Added option to copy data when combining datasets

[Howuhh]

Description

Related to #56

Type of change

• New feature (non-breaking change which adds functionality)

Checklist:

• I have run the pre-commit checks with pre-commit run --all-files (see CONTRIBUTING.md instructions to set it up)
• I have run pytest -v and no errors are present.
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I solved any possible warnings that pytest -v has generated that are related to my code to the best of my knowledge.
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[Howuhh]

a bit uglier than initially, but unfortunately because of the limitations of h5py you can't do it like in the first commit

[balisujohn]

Overall, it looks good, and it seems to perform as intended, creating combined datasets that are not broken when the source datasets are deleted.

I think also it would be good to include a test that makes sure the true-copied combined dataset is still intact after deleting the source datasets.

In a future PR, I think the true copy behavior should be made the default for the combine_datasets() function, and also the default for the combine command in the cli, though it should still be possible to enable the external link combination behavior in the cli with the optional flag --external-link I think we should make there be a check to see if combined datasets depend on other datasets, because right now you can break combined datasets with no warning by deleting their dependency datasets using minari delete.

Curious to hear your thoughts on this.

[Howuhh]

@balisujohn yup, I will add the test for deletion. I think the default behavior should still be to create a link, so that it does not take up too much disk space. Usually it is still a combination of datasets for the convenience of working with them, and not to move it somewhere or delete old ones.

[balisujohn]

LGTM :^)

[balisujohn]

@Howuhh Thanks for your thoughts on this. I can understand the argument against switching to true copy as the primary method, so I'll hold off on making that change for the time being. I will make a task to add am optional command line flag to enable true copy to the cli command minari combine.