Notebook pairings are bounded by the config directory

jupytext/config.py

@@ -10,10 +10,6 @@
     long_form_multiple_formats,
     rearrange_jupytext_metadata,
 )
-from .paired_paths import (
-    base_path,
-    InconsistentPath,
-)
 
 JUPYTEXT_CONFIG_FILES = [
     "jupytext",
@@ -138,6 +134,11 @@ def set_default_format_options(self, format_options, read=False):
 
     def default_formats(self, path):
         """Return the default formats, if they apply to the current path #157"""
+        from .paired_paths import (
+            base_path,
+            InconsistentPath,
+        )
+
         formats = long_form_multiple_formats(self.default_jupytext_formats)
         for fmt in formats:
             try:

jupytext/paired_paths.py

@@ -4,6 +4,7 @@
 from .formats import long_form_one_format, long_form_multiple_formats
 from .formats import short_form_one_format, short_form_multiple_formats
 from .formats import NOTEBOOK_EXTENSIONS
+from .config import find_jupytext_configuration_file
 
 
 class InconsistentPath(ValueError):
@@ -67,6 +68,14 @@ def base_path(main_path, fmt):
     notebook_dir, notebook_file_name = split(base)
     sep = base[len(notebook_dir) : -len(notebook_file_name)]
 
+    base_dir = None
+    config_file = find_jupytext_configuration_file(notebook_dir)
+    if config_file:
+        config_file_dir = os.path.dirname(config_file)
+        if notebook_dir.startswith(config_file_dir):
+            base_dir = config_file_dir
+            notebook_dir = notebook_dir[len(config_file_dir) :]
+
     if prefix_file_name:
         if not notebook_file_name.startswith(prefix_file_name):
             raise InconsistentPath(
@@ -116,6 +125,9 @@ def base_path(main_path, fmt):
         notebook_dir = "///".join(long_notebook_dir.rsplit(long_prefix_root, 1))
         notebook_dir = notebook_dir[len(sep) : -len(sep)]
 
+    if base_dir:
+        notebook_dir = base_dir + notebook_dir
+
     if not notebook_dir:
         return notebook_file_name
 

tests/test_paired_paths.py

@@ -66,6 +66,47 @@ def test_full_path_in_tree_from_non_root():
     )
 
 
+def test_path_in_tree_limited_to_config_dir(tmpdir):
+    root_nb_dir = tmpdir.mkdir("notebooks")
+    nb_dir = root_nb_dir.mkdir("notebooks")
+    src_dir = root_nb_dir.mkdir("scripts")
+    other_dir = root_nb_dir.mkdir("other")
+
+    formats = "notebooks///ipynb,scripts///py"
+    fmt = long_form_multiple_formats(formats)[0]
+
+    # Notebook in nested 'notebook' dir is paired
+    notebook_in_nb_dir = nb_dir.join("subfolder").join("nb.ipynb")
+
+    assert set(
+        path for (path, _) in paired_paths(str(notebook_in_nb_dir), fmt, formats)
+    ) == {str(notebook_in_nb_dir), str(src_dir.join("subfolder").join("nb.py"))}
+
+    # Notebook in base 'notebook' dir is paired if no config file is found
+    notebook_in_other_dir = other_dir.mkdir("subfolder").join("nb.ipynb")
+    assert set(
+        path for (path, _) in paired_paths(str(notebook_in_other_dir), fmt, formats)
+    ) == {
+        str(notebook_in_other_dir),
+        str(tmpdir.join("scripts").join("other").join("subfolder").join("nb.py")),
+    }
+
+    # When a config file exists
+    root_nb_dir.join("jupytext.toml").write("\n")
+
+    # Notebook in nested 'notebook' dir is still paired
+    assert set(
+        path for (path, _) in paired_paths(str(notebook_in_nb_dir), fmt, formats)
+    ) == {str(notebook_in_nb_dir), str(src_dir.join("subfolder").join("nb.py"))}
+
+    # But the notebook in base 'notebook' dir is not paired any more
+    with pytest.raises(
+        InconsistentPath,
+        match="Notebook directory '/other/subfolder' does not match prefix root 'notebooks'",
+    ):
+        paired_paths(str(notebook_in_other_dir), fmt, formats)
+
+
 def test_many_and_suffix():
     formats = long_form_multiple_formats("ipynb,.pct.py,_lgt.py")
     expected_paths = ["notebook.ipynb", "notebook.pct.py", "notebook_lgt.py"]