Changes to work with recent versions of Sphinx (#3138)

* Changes to work with recent versions of Sphinx

* Updated Sphinx version used for CI

devtools/ci/gh-actions/conda-envs/docs.yml

@@ -13,7 +13,7 @@ dependencies:
 - swig
 - doxygen 1.8.14
 - pip:
-  - sphinx==2.3.1
-  - sphinxcontrib-bibtex<2.0.0
+  - sphinx==4.0.2
+  - sphinxcontrib-bibtex
   - sphinxcontrib-lunrsearch
   - sphinxcontrib-autodoc_doxygen
\ No newline at end of file

docs-source/api-python/conf.py

@@ -9,8 +9,11 @@ extensions = ['sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.autosumma
               'sphinxcontrib.lunrsearch']
 
 autosummary_generate = True
-autodoc_default_flags = ['members', 'inherited-members']
-autodoc_member_order = 'bysource'
+autodoc_default_options = {
+    'members': True,
+    'inherited-members': True,
+    'member-order': 'bysource'
+}
 
 source_suffix = '.rst'
 master_doc = 'index'

docs-source/sphinx/numsec.py

@@ -47,6 +47,5 @@ def doctree_resolved(app, doctree, docname):
                 node.replace(emphnode, nodes.Text(linktext))
 
 def setup(app):
-    app.override_domain(CustomStandardDomain)
     app.connect('doctree-resolved', doctree_resolved)
 

docs-source/usersguide/conf.py

@@ -27,6 +27,7 @@ sys.path.append(os.path.abspath('../sphinx'))
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.mathjax', 'sphinxcontrib.bibtex', 'autonumber', 'samepage', 'caption', 'numsec']
+bibtex_bibfiles = ['references.bib']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']