shutil.copystat fails on panfs if the source file lacks u+w, because setting extended attributes results in a PermissionError. This leads to higher end functions such as shutil.copytree to fail. More seriously, it leads to pip install . to fail, as I reported here:

In [55]: shutil.copystat("/src/on/panfs", "/tmp/fubar")
\---------------------------------------------------------------------------

    PermissionError                           Traceback (most recent call last)
    <ipython-input-55-139c9fc77184> in <module>()
    ----> 1 shutil.copystat("/home/users/gholl/checkouts/pyatmlab/.git/objects/pack/pack-c1449559ec4287b3830efe2913608dddf2f21391.pack", "/tmp/fubar")
    
    /home/users/gholl/lib/python3.4/shutil.py in copystat(src, dst, follow_symlinks)
        211             else:
        212                 raise
    --> 213     _copyxattr(src, dst, follow_symlinks=follow)
        214
        215 def copy(src, dst, *, follow_symlinks=True):
    
    /home/users/gholl/lib/python3.4/shutil.py in _copyxattr(src, dst, follow_symlinks)
        151             try:
        152                 value = os.getxattr(src, name, follow_symlinks=follow_symlinks)
    --> 153                 os.setxattr(dst, name, value, follow_symlinks=follow_symlinks)
        154             except OSError as e:
        155                 if e.errno not in (errno.EPERM, errno.ENOTSUP, errno.ENODATA):
    
    PermissionError: [Errno 13] Permission denied: '/tmp/fubar'

This occurs for any source file where the user write bit is not set.

Now, I'm not sure if this should be addressed in pip, shutil.copytree, shutil.copystat, setxattr, panfs, or in none of the above. I'm reporting it in different places; please close this issue if this is the wrong place.

There are a couple of related open issues. I think there is an stdlib problem here, but I"m not sure what the solution is.

Perhaps the solution would be some kind of flag, at least for copytree and possibly others, on what to do when attributes cannot be completely copied — a bit like numpys options to raise, warn, or ignore?

The issue can be avoided by calling _copyxattr *before* instead of after os.chmod in shutil.copystat. That way the file is still writable.

The same issue happens on the Lustre parallel file system, with the lustre.lov extended attribute.

This old bug now has a PR on Github authored by myself that may be reviewed.

Patch LGTM. I'd like to point out one thing for posterity. Current shutil code catches EPERM but not EACCES. While reviewing the patch I wondered whether simply catching (and ignoring) both error codes instead, but it turns out they are supposed to have 2 different meanings:
https://stackoverflow.com/a/35879961/376587
Especially after _copyxattr is moved before chmod() EACCES (permission denied) should propagate instead of being silenced, and EPERM should be left in place because in this case EPERM acts more like an ENOTSUP (operation not supported) than EACCES (permission denied) and as such should rightly be ignored.

New changeset 79efbb7 by Giampaolo Rodola (Olexa Bilaniuk) in branch 'master':
bpo-24538: Fix bug in shutil involving the copying of xattrs to read-only files. (PR-13212)
79efbb7

New changeset 0a5b88e by Giampaolo Rodola (Miss Islington (bot)) in branch '3.7':
bpo-24538: Fix bug in shutil involving the copying of xattrs to read-only files. (PR-13212) (bpo-13234)
0a5b88e

This seems complete, can it be closed?

Yes, it may be closed. The fix was merged in time to make it into Python 3.7.4 and 3.8.0, and solved the problems we were facing with fancy filesystem xattrs on read-only files.