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

[altendky]

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)

[altendky]

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,

[altendky]

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]

Better 'workaround':

tree = repo.tree('master')
repo.git.clear_cache()

[Byron]

@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.