improvement: add `Atoms.clone()` and `remove sites by indices`, including in-place. Use `develop` branch for the PR.

[timurbazhirov]

@knc6 The action is awaiting approval to run, it seems:

[knc6]

Could you try the following: pip install black black -l 79 jarvis/core/atoms.py (and any other files you modified) add, commit,push

[timurbazhirov]

OK, should be done now. We can also consider a pre-commit hook to lint before each commit similar to https://github.com/Exabyte-io/express/blob/dev/.pre-commit-config.yaml.

[knc6]

I found a couple of issues with the PR, which should be resolved by now: 1) for numpy array, simple assert doesnt work e.g. np.testing.assert_array_equal(Si2.coords, Si.coords) is needed, 2) for remove_sies_by_indices there was a not statement missing in the if statement.

[timurbazhirov]