adapt to BundleWorkflow interface

README.md

@@ -76,24 +76,24 @@ For more details usage instructions, visit the [MONAI Bundle Configuration Page]
 
 #### Execute training:
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf
+python -m monai.bundle run --config_file configs/train.json
 ```
 
 #### Override the `train` config to execute multi-GPU training:
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=8 -m monai.bundle run training --meta_file configs/metadata.json --config_file "['configs/train.json','configs/multi_gpu_train.json']" --logging_file configs/logging.conf
+torchrun --standalone --nnodes=1 --nproc_per_node=8 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
 ```
 
 Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
 
 #### Override the `train` config to execute evaluation with the trained model:
 ```
-python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file "['configs/train.json','configs/evaluate.json']" --logging_file configs/logging.conf
+python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
 ```
 
 #### Execute inference:
 ```
-python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
+python -m monai.bundle run --config_file configs/inference.json
 ```
 
 # References

configs/evaluate.json

@@ -85,8 +85,10 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }

configs/inference.json

@@ -35,7 +35,8 @@
         "transforms": [
             {
                 "_target_": "LoadImaged",
-                "keys": "image"
+                "keys": "image",
+                "image_only": false
             },
             {
                 "_target_": "NormalizeIntensityd",
@@ -129,8 +130,10 @@
         "val_handlers": "@handlers",
         "amp": true
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "[email protected]()"
     ]
 }

configs/metadata.json

@@ -1,7 +1,8 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
-    "version": "0.3.9",
+    "version": "0.4.0",
     "changelog": {
+        "0.4.0": "adapt to BundleWorkflow interface",
         "0.3.9": "black autofix format and add name tag",
         "0.3.8": "modify dataset key name",
         "0.3.7": "restructure readme to match updated template",
@@ -17,9 +18,9 @@
         "0.1.1": "update for MetaTensor",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.0.1",
-    "pytorch_version": "1.13.0",
-    "numpy_version": "1.22.4",
+    "monai_version": "1.2.0rc3",
+    "pytorch_version": "1.13.1",
+    "numpy_version": "1.22.2",
     "optional_packages_version": {
         "nibabel": "4.0.1",
         "pytorch-ignite": "0.4.9",

configs/multi_gpu_train.json

@@ -24,13 +24,17 @@
     },
     "validate#dataloader#sampler": "@validate#sampler",
     "validate#evaluator#val_handlers": "$None if dist.get_rank() > 0 else @validate#handlers",
-    "training": [
+    "initialize": [
         "$import torch.distributed as dist",
-        "$dist.init_process_group(backend='nccl')",
+        "$dist.is_initialized() or dist.init_process_group(backend='nccl')",
         "$torch.cuda.set_device(@device)",
         "$monai.utils.set_determinism(seed=123)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
-        "$@train#trainer.run()",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
+        "$@train#trainer.run()"
+    ],
+    "finalize": [
         "$dist.destroy_process_group()"
     ]
 }

configs/train.json

@@ -60,7 +60,8 @@
                 "keys": [
                     "image",
                     "label"
-                ]
+                ],
+                "image_only": false
             },
             {
                 "_target_": "ConvertToMultiChannelBasedOnBratsClassesd",
@@ -318,9 +319,11 @@
             "amp": "@amp"
         }
     },
-    "training": [
+    "initialize": [
         "$monai.utils.set_determinism(seed=123)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@train#trainer.run()"
     ]
 }

docs/README.md

@@ -69,24 +69,24 @@ For more details usage instructions, visit the [MONAI Bundle Configuration Page]
 
 #### Execute training:
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf
+python -m monai.bundle run --config_file configs/train.json
 ```
 
 #### Override the `train` config to execute multi-GPU training:
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=8 -m monai.bundle run training --meta_file configs/metadata.json --config_file "['configs/train.json','configs/multi_gpu_train.json']" --logging_file configs/logging.conf
+torchrun --standalone --nnodes=1 --nproc_per_node=8 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
 ```
 
 Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
 
 #### Override the `train` config to execute evaluation with the trained model:
 ```
-python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file "['configs/train.json','configs/evaluate.json']" --logging_file configs/logging.conf
+python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
 ```
 
 #### Execute inference:
 ```
-python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
+python -m monai.bundle run --config_file configs/inference.json
 ```
 
 # References