Update SDK to support typeguard v3.0 and above, which has a breaking change in its API, and updated notebooks

.github/workflows/pr.yml

@@ -14,10 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: "3.7"
+          python-version: "3.8"
       - name: Setup Dev Environment
         run: |
           pip install virtualenv

.readthedocs.yml

@@ -18,7 +18,7 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: "3.8"
   install:
     - requirements: docs/requirements.txt
 #  system_packages: true

examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py

@@ -95,7 +95,7 @@ def compute(self, op_input: InputContext, op_output: OutputContext, context: Exe
 
 
 @md.resource(cpu=1, gpu=1, memory="1Gi")
-@md.env(pip_packages=["pydicom >= 2.3.0", "highdicom>=0.18.2", "typeguard~=2.12.1"])
+@md.env(pip_packages=["pydicom >= 2.3.0", "highdicom>=0.18.2"])  # because of the use of DICOM writer operator
 class App(Application):
     """Application class for the MedNIST classifier."""
 

monai/deploy/core/application.py

@@ -205,13 +205,13 @@ def add_flow(
         if not io_map:
             if len(op_output_labels) > 1:
                 raise IOMappingError(
-                    f"The source operator has more than one output port "
+                    "The source operator has more than one output port "
                     f"({', '.join(op_output_labels)}) so mapping should be specified explicitly!"
                 )
             if len(op_input_labels) > 1:
                 raise IOMappingError(
                     f"The destination operator has more than one output port ({', '.join(op_input_labels)}) "
-                    f"so mapping should be specified explicitly!"
+                    "so mapping should be specified explicitly!"
                 )
             io_map = {"": {""}}
 
@@ -227,7 +227,7 @@ def add_flow(
         if len(op_output_labels) == 1 and len(output_labels) != 1:
             raise IOMappingError(
                 f"The source operator({source_op.name}) has only one port with label "
-                f"'{next(iter(op_output_labels))}' but io_map specifies {len(output_labels)} "
+                f"{next(iter(op_output_labels))!r} but io_map specifies {len(output_labels)} "
                 f"labels({', '.join(output_labels)}) to the source operator's output port"
             )
 
@@ -239,7 +239,7 @@ def add_flow(
                     del io_maps[output_label]
                     break
                 raise IOMappingError(
-                    f"The source operator({source_op.name}) has no output port with label '{output_label}'. "
+                    f"The source operator({source_op.name}) has no output port with label {output_label!r}. "
                     f"It should be one of ({', '.join(op_output_labels)})."
                 )
 
@@ -250,7 +250,7 @@ def add_flow(
             if len(op_input_labels) == 1 and len(input_labels) != 1:
                 raise IOMappingError(
                     f"The destination operator({destination_op.name}) has only one port with label "
-                    f"'{next(iter(op_input_labels))}' but io_map specifies {len(input_labels)} "
+                    f"{next(iter(op_input_labels))!r} but io_map specifies {len(input_labels)} "
                     f"labels({', '.join(input_labels)}) to the destination operator's input port"
                 )
 
@@ -262,8 +262,8 @@ def add_flow(
                         input_labels.add(next(iter(op_input_labels)))
                         break
                     raise IOMappingError(
-                        f"The destination operator({destination_op.name}) has no input port with label '{input_label}'. "
-                        f"It should be one of ({', '.join(op_input_labels)})."
+                        f"The destination operator({destination_op.name}) has no input port with label {input_label!r}."
+                        f" It should be one of ({', '.join(op_input_labels)})."
                     )
 
         self._graph.add_flow(source_op, destination_op, io_maps)

monai/deploy/core/domain/datapath.py

@@ -67,10 +67,10 @@ def get(self, name: Optional[str] = "") -> DataPath:
                 return next(iter(self._paths.values()))
             else:
                 raise IOMappingError(
-                    f"'{name}' is not a valid name. It should be one of ({', '.join(self._paths.keys())})."
+                    f"{name!r} is not a valid name. It should be one of ({', '.join(self._paths.keys())})."
                 )
         else:
             datapath = self._paths.get(name)
             if not datapath:
-                raise ItemNotExistsError(f"A DataPath instance for '{name}' does not exist.")
+                raise ItemNotExistsError(f"A DataPath instance for {name!r} does not exist.")
             return datapath

monai/deploy/core/env.py

@@ -37,7 +37,7 @@ def __init__(self, pip_packages: Optional[Union[str, List[str]]] = None):
             if requirements_path.exists():
                 pip_packages = requirements_path.read_text().strip().splitlines()  # make it a list
             else:
-                raise FileNotFoundError(f"The '{requirements_path}' file does not exist!")
+                raise FileNotFoundError(f"The {requirements_path!r} file does not exist!")
 
         self._pip_packages = list(pip_packages or [])
 

monai/deploy/core/io_context.py

@@ -49,7 +49,7 @@ def get_default_label(self, label: str = "") -> str:
                 label = next(iter(self._labels))
             else:
                 raise IOMappingError(
-                    f"'{label}' is not a valid {self._io_kind} of the operator({self._op.name}). "
+                    f"{label!r} is not a valid {self._io_kind} of the operator({self._op.name}). "
                     f"It should be one of ({', '.join(self._labels)})."
                 )
         return label
@@ -82,7 +82,7 @@ def get(self, label: str = "") -> Any:
         key = self.get_group_path(f"{self._io_kind}/{label}")
         storage = self._storage
         if not storage.exists(key):
-            raise ItemNotExistsError(f"'{key}' does not exist.")
+            raise ItemNotExistsError(f"{key!r} does not exist.")
         return storage.get(key)
 
     def set(self, value: Any, label: str = ""):
@@ -109,10 +109,10 @@ def set(self, value: Any, label: str = ""):
             # checking: https://www.python.org/dev/peps/pep-0585/#id15
             data_type = self._op_info.get_data_type(self._io_kind, label)
             try:
-                check_type("value", value, data_type)
+                check_type(value, data_type)
             except TypeError as err:
                 raise IOMappingError(
-                    f"The data type of '{label}' in the {self._io_kind} of '{self._op}' is {data_type}, but the value"
+                    f"The data type of {label!r} in the {self._io_kind} of {self._op!r} is {data_type}, but the value"
                     f" to set is the data type of {type(value)}."
                 ) from err
 

monai/deploy/core/models/model.py

@@ -164,7 +164,7 @@ def get(self, name: str = "") -> "Model":
             if item:
                 return item
             else:
-                raise ItemNotExistsError(f"A model with '{name}' does not exist.")
+                raise ItemNotExistsError(f"A model with {name!r} does not exist.")
         else:
             item_count = len(self._items)
             if item_count == 1:

monai/deploy/core/models/named_model.py

@@ -83,7 +83,7 @@ def accept(cls, path: str):
             # 3) Each model folder must contain only one model definition file or folder.
             if sum(1 for _ in model_folder.iterdir()) != 1:
                 logger.warning(
-                    f"Model repository '{model_folder}' contains more than one model definition file or folder "
+                    f"Model repository {model_folder!r} contains more than one model definition file or folder "
                     "so not treated as NamedModel."
                 )
                 return False, None

monai/deploy/core/resource.py

@@ -64,15 +64,17 @@ def set_resource_limits(
                 self._cpu = cpu_limit
             else:
                 raise ItemAlreadyExistsError(
-                    f"'cpu' wouldn't be set to {cpu_limit} because it is already set to {self._cpu} by the runtime environment."
+                    f"'cpu' wouldn't be set to {cpu_limit} because it is already set to {self._cpu} by the runtime"
+                    " environment."
                 )
 
         if gpu_limit is not None:
             if self._gpu is None:
                 self._gpu = gpu_limit
             else:
                 raise ItemAlreadyExistsError(
-                    f"'gpu' wouldn't be set to {gpu_limit} because it is already set to {self._gpu} by the runtime environment."
+                    f"'gpu' wouldn't be set to {gpu_limit} because it is already set to {self._gpu} by the runtime"
+                    " environment."
                 )
 
         if type(memory_limit) == str:

monai/deploy/operators/dicom_data_loader_operator.py

@@ -308,7 +308,8 @@ def test():
                 print(f"   'StudyInstanceUID': {ds.StudyInstanceUID if ds.StudyInstanceUID else ''}")
                 print(f"  'SeriesDescription': {ds.SeriesDescription if ds.SeriesDescription else ''}")
                 print(
-                    f"  'IssuerOfPatientID': {ds.get('IssuerOfPatientID', '').repval if ds.get('IssuerOfPatientID', '') else '' }"
+                    "  'IssuerOfPatientID':"
+                    f" {ds.get('IssuerOfPatientID', '').repval if ds.get('IssuerOfPatientID', '') else '' }"
                 )
                 try:
                     print(f"  'IssuerOfPatientID': {ds.IssuerOfPatientID if ds.IssuerOfPatientID else '' }")

monai/deploy/operators/dicom_series_selector_operator.py

@@ -177,7 +177,7 @@ def _select_all_series(self, dicom_study_list: List[DICOMStudy]) -> List[StudySe
         study_selected_series_list = []
         for study in dicom_study_list:
             logging.info(f"Working on study, instance UID: {study.StudyInstanceUID}")
-            print((f"Working on study, instance UID: {study.StudyInstanceUID}"))
+            print(f"Working on study, instance UID: {study.StudyInstanceUID}")
             study_selected_series = StudySelectedSeries(study)
             for series in study.get_all_series():
                 logging.info(f"Working on series, instance UID: {str(series.SeriesInstanceUID)}")
@@ -213,7 +213,7 @@ def _select_series(self, attributes: dict, study: DICOMStudy, all_matched=False)
             matched = True
             # Simple matching on attribute value
             for key, value_to_match in attributes.items():
-                logging.info(f"On attribute: '{key}' to match value: '{value_to_match}'")
+                logging.info(f"On attribute: {key!r} to match value: {value_to_match!r}")
                 # Ignore None
                 if not value_to_match:
                     continue

monai/deploy/operators/monai_bundle_inference_operator.py

@@ -80,7 +80,7 @@ def _read_from_archive(archive, root_name: str, config_name: str, do_search=True
         for suffix in bundle_suffixes:
             path = Path(root_name, config_folder, config_name).with_suffix(suffix)
             try:
-                logging.debug(f"Trying to read config '{config_name}' content from {path}.")
+                logging.debug(f"Trying to read config {config_name!r} content from {path}.")
                 content_text = archive.read(str(path))
                 break
             except Exception:
@@ -89,12 +89,12 @@ def _read_from_archive(archive, root_name: str, config_name: str, do_search=True
 
         # Try search for the name in the name list of the archive
         if not content_text and do_search:
-            logging.debug(f"Trying to find the file in the archive for config '{config_name}'.")
+            logging.debug(f"Trying to find the file in the archive for config {config_name!r}.")
             name_list = archive.namelist()
             for suffix in bundle_suffixes:
                 for n in name_list:
                     if (f"{config_name}{suffix}").casefold in n.casefold():
-                        logging.debug(f"Trying to read content of config '{config_name}' from {n}.")
+                        logging.debug(f"Trying to read content of config {config_name!r} from {n}.")
                         content_text = archive.read(n)
                         break
 

monai/deploy/packager/util.py

@@ -93,11 +93,9 @@ def initialize_args(args: Namespace) -> Dict:
         dockerfile_type = verify_base_image(args.base)
         if not dockerfile_type:
             logger.error(
-                "Provided base image '{}' is not supported \n \
-                        Please provide a ROCm or Cuda based Pytorch image from \n \
-                        https://hub.docker.com/r/rocm/pytorch or https://ngc.nvidia.com/ (nvcr.io/nvidia)".format(
-                    args.base
-                )
+                "Provided base image '{}' is not supported \n                         Please provide a ROCm or Cuda"
+                " based Pytorch image from \n                         https://hub.docker.com/r/rocm/pytorch or"
+                " https://ngc.nvidia.com/ (nvcr.io/nvidia)".format(args.base)
             )
 
             sys.exit(1)
@@ -237,7 +235,7 @@ def build_image(args: dict, temp_dir: str):
         dockerignore_file.write(docker_ignore_template)
 
     # Build dockerfile into an MAP image
-    docker_build_cmd = f'''docker build -f "{docker_file_path}" -t {tag} "{temp_dir}"'''
+    docker_build_cmd = f"""docker build -f {docker_file_path!r} -t {tag} {temp_dir!r}"""
     if sys.platform != "win32":
         docker_build_cmd += """ --build-arg MONAI_UID=$(id -u) --build-arg MONAI_GID=$(id -g)"""
     if no_cache:

monai/deploy/runner/runner.py

@@ -41,7 +41,7 @@ def fetch_map_manifest(map_name: str) -> Tuple[dict, dict, int]:
 
     with tempfile.TemporaryDirectory() as info_dir:
         if sys.platform == "win32":
-            cmd = f'docker run --rm -a STDOUT -a STDERR -v "{info_dir}":/var/run/monai/export/config {map_name}'
+            cmd = f'docker run --rm -a STDOUT -a STDERR -v " {info_dir}":/var/run/monai/export/config {map_name}'
         else:
             cmd = f"""docker_id=$(docker create {map_name})
 docker cp $docker_id:/etc/monai/app.json "{info_dir}/app.json"
@@ -103,8 +103,8 @@ def run_app(map_name: str, input_path: Path, output_path: Path, app_info: dict,
     if not posixpath.isabs(map_output):
         map_output = posixpath.join(app_info["working-directory"], map_output)
 
-    cmd += f' -e MONAI_INPUTPATH="{map_input}"'
-    cmd += f' -e MONAI_OUTPUTPATH="{map_output}"'
+    cmd += ' -e MONAI_INPUTPATH="{}"'.format(map_input)
+    cmd += ' -e MONAI_OUTPUTPATH="{}"'.format(map_output)
     # TODO(bhatt-piyush): Handle model environment correctly (maybe solved by fixing 'monai-exec')
     cmd += " -e MONAI_MODELPATH=/opt/monai/models"
 

monai/deploy/utils/argparse_types.py

@@ -36,7 +36,7 @@ def valid_dir_path(path: str) -> Path:
         if dir_path.is_dir():
             return dir_path
         else:
-            raise argparse.ArgumentTypeError(f"Expected directory path: '{dir_path}' is not a directory")
+            raise argparse.ArgumentTypeError(f"Expected directory path: {dir_path!r} is not a directory")
 
     # create directory
     dir_path.mkdir(parents=True)
@@ -58,7 +58,7 @@ def valid_existing_dir_path(path: str) -> Path:
     dir_path = Path(path).absolute()
     if dir_path.exists() and dir_path.is_dir():
         return dir_path
-    raise argparse.ArgumentTypeError(f"No such directory: '{dir_path}'")
+    raise argparse.ArgumentTypeError(f"No such directory: {dir_path!r}")
 
 
 def valid_existing_path(path: str) -> Path:
@@ -76,4 +76,4 @@ def valid_existing_path(path: str) -> Path:
     file_path = Path(path).absolute()
     if file_path.exists():
         return file_path
-    raise argparse.ArgumentTypeError(f"No such file/folder: '{file_path}'")
+    raise argparse.ArgumentTypeError(f"No such file/folder: {file_path!r}")

monai/deploy/utils/importutil.py

@@ -238,7 +238,7 @@ def optional_import(
     # preparing lazy error message
     msg = descriptor.format(actual_cmd)
     if version and tb is None:  # a pure version issue
-        msg += f" (requires '{module} {version}' by '{version_checker.__name__}')"
+        msg += f" (requires '{module} {version}' by {version_checker.__name__!r})"
     if exception_str:
         msg += f" ({exception_str})"
 

monai/deploy/utils/sizeutil.py

@@ -66,7 +66,7 @@ def get_bytes(size: Union[str, int]) -> int:
 
     m = re.match(r"^\s*(?P<size>(([1-9]\d+)|\d)(\.\d+)?)\s*(?P<unit>[a-z]{1,3})?\s*$", size, re.IGNORECASE)
     if not m:
-        raise ValueError(f"Invalid size string ('{size}').")
+        raise ValueError(f"Invalid size string ({size!r}).")
 
     parsed_size = float(m.group("size"))
 
@@ -77,7 +77,7 @@ def get_bytes(size: Union[str, int]) -> int:
         parsed_unit = "b"  # default to bytes
 
     if parsed_unit not in BYTES_UNIT:
-        raise ValueError(f"Invalid unit ('{parsed_unit}').")
+        raise ValueError(f"Invalid unit ({parsed_unit!r}).")
 
     return int(parsed_size * BYTES_UNIT[parsed_unit])
 
@@ -115,7 +115,7 @@ def convert_bytes(num_bytes: int, unit: str = "Mi") -> Union[str, int]:
 
     unit_lowered = unit.lower()
     if unit_lowered not in BYTES_UNIT:
-        raise ValueError(f"Invalid unit ('{unit}').")
+        raise ValueError(f"Invalid unit ({unit!r}).")
 
     converted = float(num_bytes) / BYTES_UNIT[unit_lowered] * 10
 

monai/deploy/utils/version.py

@@ -123,7 +123,7 @@ def get_sdk_semver():
         if SEMVER_REGEX.match(semver_str):
             return semver_str
         else:
-            raise ValueError(f"Invalid semver string: '{semver_str}' (from '{version_str}')")
+            raise ValueError(f"Invalid semver string: {semver_str!r} (from {version_str!r})")
     else:
         raise ValueError(f"Invalid version string: {version_str}")