From 3aca041c35810bdb121115c42237c79bf795f403 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 16 Dec 2025 14:35:00 +0000
Subject: [PATCH 1/3] Initial plan


From fae42296f24d0a2af8c6a0277e5999ba1326b7ba Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 16 Dec 2025 14:38:54 +0000
Subject: [PATCH 2/3] Add back sphinx-hoverxref extension and settings

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
---
 docs/requirements.txt          |  3 ++-
 docs/source/_static/custom.css | 14 ++++++++++++++
 docs/source/conf.py            |  8 +++++++-
 requirements.txt               |  1 +
 4 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 9e442f60c..e4ebc86fe 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,8 +1,9 @@
 # Updated to use latest compatible versions as of December 2025.
-sphinx==9.0.4
+sphinx==8.2.4
 pydata-sphinx-theme
 readthedocs-sphinx-search
 sphinx-copybutton
+sphinx-hoverxref
 sphinx-remove-toctrees
 ## for pygment coloring of code snippets using ipython syntax
 ipython
diff --git a/docs/source/_static/custom.css b/docs/source/_static/custom.css
index 5fcf0d318..87ea26ec3 100644
--- a/docs/source/_static/custom.css
+++ b/docs/source/_static/custom.css
@@ -40,6 +40,20 @@ div.admonition-video > p.admonition-title::after {
   content: "\f008";
 }
 
+/*terms with tooltips*/
+
+a.hxr-hoverxref {
+  text-decoration: underline;
+  text-decoration-style: dotted;
+  text-decoration-thickness: 2px;
+  text-decoration-color: var(--color-link-underline);
+  border-bottom: none;
+}
+
+a.hxr-hoverxref:hover {
+  text-decoration-color: var(--color-link-underline--hover);
+}
+
 /* second column of API autosummaries should break more and be a bit smaller */
 table.autosummary td:nth-child(2) {
   FONT-WEIGHT: 300;
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 9219f72c3..1669991ec 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -40,7 +40,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'glossary_warnings',
+    'glossary_warnings', 'hoverxref.extension',
     'sphinx_copybutton', 'sphinx.ext.autodoc',
     'sphinx.ext.autosummary', 'sphinx.ext.mathjax',
     'sphinx_remove_toctrees',
@@ -59,6 +59,12 @@
     "apidocs/_autosummary/pyopenmssubmodules/pyopenms.plotting.*.rst"]
 autodoc_docstring_signature = True
 
+# configure tooltips
+hoverxref_roles = ['term', ]
+hoverxref_role_types = {'term': 'tooltip', }
+# specific for pyopenms documentation
+hoverxref_tooltip_lazy = True
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
diff --git a/requirements.txt b/requirements.txt
index d05d489c9..8b58c040b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,6 +12,7 @@ holoviews
 pyviz_comms
 jupyter-server-proxy
 massql
+sphinx-hoverxref
 
 
 pyopenms

From 61d9144c2d2e12d380dd9cac91c04a16d22aa65a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 16 Dec 2025 14:44:33 +0000
Subject: [PATCH 3/3] Fix Sphinx version to 8.2.3 (8.2.4 doesn't exist)

Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
---
 docs/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index e4ebc86fe..781016e97 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1,5 +1,5 @@
 # Updated to use latest compatible versions as of December 2025.
-sphinx==8.2.4
+sphinx==8.2.3
 pydata-sphinx-theme
 readthedocs-sphinx-search
 sphinx-copybutton