7601 fix mlflow artifacts (#7604)

Fixes #7601 .

### Description

Support not save artifacts.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] 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.
- [x] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [x] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [x] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: binliu <[email protected]>
Co-authored-by: Nic Ma <[email protected]>
Co-authored-by: YunLiu <[email protected]>

monai/bundle/scripts.py

@@ -778,10 +778,19 @@ def run(
             https://docs.python.org/3/library/logging.config.html#logging.config.fileConfig.
             Default to None.
         tracking: if not None, enable the experiment tracking at runtime with optionally configurable and extensible.
-            if "mlflow", will add `MLFlowHandler` to the parsed bundle with default tracking settings,
-            if other string, treat it as file path to load the tracking settings.
-            if `dict`, treat it as tracking settings.
-            will patch the target config content with `tracking handlers` and the top-level items of `configs`.
+            If "mlflow", will add `MLFlowHandler` to the parsed bundle with default tracking settings where a set of
+            common parameters shown below will be added and can be passed through the `override` parameter of this method.
+
+            - ``"output_dir"``: the path to save mlflow tracking outputs locally, default to "<bundle root>/eval".
+            - ``"tracking_uri"``: uri to save mlflow tracking outputs, default to "/output_dir/mlruns".
+            - ``"experiment_name"``: experiment name for this run, default to "monai_experiment".
+            - ``"run_name"``: the name of current run.
+            - ``"save_execute_config"``: whether to save the executed config files. It can be `False`, `/path/to/artifacts`
+              or `True`. If set to `True`, will save to the default path "<bundle_root>/eval". Default to `True`.
+
+            If other string, treat it as file path to load the tracking settings.
+            If `dict`, treat it as tracking settings.
+            Will patch the target config content with `tracking handlers` and the top-level items of `configs`.
             for detailed usage examples, please check the tutorial:
             https://github.com/Project-MONAI/tutorials/blob/main/experiment_management/bundle_integrate_mlflow.ipynb.
         args_file: a JSON or YAML file to provide default values for `run_id`, `meta_file`,

monai/bundle/utils.py

@@ -113,7 +113,7 @@
         "experiment_name": "monai_experiment",
         "run_name": None,
         # may fill it at runtime
-        "execute_config": None,
+        "save_execute_config": True,
         "is_not_rank0": (
             "$torch.distributed.is_available() \
                 and torch.distributed.is_initialized() and torch.distributed.get_rank() > 0"
@@ -125,7 +125,7 @@
             "tracking_uri": "@tracking_uri",
             "experiment_name": "@experiment_name",
             "run_name": "@run_name",
-            "artifacts": "@execute_config",
+            "artifacts": "@save_execute_config",
             "iteration_log": True,
             "epoch_log": True,
             "tag_name": "train_loss",
@@ -148,7 +148,7 @@
             "tracking_uri": "@tracking_uri",
             "experiment_name": "@experiment_name",
             "run_name": "@run_name",
-            "artifacts": "@execute_config",
+            "artifacts": "@save_execute_config",
             "iteration_log": False,
             "close_on_complete": True,
         },

monai/bundle/workflows.py

@@ -506,13 +506,19 @@ def patch_bundle_tracking(parser: ConfigParser, settings: dict) -> None:
                 parser[k] = v
         # save the executed config into file
         default_name = f"config_{time.strftime('%Y%m%d_%H%M%S')}.json"
-        filepath = parser.get("execute_config", None)
-        if filepath is None:
-            if "output_dir" not in parser:
-                # if no "output_dir" in the bundle config, default to "<bundle root>/eval"
-                parser["output_dir"] = f"{EXPR_KEY}{ID_REF_KEY}bundle_root + '/eval'"
-            # experiment management tools can refer to this config item to track the config info
-            parser["execute_config"] = parser["output_dir"] + f" + '/{default_name}'"
-            filepath = os.path.join(parser.get_parsed_content("output_dir"), default_name)
-        Path(filepath).parent.mkdir(parents=True, exist_ok=True)
-        parser.export_config_file(parser.get(), filepath)
+        # Users can set the `save_execute_config` to `False`, `/path/to/artifacts` or `True`.
+        # If set to False, nothing will be recorded. If set to True, the default path will be logged.
+        # If set to a file path, the given path will be logged.
+        filepath = parser.get("save_execute_config", True)
+        if filepath:
+            if isinstance(filepath, bool):
+                if "output_dir" not in parser:
+                    # if no "output_dir" in the bundle config, default to "<bundle root>/eval"
+                    parser["output_dir"] = f"{EXPR_KEY}{ID_REF_KEY}bundle_root + '/eval'"
+                # experiment management tools can refer to this config item to track the config info
+                parser["save_execute_config"] = parser["output_dir"] + f" + '/{default_name}'"
+                filepath = os.path.join(parser.get_parsed_content("output_dir"), default_name)
+            Path(filepath).parent.mkdir(parents=True, exist_ok=True)
+            parser.export_config_file(parser.get(), filepath)
+        else:
+            parser["save_execute_config"] = None

tests/test_fl_monai_algo.py

@@ -75,7 +75,7 @@
             tracking={
                 "handlers_id": DEFAULT_HANDLERS_ID,
                 "configs": {
-                    "execute_config": f"{_data_dir}/config_executed.json",
+                    "save_execute_config": f"{_data_dir}/config_executed.json",
                     "trainer": {
                         "_target_": "MLFlowHandler",
                         "tracking_uri": path_to_uri(_data_dir) + "/mlflow_override",
@@ -201,7 +201,7 @@ def test_train(self, input_params):
         algo.finalize()
 
         # test experiment management
-        if "execute_config" in algo.train_workflow.parser:
+        if "save_execute_config" in algo.train_workflow.parser:
             self.assertTrue(os.path.exists(f"{_data_dir}/mlflow_override"))
             shutil.rmtree(f"{_data_dir}/mlflow_override")
             self.assertTrue(os.path.exists(f"{_data_dir}/config_executed.json"))
@@ -224,7 +224,7 @@ def test_evaluate(self, input_params):
         algo.evaluate(data=data, extra={})
 
         # test experiment management
-        if "execute_config" in algo.eval_workflow.parser:
+        if "save_execute_config" in algo.eval_workflow.parser:
             self.assertGreater(len(list(glob.glob(f"{_data_dir}/mlflow_*"))), 0)
             for f in list(glob.glob(f"{_data_dir}/mlflow_*")):
                 shutil.rmtree(f)