Translate h5py soft and hard linked datasets with an optional kwarg

[ljwoods2]

Fixes #459

Linked groups can't be translated as easily as linked datasets- the h5py method visititems_links is only called once for
each link. This means that if you have this hdf5 layout for example:

/
 └── particles
     └── trajectory
         ├── box
         │   └── edges
         │       ├── step (50,) int32
         │       ├── time (50,) float32
         │       └── value (50, 3, 3) float32
         └── position
             └── value (50, 13406, 3) float32

And you try to create this hard link and translate it:

f["particles/trajectory2"] = f["particles/trajectory"]

Then visititems_links will be called on "box/edges/step", "time", and "value" during the traversal of "particles/trajectory" and therefore can't be traversed again during the traversal of "particles/trajectory2", resulting in an empty translated group. This behavior makes sense since it avoids the problem of circularly-linked groups, but it makes translating groups with h5py-builtin traversal methods difficult. If zarr-python 3.0 implements links, visititems and visititems_links may have to be replaced with custom directory traversal code as a result

This PR only allows translating linked datasets by traversing the h5py directory twice and using require_dataset instead of create_dataset to avoid duplicating non-linked groups and datasets.

[martindurant]

I'll look into the test failure, which looks unrelated. Maybe something about numpy 2, which just came out.

[martindurant]

(update: I have fixed one test failure so far, so one more to go)

[martindurant]

If you sync your branch, things should pass now.

[hmacdope]

@martindurant thanks for helping @ljwoods2 with this! This is part of his GSOC 2024 work with MDAnalysis, which I am co-supervising. With that hat on would you be able to approve the workflows here by any chance? Getting this merged would help us a lot moving forward. Let me know if I can help in any way. 😄

[martindurant]

Sorry, new commits by themselves don't send a notification. Would you like me to add a label to this PR for gsoc?

[ljwoods2]

I switched out the string version compatibility with a direct check of if the visititems_links method is present- not sure if this is the most pythonic way to do it, let me know what you think. Also integrated your other suggestions

[hmacdope]

Thanks a lot @martindurant! Appreciate your help here 👍