Enable Ruff E, W, F, RUF, NPY, and DTZ rules

1. In the `pre-commit` configuration file, upgrade Ruff to the latest version;
2. Enable Ruff E, W, F, RUF, NPY, and DTZ rules, i.e.
```toml
# pyproject.toml
[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "E", # errors
    "W", # warning
    "F", # pyflakes
    "RUF", # ruff
    "NPY", # numpy
    "DTZ", # datetime
]
```
3. Fix all Ruff errors.