From 572d534692b00161e7dae78db43ecaed9eb6de28 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 11 Oct 2024 11:16:40 -0700
Subject: [PATCH 1/4] Restore attached flyout
MIME-Version: 1.0
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sphinx-rtd-theme 3.0.0 changed the default behavior to hide this flyout
in favor of the Read the Docs flyout which was enabled by default along
with the 3.0.0 release.¹ I'll plan to disable the RTD flyout on the RTD
dashboard when this commit makes its way into RTD-hosted builds.

¹ https://about.readthedocs.com/blog/2024/07/addons-by-default/
---
 doc/conf.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/conf.py b/doc/conf.py
index a81120b..42257bc 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -48,3 +48,7 @@
 # a list of builtin themes.
 #
 html_theme = 'nextstrain-sphinx-theme'
+
+html_theme_options = {
+    'flyout_display': 'attached',
+}
\ No newline at end of file

From 8866eba5ebde40149eaa5707a78402a44fc84c0e Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 11 Oct 2024 11:49:49 -0700
Subject: [PATCH 2/4] fixup! Restore attached flyout

---
 doc/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/conf.py b/doc/conf.py
index 42257bc..3a2ab1f 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -51,4 +51,4 @@
 
 html_theme_options = {
     'flyout_display': 'attached',
-}
\ No newline at end of file
+}

From f9e97c383ca2dc11d6f85205d2bf911d5ba11c5a Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 11 Oct 2024 11:50:00 -0700
Subject: [PATCH 3/4] =?UTF-8?q?=F0=9F=9A=A7=20add=20section=20for=20Read?=
 =?UTF-8?q?=20the=20Docs=20configuration?=
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Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 doc/conf.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/doc/conf.py b/doc/conf.py
index 3a2ab1f..5ab6318 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -52,3 +52,14 @@
 html_theme_options = {
     'flyout_display': 'attached',
 }
+
+# -- Read the Docs configuration ---------------------------------------------
+
+# Define the canonical URL if you are using a custom domain on Read the Docs
+html_baseurl = os.environ.get("READTHEDOCS_CANONICAL_URL", "")
+
+# Tell Jinja2 templates the build is running on Read the Docs
+if os.environ.get("READTHEDOCS", "") == "True":
+    if "html_context" not in globals():
+        html_context = {}
+    html_context["READTHEDOCS"] = True

From 1c874d188788e3779b873b5f4aac3ecb681469bb Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 11 Oct 2024 11:55:05 -0700
Subject: [PATCH 4/4] Remove script block on RTD JS injection
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

RTD no longer adds its own JS on new builds as of October 7, 2024.¹

¹ https://about.readthedocs.com/blog/2024/07/addons-by-default/
---
 lib/nextstrain/sphinx/theme/layout.html | 46 -------------------------
 1 file changed, 46 deletions(-)

diff --git a/lib/nextstrain/sphinx/theme/layout.html b/lib/nextstrain/sphinx/theme/layout.html
index a5c9db2..edec100 100644
--- a/lib/nextstrain/sphinx/theme/layout.html
+++ b/lib/nextstrain/sphinx/theme/layout.html
@@ -69,49 +69,3 @@
 {% include "searchbox.html" %}
 
 {% endblock %}
-
-
-{% block extrabody %}
-  <!--
-    Lie about what theme we really are when some RTD-injected JS fetches the
-    full versions panel from the RTD API.  RTD's JS replaces the stub versions
-    panel in the Sphinx-generated HTML with the full versions panel it fetches
-    from the RTD API.  If the API thinks we're not sphinx_rtd_theme, it will
-    serve us the wrong HTML and the panel will float as a "badge" when it
-    shouldn't.  As a customized version of sphinx_rtd_theme, we really do want
-    the same HTML it gets.  See also the diagnoses in
-    <https://github.com/nextstrain/docs.nextstrain.org/issues/76>.
-
-    This bit of JS finds the data RTD injects into the page and modifies it
-    before the code that RTD injects runs and looks at the data.  RTD's
-    <script>s (in <head>) run before this JS, but they wait until the DOM is
-    ready to actually do any work.  This gives us a chance to modify the data
-    during DOM load before the RTD code actually uses it.
-
-      -trs, 27 Jan 2022
-  -->
-  <script>
-    (() => {
-      try {
-        console.log("Lying about the theme to RTD's JS so the versions panel works properly. 🙈");
-
-        /* Update global variable, which is used in the request to get the RTD
-         * "footer" that includes the versions panel.
-         */
-        if (window.READTHEDOCS_DATA)
-          window.READTHEDOCS_DATA.theme = "sphinx_rtd_theme";
-
-        /* Update stored JSON in case anything else deserializes it later.
-         * Comments in the RTD-injected HTML source claim the global variable
-         * above is deprecated.
-         */
-        var script = document.querySelector("#READTHEDOCS_DATA");
-        if (script)
-          script.innerHTML = JSON.stringify({ ...JSON.parse(script.innerHTML), theme: "sphinx_rtd_theme" });
-      }
-      catch (err) {
-        console.log("Lying about the theme to RTD's JS failed… oh well. 🤷", err);
-      }
-    })();
-  </script>
-{% endblock %}