
backend_args: dict[str, Any] | None = None,
mode: FileMode = FileMode.write,
Expand Down Expand Up @@ -277,7 +277,7 @@ def write_mesh(

def read_mesh_data(
filename: Path | str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None = 0.0,
read_from_partition: bool = False,
backend_args: dict[str, Any] | None = None,
Expand Down Expand Up @@ -409,7 +409,7 @@ def read_mesh_data(

def write_meshtags(
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
data: MeshTagsData,
backend_args: dict[str, Any] | None = None,
):
Expand Down Expand Up @@ -462,7 +462,7 @@ def write_meshtags(


def read_meshtags_data(
filename: str | Path, comm: MPI.Intracomm, name: str, backend_args: dict[str, Any] | None = None
filename: str | Path, comm: MPI.Comm, name: str, backend_args: dict[str, Any] | None = None
) -> MeshTagsData:
"""Read mesh tags from file.

Expand Down Expand Up @@ -600,7 +600,7 @@ def read_meshtags_data(


def read_dofmap(
filename: str | Path, comm: MPI.Intracomm, name: str, backend_args: dict[str, Any] | None = None
filename: str | Path, comm: MPI.Comm, name: str, backend_args: dict[str, Any] | None = None
) -> dolfinx.graph.AdjacencyList:
"""Read the dofmap of a function with a given name.

Expand Down Expand Up @@ -641,7 +641,7 @@ def read_dofmap(

def read_dofs(
filename: str | Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
name: str,
time: float,
backend_args: dict[str, Any] | None = None,
Expand Down Expand Up @@ -698,7 +698,7 @@ def read_dofs(


def read_cell_perms(
comm: MPI.Intracomm, filename: Path | str, backend_args: dict[str, Any] | None = None
comm: MPI.Comm, filename: Path | str, backend_args: dict[str, Any] | None = None
) -> npt.NDArray[np.uint32]:
"""
Read cell permutation from file with given communicator,
Expand Down Expand Up @@ -733,7 +733,7 @@ def read_cell_perms(


def read_hdf5_array(
comm: MPI.Intracomm,
comm: MPI.Comm,
filename: Path | str,
group: str,
backend_args: dict[str, Any] | None = None,
Expand All @@ -758,7 +758,7 @@ def read_hdf5_array(

def write_function(
filename: Path,
comm: MPI.Intracomm,
comm: MPI.Comm,
u: FunctionData,
time: float = 0.0,
mode: FileMode = FileMode.append,
Expand Down Expand Up @@ -854,7 +854,7 @@ def write_function(


def read_legacy_mesh(
filename: Path | str, comm: MPI.Intracomm, group: str
filename: Path | str, comm: MPI.Comm, group: str
) -> tuple[npt.NDArray[np.int64], npt.NDArray[np.floating], str | None]:
"""Read in the mesh topology, geometry and (optionally) cell type from a
legacy DOLFIN HDF5-file.
Expand Down Expand Up @@ -970,7 +970,7 @@ def snapshot_checkpoint(


def read_function_names(
filename: Path | str, comm: MPI.Intracomm, backend_args: dict[str, Any] | None
filename: Path | str, comm: MPI.Comm, backend_args: dict[str, Any] | None
) -> list[str]:
"""Read all function names from a file.

Expand All @@ -988,7 +988,7 @@ def read_function_names(
def read_point_data(
filename: Path | str,
name: str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: float | str | None,
backend_args: dict[str, Any] | None,
) -> tuple[np.ndarray, int]:
Expand All @@ -1010,7 +1010,7 @@ def read_point_data(
def read_cell_data(
filename: Path | str,
name: str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
backend_args: dict[str, Any] | None,
) -> tuple[npt.NDArray[np.int64], np.ndarray]:
Expand All @@ -1033,7 +1033,7 @@ def read_cell_data(
def write_data(
filename: Path | str,
array_data: ArrayData,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: str | float | None,
mode: FileMode,
backend_args: dict[str, Any] | None,
Expand Down
9 changes: 4 additions & 5 deletions src/io4dolfinx/backends/adios2/helpers.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,11 @@
from mpi4py import MPI

import adios2
import dolfinx.cpp.graph
import dolfinx.graph
import numpy as np
import numpy.typing as npt

from io4dolfinx.utils import compute_local_range, valid_function_types
from ...utils import compute_local_range, valid_function_types


def resolve_adios_scope(adios2):
Expand Down Expand Up @@ -60,7 +59,7 @@ def ADIOSFile(
engine: str,
mode: adios2.Mode,
io_name: str,
comm: MPI.Intracomm | None = None,
comm: MPI.Comm | None = None,
):
io = adios.DeclareIO(io_name)
io.SetEngine(engine)
Expand Down Expand Up @@ -118,7 +117,7 @@ def check_variable_exists(

def read_adjacency_list(
adios: adios2.ADIOS,
comm: MPI.Intracomm,
comm: MPI.Comm,
filename: Path | str,
data_name: str,
offsets_name: str,
Expand Down Expand Up @@ -221,7 +220,7 @@ def read_array(
filename: Path | str,
array_name: str,
engine: str,
comm: MPI.Intracomm,
comm: MPI.Comm,
time: float = 0.0,
time_name: str = "",
legacy: bool = False,
Expand Down
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