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transformers - ✅(Solved) Fix save_pretrained` (with `register_for_auto_class`) propagates read-only permissions from custom-model source files [1 pull requests, 1 comments, 1 participants]

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huggingface/transformers#45684•Fetched 2026-04-29 06:11:23
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Error Message

$ chmod u-w custom_model.py $ python main.py save --path=pretrained_c --magic="Magic C" ... PermissionError: [Errno 13] Permission denied: 'pretrained_c/custom_model.py'

Root Cause

transformers/dynamic_module_utils.py, in custom_object_save() (lines 646–659):

result = []
# Copy module file to the output folder.
object_file = sys.modules[obj.__module__].__file__
dest_file = Path(folder) / (Path(object_file).name)
shutil.copy(object_file, dest_file)
result.append(dest_file)

# Gather all relative imports recursively and make sure they are copied as well.
for needed_file in get_relative_import_files(object_file):
    dest_file = Path(folder) / (Path(needed_file).name)
    shutil.copy(needed_file, dest_file)
    result.append(dest_file)

return result

shutil.copy preserves permission bits. The same applies to the three call sites in get_cached_module_file (lines 423, 431, 445).

Fix Action

Fix / Workaround

This:

  1. Breaks any post-save tooling that wants to rewrite the saved module file (in our real workflow we patch the saved file after save_pretrained returns; in the minimal repro below, the patching step fails with PermissionError).
  2. Leaves users with a saved-model directory full of read-only files that are surprising and awkward to operate on.

PR fix notes

PR #45686: Fix custom-module copies inheriting read-only permissions

Description (problem / solution / changelog)

What does this PR do?

Fixes #45684.

shutil.copy is copyfile + copymode, so when source files are read-only (common with version-control systems like Perforce that check files out as r--r--r-- until edit), the destination inherits those permissions. This breaks post-save tooling that wants to rewrite the saved module file, and leaves users with read-only files in their saved-model directories.

The fix swaps shutil.copy for shutil.copyfile at all five call sites in dynamic_module_utils.py (one in custom_object_save, four in get_cached_module_file). copyfile copies file contents only; the destination, when newly created, gets standard umask-based permissions, which is what callers of save_pretrained expect.

A regression test is added to tests/utils/test_dynamic_module_utils.py: it makes a source module read-only, calls custom_object_save, and asserts the destination is writable. The test fails on main and passes with this fix.

Code Agent Policy

  • I confirm that this is not a pure code agent PR.
    • AI was used for making the change, but I hand-edited, reviewed and added tests myself.

Before submitting

Who can review?

@Cyrilvallez (model loading)

Changed files

  • src/transformers/dynamic_module_utils.py (modified, +5/-5)
  • tests/utils/test_dynamic_module_utils.py (modified, +31/-1)

Code Example

$ chmod u-w custom_model.py
$ python main.py save --path=pretrained_c --magic="Magic C"
...
PermissionError: [Errno 13] Permission denied: 'pretrained_c/custom_model.py'

---

result = []
# Copy module file to the output folder.
object_file = sys.modules[obj.__module__].__file__
dest_file = Path(folder) / (Path(object_file).name)
shutil.copy(object_file, dest_file)
result.append(dest_file)

# Gather all relative imports recursively and make sure they are copied as well.
for needed_file in get_relative_import_files(object_file):
    dest_file = Path(folder) / (Path(needed_file).name)
    shutil.copy(needed_file, dest_file)
    result.append(dest_file)

return result

---

-    shutil.copy(object_file, dest_file)
+    shutil.copyfile(object_file, dest_file)
RAW_BUFFERClick to expand / collapse

System Info

  • transformers version: 5.5.3
  • Python: 3.13
  • Platform: Linux

Who can help?

@Cyrilvallez (model loading)

Information

  • The official example scripts
  • My own modified scripts

Tasks

  • An officially supported task in the examples folder (such as GLUE/SQuAD, ...)
  • My own task or dataset (give details below)

Reproduction

When a model is registered via register_for_auto_class, save_pretrained copies the user's custom-model .py file(s) into the output folder using shutil.copy. Since shutil.copy is copyfile + copymode, the destination inherits the source file's permission bits. If the source is read-only -- a common state for files managed by Perforce, which checks files out as r--r--r-- until p4 edit -- the saved copy in the output dir is also read-only.

This:

  1. Breaks any post-save tooling that wants to rewrite the saved module file (in our real workflow we patch the saved file after save_pretrained returns; in the minimal repro below, the patching step fails with PermissionError).
  2. Leaves users with a saved-model directory full of read-only files that are surprising and awkward to operate on.

Repro:

Run:

$ chmod u-w custom_model.py
$ python main.py save --path=pretrained_c --magic="Magic C"
...
PermissionError: [Errno 13] Permission denied: 'pretrained_c/custom_model.py'

main.py custom_model.py

Expected behavior

Files written into the save directory should be writable by the user (subject to the standard umask), independent of the source file's mode bits.

Root cause

transformers/dynamic_module_utils.py, in custom_object_save() (lines 646–659):

result = []
# Copy module file to the output folder.
object_file = sys.modules[obj.__module__].__file__
dest_file = Path(folder) / (Path(object_file).name)
shutil.copy(object_file, dest_file)
result.append(dest_file)

# Gather all relative imports recursively and make sure they are copied as well.
for needed_file in get_relative_import_files(object_file):
    dest_file = Path(folder) / (Path(needed_file).name)
    shutil.copy(needed_file, dest_file)
    result.append(dest_file)

return result

shutil.copy preserves permission bits. The same applies to the three call sites in get_cached_module_file (lines 423, 431, 445).

Suggested fix

Replace shutil.copy with shutil.copyfile at all five call sites in dynamic_module_utils.py. copyfile copies file contents only; the destination, when newly created, gets standard umask-based permissions, which is what callers of save_pretrained reasonably expect.

-    shutil.copy(object_file, dest_file)
+    shutil.copyfile(object_file, dest_file)

Happy to send a PR if this looks right.

extent analysis

TL;DR

Replace shutil.copy with shutil.copyfile in dynamic_module_utils.py to ensure saved files have writable permissions.

Guidance

  • Identify the call sites of shutil.copy in dynamic_module_utils.py and replace them with shutil.copyfile to change the permission behavior.
  • Verify the fix by checking the permissions of the saved files after running save_pretrained.
  • Test the post-save tooling to ensure it can rewrite the saved module files without encountering PermissionError.
  • Consider sending a PR with the suggested fix to update the transformers library.

Example

# Before
shutil.copy(object_file, dest_file)

# After
shutil.copyfile(object_file, dest_file)

Notes

This fix assumes that the standard umask-based permissions are desired for the saved files. If custom permissions are required, additional modifications may be needed.

Recommendation

Apply the workaround by replacing shutil.copy with shutil.copyfile in dynamic_module_utils.py, as this change should resolve the permission issue without introducing significant side effects.

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FAQ

Expected behavior

Files written into the save directory should be writable by the user (subject to the standard umask), independent of the source file's mode bits.

#model save/load#optimization#mixed precision#training loop#model loading

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transformers - ✅(Solved) Fix save_pretrained` (with `register_for_auto_class`) propagates read-only permissions from custom-model source files [1 pull requests, 1 comments, 1 participants]