Enhance Packager to make the MAP more secure, easier to use, and based on new version of PyTorch image for newer CUDA versions. (#381)

* Update the default base image to 22.08 version

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

* Remove unused file path contain "/tmp/" which caused security warning

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

* Add env var and remove /tmp is packager, update dependent package min version

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

* Update the Gaussian due to new param introduced in sciki-image 0.19

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

* Formatting fix

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

* Fix simple_app Jupyter notebook imshow failure with the new scikit-image

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

* Keep Numpy at 1.21.6 for Python 3.7 support

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

* Fix Flake8 error

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

* For Python 3.7 compatibility

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

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

Author: MMelQin

docs/requirements.txt

@@ -1,7 +1,7 @@
 Sphinx==4.1.2
 sphinx-autobuild==2021.3.14
 myst-parser==0.15.2
-numpy>=1.21.2  # CVE-2021-33430
+numpy>=1.21.6
 matplotlib==3.3.4
 ipywidgets==7.6.4
 pandas==1.1.5
@@ -23,7 +23,7 @@ scikit-image>=0.17.2
 plotly
 nibabel>=3.2.1
 monai>=1.0.0
-torch>=1.10.0
+torch>=1.12.0
 numpy-stl>=2.12.0
 trimesh>=3.8.11
 pydicom

docs/source/developing_with_sdk/packaging_app.md

@@ -46,7 +46,7 @@ However, the user can choose to override these values by invoking these optional
 * `--requirements, -r <FILE_PATH>`: Optional path to requirements.txt containing package dependencies of the application
 * `--log-level, -l <LEVEL>`: Set the logging level (`"DEBUG"`, `"INFO"`, `"WARN"`, `"ERROR"`, or `"CRITICAL"`).
 
-* `--base <BASE_IMAGE>`: Base Docker Image (overrides default `"nvcr.io/nvidia/pytorch:21.07-py3"`).
+* `--base <BASE_IMAGE>`: Base Docker Image (overrides default `"nvcr.io/nvidia/pytorch:22.08-py3"`).
 * `--input-dir, -i <INPUT_DIR>`: Directory mounted in container for Application Input (overrides default `"input"`).
 * `--models-dir <MODELS_DIR>`: Directory mounted in container for Models Path (overrides default `"/opt/monai/models"`).
 * `--output-dir, -o <OUTPUT_DIR>`: Directory mounted in container for Application Output (overrides default `"output"`).

docs/source/getting_started/installing_app_sdk.md

@@ -19,12 +19,12 @@ For packaging your application, [MONAI Application Packager](/developing_with_sd
 
 <https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker>
 
-Currently, `nvcr.io/nvidia/pytorch:21.07-py3` base Docker image is used by [MONAI Application Packager](/developing_with_sdk/packaging_app) by default.
+Currently, `nvcr.io/nvidia/pytorch:22.08-py3` base Docker image is used by [MONAI Application Packager](/developing_with_sdk/packaging_app) by default.
 
 The image size is large so please pull the image in advance to save time.
 
 ```bash
-docker pull nvcr.io/nvidia/pytorch:21.07-py3
+docker pull nvcr.io/nvidia/pytorch:22.08-py3
 ```
 
 :::

examples/apps/ai_pancrea_seg_app/__main__.py

@@ -1,4 +1,4 @@
-from app import AISpleenSegApp
+from app import AIPancreasSegApp
 
 if __name__ == "__main__":
-    AISpleenSegApp(do_run=True)
+    AIPancreasSegApp(do_run=True)

examples/apps/simple_imaging_app/gaussian_operator.py

@@ -29,7 +29,7 @@ def compute(self, op_input: InputContext, op_output: OutputContext, context: Exe
         from skimage.io import imsave
 
         data_in = op_input.get().asnumpy()
-        data_out = gaussian(data_in, sigma=0.2)
+        data_out = gaussian(data_in, sigma=0.2, channel_axis=2)  # Add the param introduced in 0.19.
 
         output_folder = op_output.get().path
         output_path = output_folder / "final_output.png"

monai/deploy/packager/constants.py

@@ -16,7 +16,7 @@ class DefaultValues:
     """
 
     DOCKER_FILE_NAME = "dockerfile"
-    BASE_IMAGE = "nvcr.io/nvidia/pytorch:21.07-py3"
+    BASE_IMAGE = "nvcr.io/nvidia/pytorch:22.08-py3"
     DOCKERFILE_TYPE = "pytorch"
     WORK_DIR = "/var/monai/"
     INPUT_DIR = "input"

monai/deploy/packager/templates.py

@@ -1,4 +1,4 @@
-# Copyright 2021 MONAI Consortium
+# Copyright 2021-2022 MONAI Consortium
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +12,7 @@
 COMMON_FOOTPRINT = """
     USER root
 
-    RUN pip install --no-cache-dir --upgrade setuptools==57.4.0 pip==21.3.1 wheel==0.37.0 numpy>=1.21
+    RUN pip install --no-cache-dir --upgrade setuptools==59.5.0 pip==22.3 wheel==0.37.1 numpy>=1.21.6
 
     RUN mkdir -p /etc/monai/ \\
      && mkdir -p /opt/monai/ \\
@@ -72,6 +72,7 @@
     ENV MONAI_WORKDIR={working_dir}
     ENV MONAI_APPLICATION={app_dir}
     ENV MONAI_TIMEOUT={timeout}
+    ENV MONAI_MODELPATH={models_dir}
 
     RUN apt update \\
      && apt upgrade -y --no-install-recommends \\
@@ -106,6 +107,7 @@
     ENV MONAI_WORKDIR={working_dir}
     ENV MONAI_APPLICATION={app_dir}
     ENV MONAI_TIMEOUT={timeout}
+    ENV MONAI_MODELPATH={models_dir}
 
     RUN apt update \\
      && apt upgrade -y --no-install-recommends \\

monai/deploy/packager/util.py

@@ -17,6 +17,7 @@
 import sys
 import tempfile
 from argparse import Namespace
+from pathlib import Path
 from typing import Dict
 
 from monai.deploy.exceptions import WrongValueError
@@ -177,7 +178,9 @@ def build_image(args: dict, temp_dir: str):
                     requirements_file.write(line)
         else:
             requirements_file.writelines("\n".join(pip_packages))
-    map_requirements_path = "/tmp/requirements.txt"
+
+    # Parameter for the Dockerfile for copying content to internal path
+    map_requirements_path = str(Path(app_dir) / "requirements.txt")
 
     # Copy model files to temp directory (under 'model' folder)
     target_models_path = os.path.join(temp_dir, "models")

notebooks/tutorials/01_simple_app.ipynb

@@ -1646,7 +1646,7 @@
     }
    ],
    "source": [
-    "!monai-deploy package -b nvcr.io/nvidia/pytorch:21.11-py3 my_app --tag my_app:latest -m model.ts"
+    "!monai-deploy package -b nvcr.io/nvidia/pytorch:22.08-py3 my_app --tag my_app:latest -m model.ts"
    ]
   },
   {

notebooks/tutorials/03_segmentation_app.ipynb

@@ -1337,7 +1337,7 @@
     }
    ],
    "source": [
-    "!monai-deploy package -b nvcr.io/nvidia/pytorch:21.11-py3 my_app --tag my_app:latest -m model.ts"
+    "!monai-deploy package -b nvcr.io/nvidia/pytorch:22.08-py3 my_app --tag my_app:latest -m model.ts"
    ]
   },
   {

notebooks/tutorials/06_monai_bundle_app.ipynb

@@ -35,4 +35,4 @@ scikit-image>=0.17.2
 nibabel>=3.2.1
 numpy-stl>=2.12.0
 trimesh>=3.8.11
-torch>=1.10.0
+torch>=1.12.0

requirements-dev.txt

@@ -9,5 +9,5 @@ trimesh>=3.8.11
 nibabel>=3.2.1
 numpy-stl>=2.12.0
 trimesh>=3.8.11
-torch>=1.10.0
+torch>=1.12.0
 monai>=1.0.0

requirements-examples.txt

@@ -1,5 +1,5 @@
 # Requirements for minimal tests
 -r requirements.txt
-setuptools>=50.3.0
+setuptools>=59.5.0
 coverage>=5.5
 parameterized

requirements-min.txt

@@ -1,4 +1,4 @@
-numpy>=1.21.2
+numpy>=1.21.6
 networkx>=2.4
 colorama>=0.4.1
 typeguard>=2.12.1

requirements.txt

@@ -23,7 +23,7 @@ python_requires = >= 3.7
 # setup_requires =
 #     cucim
 install_requires =
-    numpy>=1.21.2  # CVE-2021-33430
+    numpy>=1.21.6
     networkx>=2.4
     colorama>=0.4.1
     typeguard>=2.12.1