[Code scan] Extend Dependabot coverage beyond GitHub Actions

[njzjz]

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

Problem

Dependabot currently updates only the github-actions ecosystem. Python package dependencies, documentation dependencies, and pre-commit hooks are declared elsewhere but do not receive automated update PRs.

Code references:

deepmodeling_sphinx/.github/dependabot.yml

Lines 1 to 6 in 156679f

	version: 2
	updates:
	- package-ecosystem: "github-actions"
	directory: "/"
	schedule:
	interval: "weekly"

deepmodeling_sphinx/pyproject.toml

Lines 17 to 24 in 156679f

	dependencies = [
	'sphinx',
	'minify-html!=0.16.*,!=0.17.0',
	'jsmin',
	'cssmin',
	'jinja2',
	]
	requires-python = ">=3.7"

deepmodeling_sphinx/docs/requirements.txt

Lines 1 to 6 in 156679f

	sphinx >=4.2
	sphinx-book-theme
	.
	myst_parser
	docutils >=0.17
	numpydoc

deepmodeling_sphinx/.pre-commit-config.yaml

Lines 3 to 29 in 156679f

	repos:
	- repo: https://github.com/pre-commit/pre-commit-hooks
	rev: v6.0.0
	hooks:
	- id: trailing-whitespace
	- id: end-of-file-fixer
	- id: check-yaml
	- id: check-json
	- id: check-added-large-files
	- id: check-merge-conflict
	- id: check-symlinks
	- id: check-toml
	# Python
	- repo: https://github.com/astral-sh/ruff-pre-commit
	rev: v0.15.14
	hooks:
	- id: ruff
	args: ["--fix"]
	- id: ruff-format
	# markdown, yaml
	- repo: https://github.com/pre-commit/mirrors-prettier
	rev: v4.0.0-alpha.8
	hooks:
	- id: prettier
	types_or: [markdown, yaml, html, javascript, css]
	# workflow files cannot be modified by pre-commit.ci
	exclude: ^(\.github/workflows)

Impact

Runtime, docs, and linting dependencies can go stale without automated visibility, while workflow actions do get update coverage.

Suggested fix

Add Dependabot entries for pip dependency files and pre-commit, or document that these dependencies are intentionally maintained manually.