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Add tests for cli, helpers, molecule, visualization and remaining graph branches. Make Atom hashable via eq=False so Bond.atoms and Bond.__contains__ work, and skip the cli __main__ guard from coverage.
Aligns the pre-commit mypy hook with pyproject.toml's mypy.files setting so source and tests are checked the same way locally and in CI. Reverts the cast/type-ignore workarounds added in the previous commit.
test: bring coverage to 100%
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