docs: replace sphinx-rtd-theme with sphinx-book-theme (#4266)

Compared to `sphinx-rtd-theme`, `sphinx-book-theme` is a clean and
modern Sphinx theme.

Generated by the task: njzjz-bot/njzjz-bot#11.


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Updated documentation theme to enhance visual presentation with the
new "sphinx_book_theme."
	- Introduced a new extension to manage table of contents visibility.
	- Enhanced dark mode styles for improved user experience.

- **Bug Fixes**
- Improved compatibility with documentation tools by updating
dependencies in the project configuration.
	- Updated version constraints for documentation-related dependencies.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

doc/_static/css/custom.css

@@ -11,7 +11,7 @@ pre {
 img.platform-icon {
   height: 2ex;
 }
-@media (prefers-color-scheme: dark) {
+html[data-theme="dark"] {
   .wy-side-nav-search .wy-dropdown > a img.logo,
   .wy-side-nav-search > a img.logo {
     content: url("../logo-dark.svg");

doc/conf.py

@@ -44,7 +44,7 @@
 # ones.
 # extensions = [
 #     'recommonmark',
-#     "sphinx_rtd_theme",
+#     "sphinx_book_theme",
 #     'myst_parser',
 #     'sphinx_markdown_tables',
 #     'sphinx.ext.autosummary'
@@ -53,7 +53,7 @@
 extensions = [
     "deepmodeling_sphinx",
     "dargs.sphinx",
-    "sphinx_rtd_theme",
+    "sphinx_book_theme",
     "myst_nb",
     "sphinx.ext.autosummary",
     "sphinx.ext.mathjax",
@@ -70,6 +70,7 @@
     "autoapi.extension",
     "sphinxcontrib.programoutput",
     "sphinxcontrib.moderncmakedomain",
+    "sphinx_remove_toctrees",
 ]
 
 # breathe_domain_by_extension = {
@@ -175,9 +176,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "sphinx_book_theme"
 html_logo = "_static/logo.svg"
 
+html_theme_options = {
+    "logo": {
+        "image_light": "_static/logo.svg",
+        "image_dark": "_static/logo-dark.svg",
+    }
+}
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
@@ -215,3 +222,5 @@
 napoleon_numpy_docstring = False
 
 bibtex_bibfiles = ["../CITATIONS.bib"]
+
+remove_from_toctrees = ["autoapi/**/*", "API_CC/*", "api_c/*", "api_core/*"]

pyproject.toml

@@ -89,22 +89,23 @@ test = [
 ]
 docs = [
     "sphinx>=3.1.1",
-    "sphinx_rtd_theme>=1.0.0rc1",
+    "sphinx-book-theme",
     "myst-nb>=1.0.0rc0",
     "myst-parser>=0.19.2",
     "sphinx-design",
     "breathe",
     "exhale>=0.3.7",
     "numpydoc",
     "ase",
-    "deepmodeling-sphinx>=0.1.0",
+    "deepmodeling-sphinx>=0.3.0",
     "dargs>=0.3.4",
     "sphinx-argparse<0.5.0",
     "pygments-lammps",
     "sphinxcontrib-bibtex",
     "sphinx-autoapi>=3.0.0",
     "sphinxcontrib-programoutput",
     "sphinxcontrib-moderncmakedomain",
+    "sphinx-remove-toctrees",
 ]
 lmp = [
     "lammps~=2024.8.29.1.0",