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The packaging.command.Command.copy_file method does not honour the preserve_mode and preserve_times keyword arguments.
Likewise, packaging.command.Command.copy_tree does not honour the preserve_mode, preserve_times and preserve_symlinks keyword arguments.

Thanks for the report. Have you found the bug with a real setup.cfg or hook, or were you just reading the code?
I’m not sure how hard to fix this will be. The copy_file method delegates to shutil.copyfile, but this does not have the arguments we need, contrary to the former distutils file_util.copy_file function.
Currently it’s only build_py that uses this parameter: 
 # if a file is read-only in the working
 # directory, we want it to be installed read/write so that the next
 # installation of the same module distribution can overwrite it
 # without problems. (This might be a Unix-specific issue.) Thus
 # we turn off 'preserve_mode' when copying to the build directory,
 # since the build directory is supposed to be exactly what the
 # installation will look like (ie. we preserve mode when
 # installing).
Depending on whether shutil supports what we need, different patches could be made:
- Change code to use the right shutil function
- Add code in copy_file to walk and chmod
- Remove the preserve_* arguments and add another method for build_py

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> 
> Éric Araujo <merwok@netwok.org> added the comment:
> 
> Thanks for the report. Have you found the bug with a real setup.cfg or hook, or 
> were you just reading the code?
> 
I found the bug with a real setup.cfg (executable permission not set IIRC) and tracked it to copy_file. The copy_tree function wasn't used, I was just making an observation from scanning the code.