Copy file metadata in atomic save

Closes gh-6405

IPython/utils/io.py

@@ -19,6 +19,8 b' import codecs'
 from contextlib import contextmanager
 import io
 import os
+import shutil
+import stat
 import sys
 import tempfile
 from .capture import CapturedIO, capture_output
@@ -219,6 +221,17 b" def temp_pyfile(src, ext='.py'):"
     f.flush()
     return fname, f
 
+def _copy_metadata(src, dst):
+    """Copy the set of metadata we want for atomic_writing.
+    
+    Permission bits and flags. We'd like to copy file ownership as well, but we
+    can't do that.
+    """
+    shutil.copymode(src, dst)
+    st = os.stat(src)
+    if hasattr(os, 'chflags') and hasattr(st, 'st_flags'):
+        os.chflags(st.st_flags)
+
 @contextmanager
 def atomic_writing(path, text=True, encoding='utf-8', **kwargs):
     """Context manager to write to a file only if the entire write is successful.
@@ -268,6 +281,13 b" def atomic_writing(path, text=True, encoding='utf-8', **kwargs):"
     # Written successfully, now rename it
     fileobj.close()
 
+    # Copy permission bits, access time, etc.
+    try:
+        _copy_metadata(path, tmp_path)
+    except OSError:
+        # e.g. the file didn't already exist. Ignore any failure to copy metadata
+        pass
+
     if os.name == 'nt' and os.path.exists(path):
         # Rename over existing file doesn't work on Windows
         os.remove(path)

IPython/utils/tests/test_io.py

@@ -16,6 +16,7 b' from __future__ import absolute_import'
 
 import io as stdlib_io
 import os.path
+import stat
 import sys
 
 from subprocess import Popen, PIPE
@@ -134,6 +135,10 b' def test_atomic_writing():'
         f1 = os.path.join(td, 'penguin')
         with stdlib_io.open(f1, 'w') as f:
             f.write(u'Before')
+        
+        if os.name != 'nt':
+            os.chmod(f1, 0o701)
+            orig_mode = stat.S_IMODE(os.stat(f1).st_mode)
 
         with nt.assert_raises(CustomExc):
             with atomic_writing(f1) as f:
@@ -149,3 +154,7 b' def test_atomic_writing():'
 
         with stdlib_io.open(f1, 'r') as f:
             nt.assert_equal(f.read(), u'Overwritten')
+
+        if os.name != 'nt':
+            mode = stat.S_IMODE(os.stat(f1).st_mode)
+            nt.assert_equal(mode, orig_mode)