Preserve executable and encoding information in scripts with metadata

Fixes #241

HISTORY.rst

@@ -15,7 +15,7 @@ Release History
 - Invalid notebooks may cause a warning, but not a fatal error (#234)
 - Jupyter server extension leaves the contents manager unchanged if it is a sub-class of Jupytext's CM (#236)
 - Fixed format inference when metadata is present but not format information (#239)
-
+- Preserve executable and encoding information in scripts with metadata (#241)
 
 1.1.3 (2019-05-22)
 ++++++++++++++++++++++

jupytext/cli.py

@@ -12,6 +12,7 @@
 from .jupytext import readf, reads, writef, writes
 from .formats import _VALID_FORMAT_OPTIONS, _BINARY_FORMAT_OPTIONS, check_file_version
 from .formats import long_form_one_format, long_form_multiple_formats, short_form_one_format, auto_ext_from_metadata
+from .header import recursive_update
 from .paired_paths import paired_paths, base_path, full_path, InconsistentPath
 from .combine import combine_inputs_with_outputs
 from .compare import test_round_trip_conversion, NotebookDifference
@@ -404,21 +405,6 @@ def print_paired_paths(nb_file, fmt):
                 sys.stdout.write(path + '\n')
 
 
-def recursive_update(target, update):
-    """ Update recursively a (nested) dictionary with the content of another.
-    Inspired from https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
-    """
-    for key in update:
-        value = update[key]
-        if value is None:
-            del target[key]
-        elif isinstance(value, dict):
-            target[key] = recursive_update(target.get(key, {}), value)
-        else:
-            target[key] = value
-    return target
-
-
 def set_format_options(fmt, format_options):
     """Apply the desired format options to the format description fmt"""
     if not format_options:

jupytext/header.py

@@ -118,6 +118,21 @@ def metadata_and_cell_to_header(notebook, metadata, text_format, ext):
     return comment_lines(header, text_format.header_prefix), lines_to_next_cell
 
 
+def recursive_update(target, update):
+    """ Update recursively a (nested) dictionary with the content of another.
+    Inspired from https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
+    """
+    for key in update:
+        value = update[key]
+        if value is None:
+            del target[key]
+        elif isinstance(value, dict):
+            target[key] = recursive_update(target.get(key, {}), value)
+        else:
+            target[key] = value
+    return target
+
+
 def header_to_metadata_and_cell(lines, header_prefix, ext=None):
     """
     Return the metadata, a boolean to indicate if a jupyter section was found,
@@ -177,7 +192,7 @@ def header_to_metadata_and_cell(lines, header_prefix, ext=None):
 
     if ended:
         if jupyter:
-            metadata.update(yaml.safe_load('\n'.join(jupyter))['jupyter'])
+            recursive_update(metadata, yaml.safe_load('\n'.join(jupyter))['jupyter'])
 
         lines_to_next_cell = 1
         if len(lines) > i + 1:

tests/test_read_simple_python.py

@@ -448,6 +448,38 @@ def test_read_write_script(pynb="""#!/usr/bin/env python
     compare(pynb, pynb2)
 
 
+def test_read_write_script_with_metadata_241(pynb="""#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.4'
+#       jupytext_version: 1.1.2
+#   kernelspec:
+#     display_name: Python 3
+#     language: python
+#     name: python3
+# ---
+
+a = 2
+
+a + 1
+"""):
+    nb = jupytext.reads(pynb, 'py')
+    assert 'executable' in nb.metadata['jupytext']
+    assert 'encoding' in nb.metadata['jupytext']
+    pynb2 = jupytext.writes(nb, 'py')
+
+    # remove version information
+    def remove_version_info(text):
+        return '\n'.join([line for line in text.splitlines() if 'version' not in line])
+
+    compare(remove_version_info(pynb), remove_version_info(pynb2))
+
+
 def test_notebook_blank_lines(script="""# +
 # This is a comment
 # followed by two variables