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Distutils ignores file permissions when copying modules and package_data
files to the build directory, and consequently to the installation
directory too. According to an XXX comment at
distutils/command/build_py.py, this is deliberate so that the built
files are not read-only, which would be a nuisance when rebuilding. This
problem though could be solved by just setting the write flag for the
user (chmod u+w) instead of overwriting all the flags. In my case, some
executable files ceased to be executable after installation.
I believe that the default behavior should be changed to preserve all
permissions, with the possible exception of setting u+w. Even that might
be unnecessary; AFAIK to delete a file you need write permissions only
to its parent directory, not to the file itself.
Even if the current behavior is deemed correct, at the very least the
code should be refactored to allow easy overriding. Currently
build_module and build_package_data pass preserve_mode=False in their
body, so I had to copy and paste the whole methods just to set
preserve_mode=True.

> I believe that the default behavior should be changed to preserve 
> all permissions, with the possible exception of setting u+w. 
> Even that might be unnecessary; AFAIK to delete a file you need 
> write permissions only to its parent directory, not to the 
> file itself.
The u+w setting could also be done on the fly by copy_file at
installation time. e.g. when overwriting a read-only file.
> In my case, some 
> executable files ceased to be executable after installation.
what is your use case of having executable file here ?
I'd use the 'scripts' metadata for that ?
> Even if the current behavior is deemed correct, at the very least 
> the code should be refactored to allow easy overriding.
> Currently build_module and build_package_data pass 
> preserve_mode=False in their
> body, so I had to copy and paste the whole methods 
> just to set preserve_mode=True.
But How do you handle the overwrite of a read-only file in your code then ?

> what is your use case of having executable file here ?
>
> I'd use the 'scripts' metadata for that ?
For one thing they are external binaries, not python scripts, and second
they are used internally only (through Subprocess), they are not
supposed to be called directly by clients.
> But How do you handle the overwrite of a read-only file in your code 
> then ?
I didn't, all my files were writable (by me), but if I had to, I'd look
at tweaking the directory write permissions; as I mentioned, I don't
think file permissions affect whether you can delete the file.

FTR it looks like http://mail.python.org/pipermail/python-list/2009-January/1188084.html was the original report for this.

The whole permissions setting operation seems a bit convoluted.
I was hoping there was something formalized with install_data.py where I could specify a default or fine-grained user/group/mode for files, but it doesn't appear to be possible. I'll investigate applying a custom rule after install is run, but I would prefer for this to be formalized in the future.

Distutils is now deprecated (see PEP 632) and all tagged issues are being closed. From now until removal, only release blocking issues will be considered for distutils.
If this issue does not relate to distutils, please remove the component and reopen it. If you believe it still requires a fix, most likely the issue should be re-reported at https://github.com/pypa/setuptools