$ PETSC_DIR=/usr/lib/petscdir/petsc-complex pytest-3 -v test_xdmf.py
=============================================================================================== test session starts ===============================================================================================
platform linux -- Python 3.13.12, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3
cachedir: .pytest_cache
Test order randomisation NOT enabled. Enable with --random-order or --random-order-bucket=<bucket_type>
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
hypothesis profile 'default'
rootdir: /projects/fenics/build/io4dolfinx
configfile: pyproject.toml
plugins: rerunfailures-16.1, remotedata-0.4.1, anyio-4.11.0, cov-5.0.0, arraydiff-0.6.1, xdist-3.8.0, mock-3.15.1, filter-subpackage-0.2.0, timeout-2.4.0, typeguard-4.4.4, xvfb-3.0.0, astropy-0.11.0, random-order-0.0.0, openfiles-0.6.0, flaky-3.8.1, benchmark-5.2.3, mpi-0.6, asyncio-1.3.0, astropy-header-0.2.2, hypothesis-6.151.5, doctestplus-1.7.1
asyncio: mode=Mode.STRICT, debug=False, asyncio_default_fixture_loop_scope=None, asyncio_default_test_loop_scope=function
collected 2 items
test_xdmf.py::test_xdmf_mesh PASSED [ 50%]
test_xdmf.py::test_xdmf_function FAILED [100%]
==================================================================================================== FAILURES =====================================================================================================
_______________________________________________________________________________________________ test_xdmf_function ________________________________________________________________________________________________
tmp_path = PosixPath('/tmp/pytest-of-me/pytest-40/test_xdmf_function0')
def test_xdmf_function(tmp_path):
tmp_path = MPI.COMM_WORLD.bcast(tmp_path, root=0)
mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 8, 10)
def f(x):
return (x[0], x[1], -2 * x[1], 3 * x[0])
V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1, (4,)))
u = dolfinx.fem.Function(V, name="u")
u.interpolate(f)
tmp_file = tmp_path / "function.xdmf"
with dolfinx.io.XDMFFile(MPI.COMM_WORLD, tmp_file, "w") as xdmf:
xdmf.write_mesh(mesh)
xdmf.write_function(u)
MPI.COMM_WORLD.barrier()
in_grid = io4dolfinx.read_mesh(tmp_file, MPI.COMM_WORLD, backend="xdmf")
names = io4dolfinx.read_function_names(
tmp_file, MPI.COMM_WORLD, backend_args={}, backend="xdmf"
)
assert len(names) == 1
assert names[0] == "u"
> u = io4dolfinx.read_point_data(tmp_file, "u", in_grid, backend="xdmf")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
test_xdmf.py:64:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3/dist-packages/io4dolfinx/readers.py:402: in read_point_data
dataset, local_range_start = backend_cls.read_point_data(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
filename = PosixPath('/tmp/pytest-of-me/pytest-40/test_xdmf_function0/function.xdmf'), name = 'u', comm = <mpi4py.MPI.Intracomm object at 0x7fb87a440540>, time = None, backend_args = {}
def read_point_data(
filename: Path | str,
name: str,
comm: MPI.Intracomm,
time: float | str | None,
backend_args: dict[str, Any] | None,
) -> tuple[np.ndarray, int]:
"""Read data from the nodes of a mesh.
Args:
filename: Path to file
name: Name of point data
comm: Communicator to launch IO on.
time: The time stamp
backend_args: The backend arguments
Returns:
Data local to process (contiguous, no mpi comm) and local start range
"""
# Find function with name u in xml tree
check_file_exists(filename)
filename = Path(filename)
tree = ElementTree.parse(filename)
root = tree.getroot()
backend_args = get_default_backend_args(backend_args)
if time is not None:
time_steps = root.findall(f".//Grid[@Name='{name}']")
time_found = False
for time_node in time_steps:
step_node = time_node.find(".//Time")
assert isinstance(step_node, ElementTree.Element)
if step_node.attrib["Value"] == time:
time_found = True
break
func_node = time_node.find(f".//Attribute[@Name='{name}']")
if not time_found:
raise RuntimeError(f"Function {name} at time={time} not found in {filename}")
else:
func_node = root.find(f".//Attribute[@Name='{name}']")
> assert isinstance(func_node, ElementTree.Element)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
E AssertionError
/usr/lib/python3/dist-packages/io4dolfinx/backends/xdmf/backend.py:134: AssertionError
============================================================================================= short test summary info =============================================================================================
FAILED test_xdmf.py::test_xdmf_function - AssertionError
=========================================================================================== 1 failed, 1 passed in 0.27s ===========================================================================================
test_xdmf_function in test_xdmf.py fails with dolfinx built with complex numbers
Is this expected?