Only run doctests in pytest when doctest-modules is specified

src/bin/sage

@@ -960,10 +960,10 @@ if [ "$1" = '-pytest' -o "$1" = '--pytest' ]; then
             for a in $*; do
                 case $a in
                     -*) ;;
-                    *)  exec pytest --rootdir="$SAGE_SRC" "$@"
+                    *)  exec pytest --rootdir="$SAGE_SRC" --doctest-modules "$@"
                 esac
             done
-            exec pytest --rootdir="$SAGE_SRC" "$@" "$SAGE_SRC"
+            exec pytest --rootdir="$SAGE_SRC" --doctest-modules "$@" "$SAGE_SRC"
         else
             echo "Run 'sage -i pytest' to install"
         fi

src/conftest.py

@@ -130,7 +130,8 @@ def pytest_collect_file(
         # hit this here if someone explicitly runs `pytest some_file.pyx`.
         return pytest.skip("Skipping Cython file")
     elif file_path.suffix == ".py":
-        return SageDoctestModule.from_parent(parent, path=file_path)
+        if parent.config.option.doctestmodules:
+            return SageDoctestModule.from_parent(parent, path=file_path)
 
 
 @pytest.fixture(autouse=True)
@@ -142,12 +143,12 @@ def add_imports(doctest_namespace: dict[str, Any]):
     """
     # Inject sage.all into each doctest
     dict_all = sage.all.__dict__
-    
+
     # Remove '__package__' item from the globals since it is not
     # always in the globals in an actual Sage session.
-    dict_all.pop('__package__', None)
+    dict_all.pop("__package__", None)
 
     sage_namespace = dict(dict_all)
-    sage_namespace['__name__'] = '__main__'
-    
+    sage_namespace["__name__"] = "__main__"
+
     doctest_namespace.update(**sage_namespace)