diff --git a/docs/_static/js/cli-page.js b/docs/_static/js/cli-page.js
deleted file mode 100644
index 79c86771..00000000
--- a/docs/_static/js/cli-page.js
+++ /dev/null
@@ -1,25 +0,0 @@
-(function () {
-    const pageMarker = "pfqnhktptyfdeomqabhq";
-
-    window.onload = (event) => {
-        let pTags = document.querySelectorAll("p");
-        let findMarker = Array.from(pTags).find(
-            paragraph => paragraph.textContent.includes(pageMarker)
-        );
-
-        // If the marker isn't on the page then this isn't
-        // the page we're looking for
-        if (findMarker == null) {
-            return;
-        }
-
-        // Remove first casanovo header and page marker
-        let firstHeader = document.querySelector("#casanovo > h2:first-of-type");
-        firstHeader.remove();
-        findMarker.remove();
-
-        // Change second header text content
-        let secondHeader = document.querySelector("#casanovo > h3:first-of-type");
-        secondHeader.textContent = "Casanovo CLI Commands";
-    }
-})();
\ No newline at end of file
diff --git a/docs/cli.rst b/docs/cli.rst
index e858ad6c..e8cc0edc 100644
--- a/docs/cli.rst
+++ b/docs/cli.rst
@@ -8,9 +8,3 @@ For Casanovo installation instructions, see the :doc:`Getting Started <getting_s
    :prog: casanovo
    :nested: full
    :commands: configure, evaluate, sequence, train, version
-
-..
-   This is just a random sequence of letters so the custom javascript can
-   ensure it is running on the correct page before running any filtering
-   operations
-pfqnhktptyfdeomqabhq
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
index 0d4bd677..d9785557 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -12,9 +12,10 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath("."))
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("."))
 
 
 # -- Project information -----------------------------------------------------
@@ -30,7 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
-extensions = ["myst_parser", "sphinx_click"]
+extensions = ["myst_parser", "sphinx_click", "sphinx_click_handlers"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
@@ -57,7 +58,7 @@
 # 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".
-html_static_path = ["_static"]
+# html_static_path = ["_static"]
 html_theme_options = {"repository_url": "https//github.com/Noble-Lab/casanovo"}
 
 html_js_files = [
diff --git a/docs/sphinx_click_handlers.py b/docs/sphinx_click_handlers.py
new file mode 100644
index 00000000..2948634f
--- /dev/null
+++ b/docs/sphinx_click_handlers.py
@@ -0,0 +1,9 @@
+def process_description(app, ctx, lines):
+    if ctx.command.name == "main":
+        del lines[:3]
+
+    print(lines)
+
+
+def setup(app):
+    app.connect("sphinx-click-process-description", process_description)