adapt to BundleWorkflow interface

README.md

@@ -95,13 +95,13 @@ Execute training:
 - Run first stage
 
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
+python -m monai.bundle run --config_file configs/train.json --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
 ```
 
 - Run second stage
 
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
+python -m monai.bundle run --config_file configs/train.json --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
 ```
 
 Override the `train` config to execute multi-GPU training:
@@ -109,25 +109,25 @@ Override the `train` config to execute multi-GPU training:
 - Run first stage
 
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=2 -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 --train#dataloader#batch_size 8 --network_def#freeze_encoder true --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']" --train#dataloader#batch_size 8 --network_def#freeze_encoder true --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
 ```
 
 - Run second stage
 
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=2 -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 --train#dataloader#batch_size 4 --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']" --train#dataloader#batch_size 4 --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
 ```
 
 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
 ```
 
 # Disclaimer

configs/evaluate.json

@@ -31,8 +31,10 @@
             "summary_ops": "*"
         }
     ],
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@validate#evaluator.run()"
     ]
 }

configs/inference.json

@@ -3,7 +3,7 @@
         "$import glob",
         "$import os"
     ],
-    "bundle_root": "$os.getcwd()",
+    "bundle_root": ".",
     "output_dir": "$os.path.join(@bundle_root, 'eval')",
     "dataset_dir": "/workspace/Data/Pathology/CoNSeP/Test/Images",
     "num_cpus": 2,
@@ -144,8 +144,10 @@
         "inferer": "@inferer",
         "amp": true
     },
-    "evaluating": [
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "initialize": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "[email protected]()"
     ]
 }

configs/metadata.json

@@ -1,14 +1,15 @@
 {
     "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_hovernet_20221124.json",
-    "version": "0.1.3",
+    "version": "0.1.4",
     "changelog": {
+        "0.1.4": "adapt to BundleWorkflow interface",
         "0.1.3": "add name tag",
         "0.1.2": "update the workflow figure",
         "0.1.1": "update to use monai 1.1.0",
         "0.1.0": "complete the model package"
     },
-    "monai_version": "1.1.0",
-    "pytorch_version": "1.13.0",
+    "monai_version": "1.2.0rc3",
+    "pytorch_version": "1.13.1",
     "numpy_version": "1.22.2",
     "optional_packages_version": {
         "scikit-image": "0.19.3",

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=321)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
-        "$@train#trainer.run()",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
+        "$@train#trainer.run()"
+    ],
+    "finalize": [
         "$dist.destroy_process_group()"
     ]
 }

configs/train.json

@@ -4,7 +4,7 @@
         "$import os",
         "$import skimage"
     ],
-    "bundle_root": "$os.getcwd()",
+    "bundle_root": ".",
     "ckpt_dir_stage0": "$os.path.join(@bundle_root, 'models', 'stage0')",
     "ckpt_dir_stage1": "$os.path.join(@bundle_root, 'models')",
     "ckpt_path_stage0": "$os.path.join(@ckpt_dir_stage0, 'model.pt')",
@@ -517,9 +517,11 @@
             "amp": "@amp"
         }
     },
-    "training": [
+    "initialize": [
         "$monai.utils.set_determinism(seed=321)",
-        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+        "$setattr(torch.backends.cudnn, 'benchmark', True)"
+    ],
+    "run": [
         "$@train#trainer.run()"
     ]
 }

docs/README.md

@@ -88,13 +88,13 @@ Execute training:
 - Run first stage
 
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
+python -m monai.bundle run --config_file configs/train.json --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
 ```
 
 - Run second stage
 
 ```
-python -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train.json --logging_file configs/logging.conf --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
+python -m monai.bundle run --config_file configs/train.json --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
 ```
 
 Override the `train` config to execute multi-GPU training:
@@ -102,25 +102,25 @@ Override the `train` config to execute multi-GPU training:
 - Run first stage
 
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=2 -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 --train#dataloader#batch_size 8 --network_def#freeze_encoder true --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']" --train#dataloader#batch_size 8 --network_def#freeze_encoder true --network_def#pretrained_url `PRETRAIN_MODEL_URL` --stage 0
 ```
 
 - Run second stage
 
 ```
-torchrun --standalone --nnodes=1 --nproc_per_node=2 -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 --train#dataloader#batch_size 4 --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']" --train#dataloader#batch_size 4 --network_def#freeze_encoder false --network_def#pretrained_url None --stage 1
 ```
 
 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
 ```
 
 # Disclaimer