Reorganize documentation to use the PyData theme

althonos · Aug 26, 2024 · 2b074b7 · 2b074b7
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diff --git a/docs/_static/css/main.css b/docs/_static/css/main.css
@@ -2,13 +2,13 @@ p {
     text-align: justify;
 }
 
-.admonition-references p {
-    text-align: left;
-}
-
-.sig-name {
+/* a.reference strong {
+    font-weight: bold;
+    font-size: 90%;
     color: #c7254e;
-}
+    box-sizing: border-box;
+    font-family: Menlo,Monaco,Consolas,"Courier New",monospace;
+} */
 
 .field-list a.reference {
     font-weight: bold;

diff --git a/docs/_static/js/apitoc.js b/docs/_static/js/apitoc.js
diff --git a/docs/_static/js/custom-icon.js b/docs/_static/js/custom-icon.js
@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * Set a custom icon for pypi as it's not available in the fa built-in brands
+ */
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "pypi",
+    icon: [
+      17.313, // viewBox width
+      19.807, // viewBox height
+      [], // ligature
+      "e001", // unicode codepoint - private use area
+      "m10.383 0.2-3.239 1.1769 3.1883 1.1614 3.239-1.1798zm-3.4152 1.2411-3.2362 1.1769 3.1855 1.1614 3.2369-1.1769zm6.7177 0.00281-3.2947 1.2009v3.8254l3.2947-1.1988zm-3.4145 1.2439-3.2926 1.1981v3.8254l0.17548-0.064132 3.1171-1.1347zm-6.6564 0.018325v3.8247l3.244 1.1805v-3.8254zm10.191 0.20931v2.3137l3.1777-1.1558zm3.2947 1.2425-3.2947 1.1988v3.8254l3.2947-1.1988zm-8.7058 0.45739c0.00929-1.931e-4 0.018327-2.977e-4 0.027485 0 0.25633 0.00851 0.4263 0.20713 0.42638 0.49826 1.953e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36226 0.13215-0.65608-0.073306-0.65613-0.4588-6.28e-5 -0.38556 0.2938-0.80504 0.65613-0.93662 0.068422-0.024919 0.13655-0.038114 0.20156-0.039466zm5.2913 0.78369-3.2947 1.1988v3.8247l3.2947-1.1981zm-10.132 1.239-3.2362 1.1769 3.1883 1.1614 3.2362-1.1769zm6.7177 0.00213-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2439-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.016195v3.8275l3.244 1.1805v-3.8254zm16.9 0.21143-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm-3.4124 1.2432-3.2947 1.1988v3.8254l3.2947-1.1988zm-6.6585 0.019027v3.8247l3.244 1.1805v-3.8254zm13.485 1.4497-3.2947 1.1988v3.8247l3.2947-1.1981zm-3.4145 1.2411-3.2926 1.2016v3.8247l3.2926-1.2009zm2.4018 0.38127c0.0093-1.83e-4 0.01833-3.16e-4 0.02749 0 0.25633 0.0085 0.4263 0.20713 0.42638 0.49826 1.97e-4 0.38532-0.29327 0.80469-0.65542 0.93662-0.36188 0.1316-0.65525-0.07375-0.65542-0.4588-1.95e-4 -0.38532 0.29328-0.80469 0.65542-0.93662 0.06842-0.02494 0.13655-0.03819 0.20156-0.03947zm-5.8142 0.86403-3.244 1.1805v1.4201l3.244 1.1805z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "sword",
+    icon: [
+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e002", // unicode codepoint - private use area
+      "M221.65723,34.34326A8.00246,8.00246,0,0,0,216,32h-.02539l-63.79883.20117A8.00073,8.00073,0,0,0,146.0332,35.106L75.637,120.32275,67.31348,111.999A16.02162,16.02162,0,0,0,44.68555,112L32.001,124.68555A15.99888,15.99888,0,0,0,32,147.31348l20.88672,20.88769L22.94531,198.14258a16.01777,16.01777,0,0,0,.001,22.62695l12.28418,12.28418a16.00007,16.00007,0,0,0,22.62793,0L87.79883,203.1123,108.68652,224.001A16.02251,16.02251,0,0,0,131.31445,224L143.999,211.31445A15.99888,15.99888,0,0,0,144,188.68652l-8.32324-8.32324,85.21679-70.39648a8.00125,8.00125,0,0,0,2.90528-6.14258L224,40.02539A8.001,8.001,0,0,0,221.65723,34.34326Zm-13.84668,65.67822-83.49829,68.97706L111.314,156l54.34327-54.34277a8.00053,8.00053,0,0,0-11.31446-11.31446L100,144.686,87.00195,131.6875,155.97852,48.189l51.99609-.16357Z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
+
+FontAwesome.library.add(
+  (faListOldStyle = {
+    prefix: "fa-custom",
+    iconName: "knife",
+    icon: [
+      256, // viewBox width
+      256, // viewBox height
+      [], // ligature
+      "e003", // unicode codepoint - private use area
+      "M231.79883,32.2002a28.05536,28.05536,0,0,0-39.667.06933L18.27441,210.41211a8,8,0,0,0,3.92676,13.38281,155.06019,155.06019,0,0,0,34.957,4.00293c33.4209-.001,66.877-10.86914,98.32813-32.1748,31.74512-21.50391,50.14551-45.79981,50.91406-46.82325a8.00114,8.00114,0,0,0-.74316-10.457L186.919,119.60547l44.97753-47.90332A28.03445,28.03445,0,0,0,231.79883,32.2002ZM189.207,144.52148a225.51045,225.51045,0,0,1-43.10351,38.13184c-34.46973,23.23145-69.999,32.665-105.83887,28.13477l106.29492-108.915,23.30176,23.30175q.208.22852.43847.44434l.082.07617Z", // svg path (https://simpleicons.org/icons/pypi.svg)
+    ],
+  }),
+);
diff --git a/docs/_static/js/example-admonition.js b/docs/_static/js/example-admonition.js
diff --git a/docs/_static/json/switcher.json b/docs/_static/json/switcher.json
@@ -0,0 +1,17 @@
+[
+    {
+        "name": "v0.3 (latest)",
+        "version": "0.3.2",
+        "url": "https://peptides.readthedocs.io/en/v0.3.1/"
+    },
+    {
+        "name": "v0.2",
+        "version": "0.2.1",
+        "url": "https://peptides.readthedocs.io/en/v0.2.1/"
+    },
+    {
+        "name": "v0.1",
+        "version": "0.1.0",
+        "url": "https://peptides.readthedocs.io/en/v0.1.0/"
+    }
+]
diff --git a/docs/api.rst → docs/api/descriptors.rst b/docs/api.rst → docs/api/descriptors.rst
@@ -1,16 +1,7 @@
-API Reference
-=============
-
-Peptide
--------
-
-.. autoclass:: peptides.Peptide(typing.Sequence[str])
-   :special-members: __init__
-   :members:
-
-
 Descriptors
------------
+===========
+
+.. currentmodule:: peptides
 
 .. autoclass:: peptides.BLOSUMIndices(typing.NamedTuple)
 
@@ -42,4 +33,4 @@ Descriptors
 
 .. autoclass:: peptides.VSTPVDescriptors(typing.NamedTuple)
 
-.. autoclass:: peptides.ZScales(typing.NamedTuple)
+.. autoclass:: peptides.ZScales(typing.NamedTuple)
diff --git a/docs/api/index.rst b/docs/api/index.rst
@@ -0,0 +1,52 @@
+API Reference
+=============
+
+.. currentmodule:: peptides
+
+Peptide
+-------
+
+.. autosummary::
+
+   Peptide
+
+.. toctree::
+   :caption: Peptide
+   :maxdepth: 1
+   :hidden:
+
+   peptide
+
+
+Descriptors
+-----------
+
+.. autosummary::
+
+   BLOSUMIndices
+   CrucianiProperties
+   FasgaiVectors
+   KideraFactors
+   MSWHIMScores
+   PhysicalDescriptors
+   PCPDescriptors
+   PRINComponents
+   ProtFPDescriptors
+   SneathVectors
+   STScales
+   SVGERDescriptors
+   TScales
+   VHSEScales
+   VSTPVDescriptors
+   ZScales
+
+
+.. toctree::
+   :caption: Descriptors
+   :maxdepth: 1
+   :hidden:
+
+   descriptors
+
+
+
diff --git a/docs/api/peptide.rst b/docs/api/peptide.rst
@@ -0,0 +1,6 @@
+Peptide
+=======
+
+.. currentmodule:: peptides
+
+.. autoclass:: peptides.Peptide(object)
diff --git a/docs/changes.md b/docs/changes.md