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`git.repo.base.repo.tree()` blocks deletion of repo directory on Windows (fine in Linux) #546

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git.repo.base.repo.tree() blocks deletion of repo directory on Windows (fine in Linux)#546

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altendky

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on Oct 27, 2016

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I am checking out repositories into a temporary directory, doing various things with them including calling tree(), and then deleting the directories and the temporary directory. This works fine in Linux but not in Windows. I have created this SSCCE to show the issue. I will take some time right now to try to attempt to fix it myself but I like to document my issues first (so others know and just in case someone else sees it and has insight).

Note that I am making an effort (del_rw()) to clear read-only items.

I am testing on:

Windows 10 Enterprise 64-bit (in VirtualBox)
Python 3.5.2 32-bit

t.py.txt

Output:

(venv) C:\Users\IEUser\Desktop\407>python t.py
Traceback (most recent call last):
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 381, in _rmtree_unsafe
    os.unlink(fullname)
PermissionError: [WinError 5] Access is denied: 'C:\\Users\\IEUser\\AppData\\Local\\Temp\\tmprbrn0gen\\tree\\.git\\objects\\pack\\pack-986f782a1c797b94e8a9fa75402bf81fbbc4d537.idx'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "t.py", line 40, in <module>
    shutil.rmtree(dir, onerror=del_rw)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 488, in rmtree
    return _rmtree_unsafe(path, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 383, in _rmtree_unsafe
    onerror(os.unlink, fullname, sys.exc_info())
  File "t.py", line 19, in del_rw
    os.remove(name)
PermissionError: [WinError 5] Access is denied: 'C:\\Users\\IEUser\\AppData\\Local\\Temp\\tmprbrn0gen\\tree\\.git\\objects\\pack\\pack-986f782a1c797b94e8a9fa75402bf81fbbc4d537.idx'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "t.py", line 40, in <module>
    shutil.rmtree(dir, onerror=del_rw)
  File "C:\Users\IEUser\Desktop\407\venv\lib\tempfile.py", line 808, in __exit__
    self.cleanup()
  File "C:\Users\IEUser\Desktop\407\venv\lib\tempfile.py", line 812, in cleanup
    _shutil.rmtree(self.name)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 488, in rmtree
    return _rmtree_unsafe(path, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 378, in _rmtree_unsafe
    _rmtree_unsafe(fullname, onerror)
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 383, in _rmtree_unsafe
    onerror(os.unlink, fullname, sys.exc_info())
  File "C:\Users\IEUser\Desktop\407\venv\lib\shutil.py", line 381, in _rmtree_unsafe
    os.unlink(fullname)
PermissionError: [WinError 5] Access is denied: 'C:\\Users\\IEUser\\AppData\\Local\\Temp\\tmprbrn0gen\\tree\\.git\\objects\\pack\\pack-986f782a1c797b94e8a9fa75402bf81fbbc4d537.idx'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "t.py", line 42, in <module>
    raise PermissionError('Failed with tree (GitPython {})'.format(gitpython_hash)) from e
PermissionError: Failed with tree (GitPython 5149c807ec5f396c1114851ffbd0f88d65d4c84f)

Reacted by Ruslan Kuprieiev

Activity

altendky commented on Oct 27, 2016

altendky

on Oct 27, 2016

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After the tree() call there are two entire Git processes that are left open... Pausing in the debugger and killing those process trees manually (via Process Explorer) does allow clean deletion of the directories.

The 'offending' instances of Git are launched per the below stack traces. I did snip the last few stack frames that were for the PyCharm debugger activities.

>>> import traceback; traceback.print_stack()
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\pydevd.py", line 1580, in <module>
    globals = debugger.run(setup['file'], None, None, is_module)
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\pydevd.py", line 964, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "C:/Users/IEUser/Desktop/407/t.py", line 40, in <module>
    tree = repo.tree('master')
  File "c:\users\ieuser\desktop\407\gitpython\git\repo\base.py", line 442, in tree
    return self.rev_parse(text_type(rev) + "^{tree}")
  File "c:\users\ieuser\desktop\407\gitpython\git\repo\fun.py", line 193, in rev_parse
    obj = name_to_object(repo, rev[:start])
  File "c:\users\ieuser\desktop\407\gitpython\git\repo\fun.py", line 130, in name_to_object
    return Object.new_from_sha(repo, hex_to_bin(hexsha))
  File "c:\users\ieuser\desktop\407\gitpython\git\objects\base.py", line 64, in new_from_sha
    oinfo = repo.odb.info(sha1)
  File "c:\users\ieuser\desktop\407\gitpython\git\db.py", line 37, in info
    hexsha, typename, size = self._git.get_object_header(bin_to_hex(sha))
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 930, in get_object_header
    cmd = self._get_persistent_cmd("cat_file_header", "cat_file", batch_check=True)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 913, in _get_persistent_cmd
    cmd = self._call_process(cmd_name, *args, **options)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 868, in _call_process
    return self.execute(call, **_kwargs)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 586, in execute
    proc = Popen(command,

and

>>> import traceback; traceback.print_stack()
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\pydevd.py", line 1580, in <module>
    globals = debugger.run(setup['file'], None, None, is_module)
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\pydevd.py", line 964, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 2016.2.3\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "C:/Users/IEUser/Desktop/407/t.py", line 40, in <module>
    tree = repo.tree('master')
  File "c:\users\ieuser\desktop\407\gitpython\git\repo\base.py", line 442, in tree
    return self.rev_parse(text_type(rev) + "^{tree}")
  File "c:\users\ieuser\desktop\407\gitpython\git\repo\fun.py", line 216, in rev_parse
    obj = to_commit(obj).tree
  File "C:\Users\IEUser\Desktop\407\venv\lib\site-packages\gitdb\util.py", line 237, in __getattr__
    self._set_cache_(attr)
  File "c:\users\ieuser\desktop\407\gitpython\git\objects\commit.py", line 143, in _set_cache_
    binsha, typename, self.size, stream = self.repo.odb.stream(self.binsha)  # @UnusedVariable
  File "c:\users\ieuser\desktop\407\gitpython\git\db.py", line 42, in stream
    hexsha, typename, size, stream = self._git.stream_object_data(bin_to_hex(sha))
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 947, in stream_object_data
    cmd = self._get_persistent_cmd("cat_file_all", "cat_file", batch=True)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 913, in _get_persistent_cmd
    cmd = self._call_process(cmd_name, *args, **options)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 868, in _call_process
    return self.execute(call, **_kwargs)
  File "c:\users\ieuser\desktop\407\gitpython\git\cmd.py", line 586, in execute
    proc = Popen(command,

ankostis
added
tag.Windows

tag.leaks
on Oct 27, 2016
altendky commented on Oct 27, 2016
altendky
on Oct 27, 2016
Author
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Does not seem to work (Still throws exception when deleting directory. I guess this just means it's not setup as a context manager):

with git.Repo.clone_from(url, dir) as repo: with repo.tree('master') as tree: pass

Does work (No exception when deleting directory):

repo = git.Repo.clone_from(url, dir) tree = repo.tree('master') del repo del tree

So, perhaps it is not a bug and I simply need to make sure that my repo and tree get deleted?
altendky commented on Oct 27, 2016
altendky
on Oct 27, 2016
Author
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Better 'workaround':

tree = repo.tree('master') repo.git.clear_cache()
Reacted by Simon Schürrle and Garrett Brenner
altendky
added a commit that references this issue on Oct 31, 2016
Workaround in collectdevices.py for bug in gitpython
6a12f70
Byron commented on Dec 8, 2016
Byron
on Dec 8, 2016
Member
More actions
@altendky Thanks for posting your progress here, as I do hope that others will find it useful! It's a known limitation of GitPython and its API, and best I can offer right now is to manually handle it by implementing some sort of workaround.
Byron
added
acknowledged
on Dec 8, 2016
TomasTomecek
added 3 commits that reference this issue on Oct 7, 2021
free GitPython resources
e33b003
free GitPython resources
466eb94
free GitPython resources
e5b1fea
softwarefactory-project-zuul
added a commit that references this issue on Oct 8, 2021
Merge pull request #1384 from TomasTomecek/git-clear-cache
a49247d
n-dusan
added 4 commits that reference this issue on Jul 18, 2022
fix: reraise original exception and windows specific cleanup errors
0f4ec36
fix: reraise original exception and windows specific cleanup errors
0598f71
fix: reraise original exception and windows specific cleanup errors
1578c4d
fix: reraise original exception and windows specific cleanup errors
f55ef7c
renatav
added a commit that references this issue on Jul 20, 2022
Fix cleanup error messages after failed update (#259)
6bc80bf
gdyrrahitis commented on Jul 29, 2023
gdyrrahitis
on Jul 29, 2023
More actions

OS Name: Microsoft Windows 10 Pro

OS Version: 10.0.19045

Python version: 3.10.9

Workaround

def main(): with git.Repo.clone_from(REPO, local_path) as repo: # omitted for brevity print(f"Removing temp destination directory {local_path}") git.rmtree(local_path)
Reacted by Mauro and Sebastian Thiel
Reacted by Mauro
reglim commented on Jan 11, 2024
reglim
on Jan 11, 2024
More actions
I had the same problem just with creating a repo and deleting it again.
Thankfully, @gdyrrahitis solution worked for me 🚀

fliiiix commented on Jun 2, 2025

fliiiix

on Jun 2, 2025

More actions

I assume there was no progress on this issue?

I'm facing something which seems the same issue but even a rmtree and a clean_cache does not help.

path = WindowsPath('C:/Users/XXXX/AppData/Local/Temp/tmp9__47p3j/template'), onexc = <function rmtree.<locals>.onexc at 0x0000

    def _rmtree_unsafe(path, onexc):
        def onerror(err):
            onexc(os.scandir, err.filename, err)
        results = os.walk(path, topdown=False, onerror=onerror, followlinks=os._walk_symlinks_as_files)
        for dirpath, dirnames, filenames in results:
            for name in dirnames:
                fullname = os.path.join(dirpath, name)
                try:
                    os.rmdir(fullname)
                except OSError as err:
                    onexc(os.rmdir, fullname, err)
            for name in filenames:
                fullname = os.path.join(dirpath, name)
                try:
>                   os.unlink(fullname)
E                   PermissionError: [WinError 5] Zugriff verweigert: 'C:\\Users\\XXXX\\AppData\\Local\\Temp\\tmp9__47p3j\\temffb21d689bc799b9a573'

..\AppData\Local\Programs\Python\Python312\Lib\shutil.py:633: PermissionError

code snipped

repo.git.clear_cache()
git.rmtree(git_repo_path / ".git")

shutil.rmtree(tmpdir)

I don't really had time to debug it more, and just went with a try, except and ignoring the cleanup.

Byron
added the
Bug
issue type on Jul 20, 2026
Byron
closed this as not planned on Jul 20, 2026

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git.repo.base.repo.tree() blocks deletion of repo directory on Windows (fine in Linux) #546

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altendky commented on Oct 27, 2016

altendky commented on Oct 27, 2016

altendky commented on Oct 27, 2016

Byron commented on Dec 8, 2016

gdyrrahitis commented on Jul 29, 2023

reglim commented on Jan 11, 2024

fliiiix commented on Jun 2, 2025

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`git.repo.base.repo.tree()` blocks deletion of repo directory on Windows (fine in Linux) #546