[FIX] Also allow errno.EBUSY during emptydirs on NFS (#3357)

* Also allow `errno.EBUSY` during `emptydirs` on NFS

- Can occur if a file is still open somewhere, so NFS will rename it to
  a hidden file in the same directory
- When `shutil` tries to delete that hidden file, we get an `OSError`
  with `errno.EBUSY`

* Ignore `.nfs` placeholder files when catching the error

- I forgot that `os.listdir` also lists hidden files in the previous
  commit

* Add unit test for `emptydirs` on NFS

- With mock for NFS silly-rename (yes, it's really called that) behavior

* Run `black`

* Update nipype/utils/tests/test_filemanip.py

Handle mock test case when no `dir_fd` is passed

Author: HippocampusGirl

nipype/utils/filemanip.py

@@ -780,8 +780,13 @@ def emptydirs(path, noexist_ok=False):
     try:
         shutil.rmtree(path)
     except OSError as ex:
-        elcont = os.listdir(path)
-        if ex.errno == errno.ENOTEMPTY and not elcont:
+        elcont = [
+            Path(root) / file
+            for root, _, files in os.walk(path)
+            for file in files
+            if not file.startswith(".nfs")
+        ]
+        if ex.errno in [errno.ENOTEMPTY, errno.EBUSY] and not elcont:
             fmlogger.warning(
                 "An exception was raised trying to remove old %s, but the path"
                 " seems empty. Is it an NFS mount?. Passing the exception.",
@@ -793,7 +798,7 @@ def emptydirs(path, noexist_ok=False):
         else:
             raise ex
 
-    os.makedirs(path)
+    os.makedirs(path, exist_ok=True)
 
 
 def silentrm(filename):

nipype/utils/tests/test_filemanip.py

@@ -31,6 +31,7 @@
     savepkl,
     path_resolve,
     write_rst_list,
+    emptydirs,
 )
 
 
@@ -670,3 +671,26 @@ def test_write_rst_list(tmp_path, items, expected):
     else:
         with pytest.raises(expected):
             write_rst_list(items)
+
+
+def nfs_unlink(pathlike, *, dir_fd=None):
+    if dir_fd is None:
+        path = Path(pathlike)
+        deleted = path.with_name(".nfs00000000")
+        path.rename(deleted)
+    else:
+        os.rename(pathlike, ".nfs1111111111", src_dir_fd=dir_fd, dst_dir_fd=dir_fd)
+
+
+def test_emptydirs_dangling_nfs(tmp_path):
+    busyfile = tmp_path / "base" / "subdir" / "busyfile"
+    busyfile.parent.mkdir(parents=True)
+    busyfile.touch()
+
+    with mock.patch("os.unlink") as mocked:
+        mocked.side_effect = nfs_unlink
+        emptydirs(tmp_path / "base")
+
+    assert Path.exists(tmp_path / "base")
+    assert not busyfile.exists()
+    assert busyfile.parent.exists()  # Couldn't remove