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

pyiron / pyiron_atomistics

pyiron_atomistics - an integrated development environment (IDE) for atomistic simulation in computational materials science.

https://pyiron-atomistics.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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Cell (along with other properties) cannot be accessed from `project_hdf5` in Sphinx #1508

Open samwaseda opened 1 month ago

samwaseda commented 1 month ago

https://github.com/pyiron/pyiron_atomistics/blob/4361b7b02f89148e249aac04d17dd6eeffdd1bff/pyiron_atomistics/atomistics/job/atomistic.py#L1032

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 1 month ago

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

pmrv commented 1 month ago

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.