Merge branch 'master' into master

Author: timosachsenberg

.readthedocs.yaml

@@ -4,13 +4,10 @@ version: 2
 sphinx:
   configuration: docs/source/conf.py
 
-# Explicitly set the version of Python and its requirements
-version: 2
-
 build:
-  os: ubuntu-20.04
+  os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.13"
 
 python:
   install:

docs/requirements.txt

@@ -1,15 +1,12 @@
-# Defining the exact version will make sure things don't break
-sphinx==6.1.0
-pydata_sphinx_theme
-readthedocs-sphinx-search==0.3.2
-sphinx-copybutton==0.5.1
-sphinx-hoverxref
+# Updated to use latest compatible versions as of December 2025.
+sphinx==9.0.4
+pydata-sphinx-theme
+readthedocs-sphinx-search
+sphinx-copybutton
 sphinx-remove-toctrees
 ## for pygment coloring of code snippets using ipython syntax
 ipython
 pygments-lexer-pseudocode
-# Dependency of Sphinx, the 3.0 release breaks it (currently)
-snowballstemmer<3
 
 --extra-index-url https://pypi.cs.uni-tuebingen.de/simple/
-pyopenms
+pyopenms

docs/source/_static/switcher.json

@@ -1,9 +1,14 @@
 [
-  {
+{
       "name": "nightly",
-      "version": "3.5.0dev",
+      "version": "3.6.0dev",
       "url": "https://pyopenms.readthedocs.io/en/latest/"
   },
+  {
+      "name": "3.5.0",
+      "version": "3.5.0",
+      "url": "https://pyopenms.readthedocs.io/en/release-3.5.0/"
+  },
   {
     "name": "3.4.0",
     "version": "3.4.0",

docs/source/conf.py

@@ -23,6 +23,7 @@
 import urllib.request
 import contextlib
 import sys
+from datetime import date
 
 sys.path.append(os.path.abspath("./_ext"))
 
@@ -39,7 +40,7 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'glossary_warnings', 'hoverxref.extension',
+    'glossary_warnings',
     'sphinx_copybutton', 'sphinx.ext.autodoc',
     'sphinx.ext.autosummary', 'sphinx.ext.mathjax',
     'sphinx_remove_toctrees',
@@ -58,12 +59,6 @@
     "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']
 
@@ -78,15 +73,15 @@
 
 # General information about the project.
 project = u'pyOpenMS'
-copyright = u'2024, OpenMS Inc'
+copyright = f'{date.today().year}, OpenMS Inc'
 author = u'OpenMS Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'3.4.0'
+version = u'3.5.0'
 # The full version, including alpha/beta/rc tags.
 release = version
 rtd_branch = os.environ.get('READTHEDOCS_GIT_IDENTIFIER', '')