Add a dummy ProjectHDFio class for generic to_dict()

[pmrv]

DummyHDFio implements a minimal subset of methods of ProjectHDFio to allow any object implementing HasHDF or the to_hdf/from_hdf convention to write itself into it. Afterwards a plain dict of everything stored to "HDF" can be obtained by DummyHDFio.to_hdf().

>>> hdf = DummyHDFio(Project(...), '/', {})
>>> obj = MyFancyObject()
>>> obj.to_hdf(hdf)
>>> hdf.to_dict()
{...}

[pmrv]

This is code copied over from tinybase. Originally my plan was to stabilize GenericStorage over in contrib and then move things here, but seeing that we already want functionality like this in atomistics I just pulled the dummy class for now. This exact implementation I've only tested for writing DataContainers, but from my testing in tinybase I expect this to work for most hdf objects.

[pmrv]

Last two commit also added support for to_object() and some bug fixes for Atoms, i.e. you can now something like

hdf = DummyHDFio(pr, '/')
cu = pr.create.structure.bulk('Cu')
cu.to_hdf(hdf, 'my_copper')
hdf['my_copper'].to_object() == cu

or maybe more interestingly

hdf = DummyHDFio(pr, '/')
cu = pr.create.structure.bulk('Cu')
cu.to_hdf(hdf, 'my_copper')
cu_dict = hdf.to_dict()
# transfer cu_dict to another machine via some executor or channel
cu == DummyHDFio(pr, '/', cu_dict)['my_copper'].to_object()

[stale]

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