[Code scan] Move Ruff lint settings out of deprecated top-level keys

This issue is from a Codex global scan of the repository. Running Ruff on the repository emits deprecation warnings because the configuration still uses top-level linter keys. Newer Ruff versions expect these settings under `[tool.ruff.lint]`, and `ignore-init-module-imports` is also deprecated. Evidence: https://github.com/deepmodeling/dpgen/blob/7af52460e1a5bc0edeb5e19cf92af5a6c79f90ec/pyproject.toml#L79-L109 Observed command: ```bash ruff check dpgen tests --select F821,F822,F823 --output-format=concise ``` Observed warning: ```text warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section. warning: The `ignore-init-module-imports` option is deprecated and will be removed in a future release. ``` Expected behavior: move `select`, `ignore`, `pydocstyle`, and related lint settings into `[tool.ruff.lint]` / `[tool.ruff.lint.pydocstyle]`, and remove or replace `ignore-init-module-imports` before a future Ruff release turns this into a harder failure.