Merge branch 'dev' into update-bundle

Project-MONAI · Oct 13, 2023 · 445347e · 445347e
2 parents 7e20dc0 + 340e65a
commit 445347e
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Showing 44 changed files with 120 additions and 105 deletions.
diff --git a/ci/run_premerge_cpu.sh b/ci/run_premerge_cpu.sh
@@ -30,6 +30,7 @@ elif [[ $# -gt 1 ]]; then
 fi
 
 verify_bundle() {
+    rm -rf /opt/hostedtoolcache
     echo 'Run verify bundle...'
     pip install -r requirements.txt
     head_ref=$(git rev-parse HEAD)

diff --git a/ci/unit_tests/test_brats_mri_axial_slices_generative_diffusion.py b/ci/unit_tests/test_brats_mri_axial_slices_generative_diffusion.py
@@ -93,7 +93,7 @@ def test_autoencoder_train(self, override):
         sys.path = [bundle_root] + sys.path
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=os.path.join(bundle_root, "configs/train_autoencoder.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -108,7 +108,7 @@ def test_autoencoder_infer(self, override):
         sys.path = [bundle_root] + sys.path
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference_autoencoder.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -125,7 +125,7 @@ def test_diffusion_train(self, override):
         diffusion_file = os.path.join(bundle_root, "configs/train_diffusion.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=[autoencoder_file, diffusion_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -140,7 +140,7 @@ def test_diffusion_infer(self, override):
         sys.path = [bundle_root] + sys.path
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_brats_mri_generative_diffusion.py b/ci/unit_tests/test_brats_mri_generative_diffusion.py
@@ -107,7 +107,7 @@ def test_autoencoder_train(self, override):
         sys.path = [bundle_root] + sys.path
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=os.path.join(bundle_root, "configs/train_autoencoder.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -122,7 +122,7 @@ def test_autoencoder_infer(self, override):
         sys.path = [bundle_root] + sys.path
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference_autoencoder.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -139,7 +139,7 @@ def test_diffusion_train(self, override):
         diffusion_file = os.path.join(bundle_root, "configs/train_diffusion.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=[autoencoder_file, diffusion_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -154,7 +154,7 @@ def test_diffusion_infer(self, override):
         sys.path = [bundle_root] + sys.path
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_brats_mri_segmentation.py b/ci/unit_tests/test_brats_mri_segmentation.py
@@ -70,7 +70,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -80,7 +80,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -94,7 +94,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_endoscopic_inbody_classification.py b/ci/unit_tests/test_endoscopic_inbody_classification.py
@@ -72,7 +72,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -82,7 +82,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -96,7 +96,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_endoscopic_tool_segmentation.py b/ci/unit_tests/test_endoscopic_tool_segmentation.py
@@ -71,7 +71,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -81,7 +81,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -95,7 +95,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_lung_nodule_ct_detection.py b/ci/unit_tests/test_lung_nodule_ct_detection.py
@@ -86,7 +86,7 @@ def test_train_eval_config(self, override):
 
         sys.path.append(bundle_root)
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -96,7 +96,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -111,7 +111,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_pancreas_ct_dints_segmentation.py b/ci/unit_tests/test_pancreas_ct_dints_segmentation.py
@@ -127,7 +127,7 @@ def test_train(self, override):
         train_file = os.path.join(bundle_root, "configs/train.yaml")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -146,7 +146,7 @@ def test_eval(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -161,7 +161,7 @@ def test_infer_config(self, override):
         arch_name = get_searched_arch(os.path.join(bundle_root, "models"))
         override["arch_ckpt_path"] = os.path.join(bundle_root, "models", arch_name)
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.yaml"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_pathology_nuclei_classification.py b/ci/unit_tests/test_pathology_nuclei_classification.py
@@ -99,7 +99,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -109,7 +109,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -124,7 +124,7 @@ def test_infer_config(self, override):
 
         sys.path.append(bundle_root)
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_pathology_nuclei_segmentation_classification.py b/ci/unit_tests/test_pathology_nuclei_segmentation_classification.py
@@ -87,7 +87,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -97,7 +97,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -111,7 +111,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_pathology_nuclick_annotation.py b/ci/unit_tests/test_pathology_nuclick_annotation.py
@@ -99,7 +99,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -109,7 +109,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -124,7 +124,7 @@ def test_infer_config(self, override):
 
         sys.path.append(bundle_root)
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_pathology_tumor_detection.py b/ci/unit_tests/test_pathology_tumor_detection.py
@@ -77,7 +77,7 @@ def test_train_infer_config(self, override, override_infer):
         train_file = os.path.join(bundle_root, "configs/train.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -89,7 +89,7 @@ def test_train_infer_config(self, override, override_infer):
         override_infer["dataset_dir"] = self.dataset_dir
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_renalStructures_CECT_segmentation.py b/ci/unit_tests/test_renalStructures_CECT_segmentation.py
@@ -93,7 +93,7 @@ def test_train_config(self, override):
         sys.path.append(bundle_root)
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=os.path.join(bundle_root, "configs/train.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -113,7 +113,7 @@ def test_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -127,7 +127,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),

diff --git a/ci/unit_tests/test_spleen_ct_segmentation.py b/ci/unit_tests/test_spleen_ct_segmentation.py
@@ -68,7 +68,7 @@ def test_train_eval_config(self, override):
         eval_file = os.path.join(bundle_root, "configs/evaluate.json")
 
         trainer = ConfigWorkflow(
-            workflow="train",
+            workflow_type="train",
             config_file=train_file,
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -78,7 +78,7 @@ def test_train_eval_config(self, override):
 
         validator = ConfigWorkflow(
             # override train.json, thus set the workflow to "train" rather than "eval"
-            workflow="train",
+            workflow_type="train",
             config_file=[train_file, eval_file],
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),
@@ -92,7 +92,7 @@ def test_infer_config(self, override):
         bundle_root = override["bundle_root"]
 
         inferrer = ConfigWorkflow(
-            workflow="infer",
+            workflow_type="infer",
             config_file=os.path.join(bundle_root, "configs/inference.json"),
             logging_file=os.path.join(bundle_root, "configs/logging.conf"),
             meta_file=os.path.join(bundle_root, "configs/metadata.json"),