[Code scan] Modernize deprecated pyproject metadata and Ruff settings

This issue is a result of a Codex global code scan of deepmodeling/deepmodeling_sphinx at commit 156679fe55fc61e8ec3b1e9be8a45fde3567b9cb.

Problem

Current build and lint tooling reports deprecation warnings for two `pyproject.toml` sections:

- Setuptools warns that `project.license` as a TOML table is deprecated and should be replaced before the 2027-02-18 removal window.
- Ruff warns that top-level linter settings are deprecated in favor of the `[tool.ruff.lint]` section.

Code references:

https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/pyproject.toml#L12-L12
https://github.com/deepmodeling/deepmodeling_sphinx/blob/156679fe55fc61e8ec3b1e9be8a45fde3567b9cb/pyproject.toml#L45-L48

Observed warnings

`uv build` reports that `project.license` as a TOML table is deprecated and recommends using a SPDX license expression and/or `project.license-files`.

`ruff check .` reports:

```text
warning: The top-level linter settings are deprecated in favour of their counterparts in the `lint` section.
```

Impact

These are not immediate runtime failures, but they create noisy CI output and will eventually require changes as packaging and lint tooling remove deprecated behavior.

Suggested fix

Move Ruff settings under `[tool.ruff.lint]`. Update license metadata to modern PEP 639-compatible fields supported by the chosen setuptools version, for example a SPDX expression plus license files where appropriate.