Rename optional_packages_version to required_packages_version (#7253)

Fixes #6959.

### Description

A few sentences describing the changes proposed in this pull request.

### 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.
- [ ] 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.

---------

Signed-off-by: KumoLiu <[email protected]>
Signed-off-by: YunLiu <[email protected]>
Co-authored-by: Eric Kerfoot <[email protected]>
Co-authored-by: Mingxin Zheng <[email protected]>

Author: 3 people

monai/bundle/config_parser.py

@@ -118,7 +118,7 @@ def __init__(
         self.ref_resolver = ReferenceResolver()
         if config is None:
             config = {self.meta_key: {}}
-        self.set(config=config)
+        self.set(config=self.ref_resolver.normalize_meta_id(config))
 
     def __repr__(self):
         return f"{self.config}"
@@ -221,7 +221,7 @@ def set(self, config: Any, id: str = "", recursive: bool = True) -> None:
                 if isinstance(conf_, dict) and k not in conf_:
                     conf_[k] = {}
                 conf_ = conf_[k if isinstance(conf_, dict) else int(k)]
-        self[ReferenceResolver.normalize_id(id)] = config
+        self[ReferenceResolver.normalize_id(id)] = self.ref_resolver.normalize_meta_id(config)
 
     def update(self, pairs: dict[str, Any]) -> None:
         """

monai/bundle/reference_resolver.py

@@ -17,7 +17,7 @@
 from typing import Any, Iterator
 
 from monai.bundle.config_item import ConfigComponent, ConfigExpression, ConfigItem
-from monai.bundle.utils import ID_REF_KEY, ID_SEP_KEY
+from monai.bundle.utils import DEPRECATED_ID_MAPPING, ID_REF_KEY, ID_SEP_KEY
 from monai.utils import allow_missing_reference, look_up_option
 
 __all__ = ["ReferenceResolver"]
@@ -202,6 +202,23 @@ def normalize_id(cls, id: str | int) -> str:
         """
         return str(id).replace("#", cls.sep)  # backward compatibility `#` is the old separator
 
+    def normalize_meta_id(self, config: Any) -> Any:
+        """
+        Update deprecated identifiers in `config` using `DEPRECATED_ID_MAPPING`.
+        This will replace names that are marked as deprecated with their replacement.
+
+        Args:
+            config: input config to be updated.
+        """
+        if isinstance(config, dict):
+            for _id, _new_id in DEPRECATED_ID_MAPPING.items():
+                if _id in config.keys():
+                    warnings.warn(
+                        f"Detected deprecated name '{_id}' in configuration file, replacing with '{_new_id}'."
+                    )
+                    config[_new_id] = config.pop(_id)
+        return config
+
     @classmethod
     def split_id(cls, id: str | int, last: bool = False) -> list[str]:
         """

monai/bundle/utils.py

@@ -36,7 +36,7 @@
     "monai_version": _conf_values["MONAI"],
     "pytorch_version": str(_conf_values["Pytorch"]).split("+")[0].split("a")[0],  # 1.9.0a0+df837d0 or 1.13.0+cu117
     "numpy_version": _conf_values["Numpy"],
-    "optional_packages_version": {},
+    "required_packages_version": {},
     "task": "Describe what the network predicts",
     "description": "A longer description of what the network does, use context, inputs, outputs, etc.",
     "authors": "Your Name Here",
@@ -157,6 +157,8 @@
 
 DEFAULT_EXP_MGMT_SETTINGS = {"mlflow": DEFAULT_MLFLOW_SETTINGS}  # default experiment management settings
 
+DEPRECATED_ID_MAPPING = {"optional_packages_version": "required_packages_version"}
+
 
 def load_bundle_config(bundle_path: str, *config_names: str, **load_kw_args: Any) -> Any:
     """

tests/testing_data/data_config.json

@@ -162,9 +162,9 @@
     },
     "configs": {
         "test_meta_file": {
-            "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
+            "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20240725.json",
             "hash_type": "md5",
-            "hash_val": "662135097106b71067cd1fc657f8720f"
+            "hash_val": "06954cad2cc5d3784e72077ac76f0fc8"
         }
     }
 }

tests/testing_data/metadata.json

@@ -1,5 +1,5 @@
 {
-    "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
+    "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20240725.json",
     "version": "0.1.0",
     "changelog": {
         "0.1.0": "complete the model package",
@@ -8,7 +8,7 @@
     "monai_version": "0.9.0",
     "pytorch_version": "1.10.0",
     "numpy_version": "1.21.2",
-    "optional_packages_version": {
+    "required_packages_version": {
         "nibabel": "3.2.1"
     },
     "task": "Decathlon spleen segmentation",