update docs

epifluidlab · Aug 11, 2024 · a15a15e · a15a15e
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diff --git a/_sources/documentation/user_guide/features.rst.txt b/_sources/documentation/user_guide/features.rst.txt
@@ -2,7 +2,7 @@
 Features
 =========================================
 
-**FinaleToolkit** has support for the following cell-free DNA features:
+**FinaleToolkit** has support for the following cell-free DNA fragmentomic features:
 
 
 -----------------------

diff --git a/_sources/documentation/user_guide/quickstart.rst.txt b/_sources/documentation/user_guide/quickstart.rst.txt
@@ -25,9 +25,9 @@ FinaleToolkit has the following modules:
 * `cli` - command line interface
 * `utils` - utilities that simplify feature generation
 
-You can load *all* of the functions by using the following command::
+You can load *all* fragmentomics functions by using the following command::
 
-    >>> import finaletoolkit as ft
+    >>> import finaletoolkit.frag as ft
     
 If you want to load a *specific* function, you can do so by using the following:
 

diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -12,6 +12,7 @@ FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) is a package and
 - **PyPI:** https://pypi.org/project/finaletoolkit/
 - **Documentation:** https://epifluidlab.github.io/finaletoolkit-docs/documentation
 - **Source code:** https://github.com/epifluidlab/finaletoolkit
+- **Changelog:** https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md
 - **Bug reports:** https://github.com/epifluidlab/finaletoolkit/issues
 
 

diff --git a/_static/basic.css b/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/_static/doctools.js b/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

diff --git a/_static/language_data.js b/_static/language_data.js
@@ -5,15 +5,15 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer