pyiron/pyiron_atomistics

Cell (along with other properties) cannot be accessed from `project_hdf5` in Sphinx

samwaseda opened this issue · 2 comments

samwaseda commented

pyiron_atomistics/pyiron_atomistics/atomistics/job/atomistic.py

Line 1032 in 4361b7b

return self._job.project_hdf5["output/generic/cells"]

The reason why this line fails is because Sphinx uses DataContainer and has tags like cells__index_2, which obviously is not the same as cells when it's accessed from project_hdf5. I guess this topic really requires an overhaul discussion because it's a recurring issue with no structural solution in the current format

jan-janssen commented

I have a prototype for accessing the output for Sphinx in the HDF5 file directly https://github.com/pyiron-dev/pyiron-hdf5-format

  • 🎉1
pmrv commented

You should be able to just change project_hdf5 to content in the sphinx output, then it'll be resolve the data container automatically. I added this to base some time ago, but never got to using it here.