5648 track bundle config in MLFlow

[Nic-Ma]

Fixes #5648 .

Description

This PR added support to track the executed bundle config in the MLFlow, also fixed #4057 (comment).

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

Hi @wyli , @binliunls ,

I tried to track the executed bundle config as a string param in MLFlow, but unfortunately MLFlow has some limitation:

mlflow.exceptions.MlflowException: Param value *** had length 2005, which exceeded length limit of 500

So I plan to save the executed bundle config in a file and put it as artifacts.
What do you think?

Thanks in advance.

[wyli]

agreed, perhaps that's better because we can track timestamp and it's reusable...

[Nic-Ma]

/build

[Nic-Ma]

/build

[wyli]

/build

[wyli]

/integration-test
/build

[Nic-Ma]

Windows test error:

Traceback (most recent call last):
  File "C:\hostedtoolcache\windows\Python\3.8.10\x64\lib\site-packages\parameterized\parameterized.py", line 533, in standalone_func
    return func(*(a + p.args), **p.kwargs)
  File "D:\a\MONAI\MONAI\tests\test_integration_bundle_run.py", line 120, in test_shape
    command_line_tests(la + ["--args_file", def_args_file] + ["--tracking", settings_file])
  File "D:\a\MONAI\MONAI\tests\utils.py", line 776, in command_line_tests
    raise RuntimeError(f"subprocess call error {e.returncode}: {errors}, {output}") from e
RuntimeError: subprocess call error 1: b'Traceback (most recent call last):\r
  File "D:\\a\\MONAI\\MONAI\\monai\\bundle\\__main__.py", line 18, in <module>\r
    fire.Fire()\r
  File "C:\\hostedtoolcache\\windows\\Python\\3.8.10\\x64\\lib\\site-packages\\fire\\core.py", line 141, in Fire\r
    component_trace = _Fire(component, args, parsed_flag_args, context, name)\r
  File "C:\\hostedtoolcache\\windows\\Python\\3.8.10\\x64\\lib\\site-packages\\fire\\core.py", line 466, in _Fire\r
    component, remaining_args = _CallAndUpdateTrace(\r
  File "C:\\hostedtoolcache\\windows\\Python\\3.8.10\\x64\\lib\\site-packages\\fire\\core.py", line 681, in _CallAndUpdateTrace\r
    component = fn(*varargs, **kwargs)\r
  File "D:\\a\\MONAI\\MONAI\\monai\\bundle\\scripts.py", line 638, in run\r
    patch_bundle_tracking(parser=parser, settings=settings_)\r
  File "D:\\a\\MONAI\\MONAI\\monai\\bundle\\scripts.py", line 500, in patch_bundle_tracking\r
    Path(filepath).parent.mkdir(parents=True, exist_ok=True)\r
  File "C:\\hostedtoolcache\\windows\\Python\\3.8.10\\x64\\lib\\pathlib.py", line 1288, in mkdir\r
    self._accessor.mkdir(self, mode)\r
OSError: [WinError 123] The filename, directory name, or volume label syntax is incorrect: \'file:\\\\C:\\\\Users\\\\RUNNER~1\\\\AppData\\\\Local\\\\Temp\\\	mp7nzhmvkh\'\r
', b"2022-12-07 20:47:06,896 - INFO - --- input summary of monai.bundle.scripts.run ---\r

Let me update the path format.

Thanks.

[Nic-Ma]

/black

[Nic-Ma]

/build

[Nic-Ma]

Windows issue fixed.

Thanks.

[wyli]

Windows issue fixed.

Thanks.

do you know what the root cause is?

[Nic-Ma]

Windows issue fixed.
Thanks.

do you know what the root cause is?

The root cause is that the previous test code changed output_dir from regular path to URI on windows:
https://github.com/Project-MONAI/MONAI/blob/dev/tests/test_integration_bundle_run.py#L108
Then can't use it to dump the config content to a file.
Already updated in the latest commit.

Thanks.

[Nic-Ma]

/black

[Nic-Ma]

/build

[wyli]

/build