update test read write on disk

[ArneDefauw]

update unit test incremental io on disk, see https://github.com/scverse/spatialdata/pull/501#issuecomment-2016568527

[LucaMarconato]

Hi @ArneDefauw, thanks for the contribution. Is this still in draft mode? If so, what's missing? Thanks!

[ArneDefauw]

I changed status of PR, there is not really something missing, but for points, there still seem to be issues with workaround 2 ,as suggested, I am not sure if this is expected or not...

[LucaMarconato]

Thanks for reporting and for the code. The use case of wanting to overwrite lazy data is an important one and now this is considered in tests. For clarify, I have split the test into 4 subcases: workaround 1 and 2, and lazy vs non-lazy data. In this way the user can see which case to use and have some code to start with.

A few more comments:

• the error messages, now made clearer, point to a discussion (https://github.com/scverse/spatialdata/discussions/520), which currently points to the test considered in this PR, to show some code to start with.
• currently we don't allow to reload single elements, or to write the sdata/element and immediately reload it; I plan to add this in the future. Tracking it here: https://github.com/scverse/spatialdata/issues/521.
• Finally, as now it is also being clarified in the test, the workaround 2 should not be used for lazy data. It is expected for it to fail for points, images and labels. Unfortunately the approach that you suggested for workaround 2 leads to data loss. The error given for points is expected and I was surprised it was working for images and labels. I looked into it better: somehow the xarray.DataArray doesn't throw an error when it tries to load from the Zarr store that had been deleted, but if you compute the data you will see that the tensor is now a tensor of zeros.