transition documentation theme and streamline

docs/source/_static/css/dscript.css

@@ -0,0 +1,9 @@
+html[data-theme="light"] {
+    --pst-color-primary: rgb(51, 122, 44);
+    --pst-color-secondary: rgb(40, 85, 129);
+}
+
+html[data-theme="dark"] {
+    --pst-color-primary: rgb(69, 171, 60);
+    --pst-color-secondary: rgb(61, 126, 191);
+}

docs/source/api.rst

@@ -4,9 +4,6 @@ API
 .. toctree::
    :maxdepth: 4
 
-   dscript.commands
-   dscript.models
-
 dscript.alphabets
 -----------------
 
@@ -72,9 +69,33 @@ dscript.pretrained
     :show-inheritance:
 
 dscript.utils
-------------- 
+-------------
 
 .. automodule:: dscript.utils
    :members:
    :undoc-members:
    :show-inheritance:
+
+dscript.models.embedding
+------------------------
+
+.. automodule:: dscript.models.embedding
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+dscript.models.contact
+----------------------
+
+.. automodule:: dscript.models.contact
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+dscript.models.interaction
+--------------------------
+
+.. automodule:: dscript.models.interaction
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api/dscript.commands.rst

@@ -1,57 +0,0 @@
-dscript.commands
-================
-
-dscript.commands.embed
-----------------------
-
-See `Embedding <../usage.html#embedding>`_ for full usage details.
-
-.. automodule:: dscript.commands.embed
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.commands.predict
-------------------------
-
-See `Prediction <../usage.html#prediction>`_ for full usage details.
-
-.. automodule:: dscript.commands.predict_block
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-.. automodule:: dscript.commands.predict_serial
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.commands.train
-----------------------
-
-See `Training <../usage.html#training>`_ for full usage details.
-
-.. automodule:: dscript.commands.train
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.commands.evaluate
--------------------------
-
-See `Evaluation <../usage.html#evaluation>`_ for full usage details.
-
-.. automodule:: dscript.commands.evaluate
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.commands.extract_3di
-----------------------------
-
-See `Extract 3Di <../usage.html#extract_3di>`_ for full usage details.
-
-.. automodule:: dscript.commands.extract_3di
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/api/dscript.models.rst

@@ -1,26 +0,0 @@
-dscript.models
-==============
-
-dscript.models.embedding
-------------------------
-
-.. automodule:: dscript.models.embedding
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.models.contact
-----------------------
-
-.. automodule:: dscript.models.contact
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-dscript.models.interaction
---------------------------
-
-.. automodule:: dscript.models.interaction
-   :members:
-   :undoc-members:
-   :show-inheritance:

docs/source/conf.py

@@ -12,6 +12,7 @@
 #
 import os.path
 import sys
+from importlib.metadata import version as _get_version
 
 sys.path.insert(0, os.path.abspath("."))
 sys.path.insert(0, os.path.abspath("../"))
@@ -21,11 +22,10 @@ sys.path.insert(0, os.path.abspath("../../"))
 # -- Project information -----------------------------------------------------
 
 project = "D-SCRIPT"
-copyright = "2021, Samuel Sledzieski, Rohit Singh"
+copyright = "2025, Samuel Sledzieski"
-author = "Samuel Sledzieski, Rohit Singh"
+author = "Samuel Sledzieski"
 
-# The full version, including alpha/beta/rc tags
+release = _get_version("dscript")
-release = "v0.3.0"
 master_doc = "index"
 
 
@@ -39,7 +39,6 @@ extensions = [
     "sphinx.ext.viewcode",
     "sphinx.ext.autodoc",
     "sphinx.ext.mathjax",
-    "sphinx_rtd_theme",
 ]
 
 
@@ -59,13 +58,22 @@ exclude_patterns = []
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
+html_css_files = [
+    "css/dscript.css",
+]
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
 # html_theme = 'default'
-html_theme = "sphinx_rtd_theme"
+# html_theme = "sphinx_rtd_theme"
-# html_theme_options = {
+html_theme = "pydata_sphinx_theme"
-#     'logo_only':  True,
+html_theme_options = {
-# }
+    "navbar_end": ["theme-switcher"],
+    "logo": {
+        "text": "D-SCRIPT",
+    },
+}
 # html_logo = '_static/dscript_architecture1.png'
+html_context = {"default_mode": "auto"}
+html_sidebars = {"**": []}

docs/source/index.rst

@@ -31,9 +31,4 @@ Table of contents
    installation
    usage
    data
-   api/index
+   api
-
-Indices and tables
-==================
-* :ref:`genindex`
-* :ref:`modindex`

pyproject.toml

@@ -41,14 +41,10 @@ dev = [
 ]
 docs = [
     "jinja2<3.1",
-    "Sphinx==3.4",
+    "Sphinx>=5.0",
-    "sphinx-rtd-theme==1.0.0",
+    "pydata-sphinx-theme>=0.16",
-    "sphinxcontrib-applehelp==1.0.2",
+    "sphinxcontrib-jsmath",
-    "sphinxcontrib-devhelp==1.0.2",
+    "sphinxcontrib-serializinghtml",
-    "sphinxcontrib-htmlhelp==1.0.3",
-    "sphinxcontrib-jsmath==1.0.1",
-    "sphinxcontrib-qthelp==1.0.3",
-    "sphinxcontrib-serializinghtml==1.1.4",
 ]
 
 [project.urls]
@@ -99,3 +95,8 @@ python_files = "test_*.py"
 testpaths = [
     "dscript/tests",
 ]
+
+[dependency-groups]
+docs = [
+    "pydata-sphinx-theme>=0.8.0",
+]