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Add nested flag for read_dict_from_hdf() (#41)

* Represent h5io groups as nodes

* Add nested flag for read_dict_from_hdf()

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Add unit test for nested parameter

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

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