Problem with xdmf files not including paths in HDF5

[DaanVanVugt]

Hello, I am trying to run some of the included cases (which run fine) but have a problem visualising the results with Paraview (and with the included postprocessing script).

The xdmf file contains lines like

<DataItem Dimensions="2145 2" Format="HDF">V_from_tstep_0.h5</DataItem>

for every reference to DataItem, while a reference xdmf file should contain a semicolon and then a path, like this example (from https://github.com/MattH688/BERNAISE/blob/master/meshes/mf_flowfocus.xdmf#L6)

<DataItem DataType="Float" Dimensions="9617 3" Format="HDF" Precision="8">mf_flowfocus.h5:/data0</DataItem>

Opening with paraview thus leads to errors like

XDMF Error in /build/paraview/src/ParaView-v5.10.1/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfValuesHDF.cxx line 76 (Can't Open Dataset V_from_tstep_0.h5)
XDMF Error in /build/paraview/src/ParaView-v5.10.1/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfDataItem.cxx line 534 (Reading Values Failed)
XDMF Error in /build/paraview/src/ParaView-v5.10.1/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfGrid.cxx line 755 (Error in Update() of Topology)
(   4.603s) [paraview        ]      vtkXdmfReader.cxx:488    ERR| vtkXdmfReader (0x55b7cb7e40a0): Failed to read data.
(   4.675s) [paraview        ]       vtkExecutive.cxx:752    ERR| vtkPVCompositeDataPipeline (0x55b7cf2f9920): Algorithm vtkFileSeriesReader(0x55b7d40b83a0) returned failure for request: vtkInformation (0x55b7cf36bd20)

Postprocess.py

Errors related to the same problem:

python postprocess.py folder=results_charged_droplet/1/ method=plot save=True                Tue 04 Oct 2022 07:56:27 PM UTC
BERNAISE: Post-processing tool
Sought fields: All
Opening folder: results_charged_droplet/1/
Traceback (most recent call last):
  File "/home/<snip>/BERNAISE/postprocess.py", line 157, in <module>
    main()
  File "/home/<snip>/BERNAISE/postprocess.py", line 145, in main
    ts = TimeSeries(folder, sought_fields=sought_fields)
  File "/home/<snip>/BERNAISE/utilities/TimeSeries.py", line 62, in __init__
    self._load_timeseries(sought_fields)
  File "/home/<snip>/BERNAISE/utilities/TimeSeries.py", line 136, in _load_timeseries
    = parse_xdmf(xml_file, get_mesh_address=True)
  File "/home/<snip>/BERNAISE/common/io.py", line 241, in parse_xdmf
    dset_address = prop[0].text.split(":")[1]
IndexError: list index out of range

Software

name	version
BERNAISE (MattH fork)	fdeff71 (master)
BERNAISE (this repo)	aa45ae5 (master)
HDF5	1.12.2
h5py	3.7.0
dolfin	2019.1.0
python	3.10.7