Don't modify fmt, instead, return an updated copy

Fix #428

jupytext/cli.py

@@ -315,7 +315,7 @@ def jupytext_single_file(nb_file, args, log):
     # Compute actual extension when using script/auto, and update nb_dest if necessary
     dest_fmt = args.to
     if dest_fmt and dest_fmt['extension'] == '.auto':
-        check_auto_ext(dest_fmt, notebook.metadata, '--to')
+        dest_fmt = check_auto_ext(dest_fmt, notebook.metadata, '--to')
         if not args.output and nb_file != '-':
             nb_dest = full_path(base_path(nb_file, args.input_format), dest_fmt)
 
@@ -625,7 +625,7 @@ def pipe_notebook(notebook, command, fmt='py:percent', update=True, prefix=None)
         command = command + ' {}'
 
     fmt = long_form_one_format(fmt, notebook.metadata, auto_ext_requires_language_info=False)
-    check_auto_ext(fmt, notebook.metadata, '--pipe-fmt')
+    fmt = check_auto_ext(fmt, notebook.metadata, '--pipe-fmt')
     text = writes(notebook, fmt)
 
     command = command.split(' ')

jupytext/formats.py

@@ -587,14 +587,15 @@ def auto_ext_from_metadata(metadata):
 
 
 def check_auto_ext(fmt, metadata, option):
-    """Raise a ValueError when the .auto extension cannot be determined"""
+    """Replace the auto extension with the actual file extension, and raise a ValueError if it cannot be determined"""
     if fmt['extension'] != '.auto':
-        return
+        return fmt
 
     auto_ext = auto_ext_from_metadata(metadata)
     if auto_ext:
+        fmt = fmt.copy()
         fmt['extension'] = auto_ext
-        return
+        return fmt
 
     raise ValueError("The notebook does not have a 'language_info' metadata. "
                      "Please replace 'auto' with the actual language extension in the {} option (currently {})."

tests/test_mirror.py

@@ -35,7 +35,7 @@ def assert_conversion_same_as_mirror(nb_file, fmt, mirror_name, compare_notebook
     file_name, org_ext = os.path.splitext(basename)
     fmt = long_form_one_format(fmt)
     notebook = jupytext.read(nb_file, fmt=fmt)
-    check_auto_ext(fmt, notebook.metadata, '')
+    fmt = check_auto_ext(fmt, notebook.metadata, '')
     ext = fmt['extension']
     mirror_file = os.path.join(dirname, '..', 'mirror', mirror_name, full_path(file_name, fmt))