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[typing] Define __all__ for modules and remove unused imports (backport #4895) (#4900)

[typing] Define __all__ for modules and remove unused imports (#4895)

* Define __all__ for modules

* Update .pre-commit-config.yaml

* Update XYDataCommands.py

* Update pyproject.toml

(cherry picked from commit f5073cb8a)

Co-authored-by: Hailin Wang <hailin.wang@connect.polyu.hk>

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