Sphinx 3 autodoc no longer accepts autodoc_default_flags and autodoc_default_options should be used

doc/conf.py

@@ -231,7 +231,11 @@ rst_epilog = """
 # Default processing flags for sphinx
 autoclass_content = "class"
 autodoc_member_order = "bysource"
-autodoc_default_flags = ["members", "undoc-members", "show-inheritance"]
+autodoc_default_options = {
+    "members": True,
+    "undoc-members": True,
+    "show-inheritance": True,
+}
 
 if not 'BOB_DOCUMENTATION_SERVER' in os.environ:
   # notice we need to overwrite this for BEAT projects - defaults from Bob are
@@ -251,25 +255,3 @@ else:
 # Adds simplejson, pyzmq links
 intersphinx_mapping["http://simplejson.readthedocs.io/en/stable/"] = None
 intersphinx_mapping["http://pyzmq.readthedocs.io/en/stable/"] = None
-
-# We want to remove all private (i.e. _. or __.__) members
-# that are not in the list of accepted functions
-accepted_private_functions = ["__array__"]
-
-
-def member_function_test(app, what, name, obj, skip, options):
-    # test if we have a private function
-    if len(name) > 1 and name[0] == "_":
-        # test if this private function should be allowed
-        if name not in accepted_private_functions:
-            # omit privat functions that are not in the list of accepted private functions
-            return skip
-        else:
-            # test if the method is documented
-            if not hasattr(obj, "__doc__") or not obj.__doc__:
-                return skip
-    return False
-
-
-def setup(app):
-    app.connect("autodoc-skip-member", member_function_test)