Aligned with the changes in v0.5.1 before rebase/merge

Signed-off-by: M Q <mingmelvinq@nvidia.com>

Author: MMelQin

.readthedocs.yml

@@ -1,28 +1,35 @@
-# .readthedocs.yml
-# Read the Docs configuration file
+# Read the Docs configuration file for Sphinx projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
-# Build documentation in the docs/ directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
-
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
 
 # Optionally build your docs in additional formats such as PDF and ePub
-# formats: all
+# formats:
+#    - pdf
+#    - epub
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.8
-  install:
-    - requirements: docs/requirements.txt
-#  system_packages: true
-
-
-build:
-  image: stable
+   install:
+   - requirements: docs/requirements.txt

examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py

@@ -201,6 +201,7 @@ def compute(self, op_input, op_output, context):
 
 
 # @md.resource(cpu=1, gpu=1, memory="1Gi")
+# @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/operators/dicom_data_loader_operator.py

@@ -358,7 +358,8 @@ 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 '' }"
+                    f"  '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

@@ -177,11 +177,9 @@ 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}"))
             study_selected_series = StudySelectedSeries(study)
             for series in study.get_all_series():
                 logging.info(f"Working on series, instance UID: {str(series.SeriesInstanceUID)}")
-                print(f"Working on series, instance UID: {str(series.SeriesInstanceUID)}")
                 selected_series = SelectedSeries("", series, None)  # No selection name or Image obj.
                 study_selected_series.add_selected_series(selected_series)
             study_selected_series_list.append(study_selected_series)

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)

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!r}:/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!r}"
-    cmd += f" -e MONAI_OUTPUTPATH={map_output!r}"
+    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"
 

requirements-dev.txt

@@ -19,8 +19,8 @@ Sphinx==4.1.2
 recommonmark==0.6.0
 sphinx-autodoc-typehints==1.12.0
 sphinx-rtd-theme==0.5.2
-pytest==6.2.4
-pytest-cov==2.12.1
+pytest==7.4.0
+pytest-cov==4.1.0
 pytest-lazy-fixture==0.6.3
 cucim~=21.06; platform_system == "Linux"
 monai>=1.0.0

requirements.txt

@@ -2,4 +2,4 @@ holoscan>=0.5.0
 numpy>=1.21.6
 networkx>=2.4
 colorama>=0.4.1
-typeguard~=2.12.1
+typeguard>=3.0.0

run

@@ -818,7 +818,7 @@ pytest_desc() { c_echo 'Run tests with pytest
 
 It executes the following command:
 
-  ' "${MONAI_PY_EXE}"' -m py.test --cache-clear -vv \
+  ' "${MONAI_PY_EXE}"' -m pytest --cache-clear -vv \
       --cov=monai \
       --junitxml="'"$TOP/junit-monai-deploy-app-sdk.xml"'" \
       --cov-config="'"$TOP/.coveragerc"'" \
@@ -837,7 +837,7 @@ pytest() {
     local result=0
 
     pushd $TOP > /dev/null
-    run_command ${MONAI_PY_EXE} -m py.test --cache-clear -vv \
+    run_command ${MONAI_PY_EXE} -m pytest --cache-clear -vv \
         --cov=monai \
         --junitxml="$TOP/junit-monai-deploy-app-sdk.xml" \
         --cov-config="$TOP/.coveragerc" \

setup.cfg

@@ -11,7 +11,7 @@ license = Apache License 2.0
 license_files =
     LICENSE
 project_urls =
-    Documentation=https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/
+    Documentation=https://docs.monai.io/projects/monai-deploy-app-sdk/en/stable/
     Bug Tracker=https://github.com/Project-MONAI/monai-deploy-app-sdk/issues
     Source Code=https://github.com/Project-MONAI/monai-deploy-app-sdk
 
@@ -27,7 +27,7 @@ install_requires =
     networkx>=2.4
     holoscan>=0.5.0
     colorama>=0.4.1
-    typeguard~=2.12.1
+    typeguard>=3.0.0
 
 [options.extras_require]
 all =

tests/unit/test_runner.py

@@ -168,8 +168,8 @@ def test_run_app_for_input_output_path_with_space(
     expected_container_output /= app_manifest["working-directory"]
 
     returncode = runner.run_app(sample_map_name, input_path, output_path, app_manifest, faux_pkg_manifest, quiet)
-    input_path_with_quotes = f"{input_path.absolute()!r}"
-    output_path_with_quotes = f"{output_path.absolute()!r}"
+    input_path_with_quotes = '"{}"'.format(input_path.absolute())  # To quiet flake8 complaint
+    output_path_with_quotes = '"{}"'.format(output_path.absolute())
 
     assert returncode == return_value
     mock_run_cmd.assert_called_once_with(ContainsString(sample_map_name))