Settings from the config file have precedence over those in the noteb…

…ook at save time

jupytext/jupytext.py

@@ -59,21 +59,14 @@ def __init__(self, fmt, config):
     def update_fmt_with_notebook_options(self, metadata, read=False):
         """Update format options with the values in the notebook metadata, and record those
         options in the notebook metadata"""
+        # The settings in the Jupytext configuration file have precedence over the metadata in the notebook
+        # when the notebook is saved. This is because the metadata in the notebook might not be visible
+        # in the text representation when e.g. notebook_metadata_filter="-all", which makes them hard to edit.
+        if not read and self.config is not None:
+            self.config.set_default_format_options(self.fmt, read)
+
         # format options in notebook have precedence over that in fmt, and precedence over the config
         for opt in _VALID_FORMAT_OPTIONS:
-            if self.config is not None:
-                # We use the config filters if provided
-                if (
-                    opt == "notebook_metadata_filter"
-                    and self.config.default_notebook_metadata_filter
-                ):
-                    continue
-                if (
-                    opt == "cell_metadata_filter"
-                    and self.config.default_cell_metadata_filter
-                ):
-                    continue
-
             if opt in metadata.get("jupytext", {}):
                 self.fmt.setdefault(opt, metadata["jupytext"][opt])
 

tests/test_contentsmanager.py

@@ -1541,21 +1541,25 @@ def test_save_file_with_default_cell_markers(tmpdir):
     nb = cm.get("nb.py")["content"]
     assert len(nb.cells) == 1
 
-    nb.metadata["jupytext"]["cell_markers"] = "+,-"
-    del nb.metadata["jupytext"]["notebook_metadata_filter"]
     cm.save(model=notebook_model(nb), path="nb.py")
 
     with open(tmp_py) as fp:
         text2 = fp.read()
 
     compare(
-        "\n".join(text2.splitlines()[-len(text.splitlines()) :]),
-        "\n".join(text.splitlines()),
+        text2,
+        """# region
+# this is a unique code cell
+1 + 1
+
+2 + 2
+# endregion
+""",
     )
 
     nb2 = cm.get("nb.py")["content"]
     compare_notebooks(nb2, nb)
-    assert nb2.metadata["jupytext"]["cell_markers"] == "+,-"
+    assert nb2.metadata["jupytext"]["cell_markers"] == "region,endregion"
 
 
 def test_notebook_extensions(tmpdir):