Project-MONAI · gigony · Jan 26, 2022 · Dec 2, 2021 · Jan 25, 2022 · Jan 25, 2022
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.0
+current_version = 0.2.1
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)((?P<release>a|b|rc)(?P<build>\d+))?
 serialize = 
 	{major}.{minor}.{patch}{release}{build}

diff --git a/README.md b/README.md
@@ -75,6 +75,10 @@ YouTube Video:
 - [Spleen Organ Segmentation - Jupyter Notebook Tutorial](https://www.youtube.com/watch?v=cqDVxzYt9lY)
 - [Spleen Organ Segmentation - Deep Dive](https://www.youtube.com/watch?v=nivgfD4pwWE)
 
+### [4) Deploying Segmentation app with MONAI Inference Service (MIS)](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/tutorials/04_mis_tutorial.html)
+
+### [5) Building and deploying Segmentation app with MONAI Inference Service (MIS)](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/tutorials/05_full_tutorial.html)
+
 ### [Examples](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/examples.html)
 
 <https://github.com/Project-MONAI/monai-deploy-app-sdk/tree/main/examples/apps> has example apps that you can see.

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,7 +1,7 @@
 Sphinx==4.1.2
 sphinx-autobuild==2021.3.14
 myst-parser==0.15.2
-numpy==1.19.5
+numpy==1.21  # CVE-2021-33430
 matplotlib==3.3.4
 ipywidgets==7.6.4
 pandas==1.1.5

diff --git a/docs/source/getting_started/tutorials/04_mis_tutorial.md b/docs/source/getting_started/tutorials/04_mis_tutorial.md
@@ -12,6 +12,12 @@ The environment from the previous section (**<a href="./03_segmentation_app.html
 ../../notebooks/tutorials/04_mis_tutorial.ipynb
 ```
 
+<!-- ```{raw} html
+<div style="text-align: center;">
+    <iframe width="560" height="315" src="https://www.youtube.com/watch?v=sISg521fdCA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+</div>
+``` -->
+
 ```{raw} html
 <p style="text-align: center;">
     <a class="sphinx-bs btn text-wrap btn-outline-primary col-md-6 reference external" href="../../_static/notebooks/tutorials/04_mis_tutorial.ipynb">

diff --git a/docs/source/getting_started/tutorials/05_full_tutorial.md b/docs/source/getting_started/tutorials/05_full_tutorial.md
@@ -12,6 +12,12 @@ The environment from the previous section (**<a href="./03_segmentation_app.html
 ../../notebooks/tutorials/05_full_tutorial.ipynb
 ```
 
+<!-- ```{raw} html
+<div style="text-align: center;">
+    <iframe width="560" height="315" src="https://www.youtube.com/watch?v=sISg521fdCA" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+</div>
+``` -->
+
 ```{raw} html
 <p style="text-align: center;">
     <a class="sphinx-bs btn text-wrap btn-outline-primary col-md-6 reference external" href="../../_static/notebooks/tutorials/05_full_tutorial.ipynb">

diff --git a/docs/source/release_notes/index.md b/docs/source/release_notes/index.md
@@ -11,6 +11,7 @@
 ```{toctree}
 :maxdepth: 1
 
+v0.2.1
 v0.2.0
 ```
 

diff --git a/docs/source/release_notes/v0.2.1.md b/docs/source/release_notes/v0.2.1.md
@@ -0,0 +1,31 @@
+# Version 0.2.1 (January 25, 2022)
+
+This is a patch release of [v0.2](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/release_notes/v0.2.0.html#).
+
+Please visit [GETTING STARTED](/getting_started/index) guide and follow tutorials.
+
+You can learn more about SDK usage through [DEVELOPING WITH SDK](/developing_with_sdk/index).
+
+Please let us know how you like it and what could be improved by [submitting an issue](https://github.com/Project-MONAI/monai-deploy-app-sdk/issues/new/choose) or [asking questions](https://github.com/Project-MONAI/monai-deploy-app-sdk/discussions)😀
+
+## What's new
+
+As per MONAI Core's [Python 3.6 drop](https://github.com/Project-MONAI/MONAI/pull/3536), drop the support for Python 3.6 from MONAI Deploy App SDK.
+
+- Drop Python 3.6 support [#248](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/248) by [@gigony](https://github.com/gigony)
+
+## What's fixed/updated
+
+- Fixed minor dependencies for fresh deployment [#208](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/208) by [@vikashg](https://github.com/vikashg)
+- Fix minor typo in chapter 4 notebook [#209](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/209) by [@KavinKrishnan](https://github.com/KavinKrishnan)
+- Bump numpy >= 1.20 to avoid MKL error in conda env, and add --upgrade for pip install app sdk [#211](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/211) by [@MMelQin](https://github.com/MMelQin)
+- Update notebooks with cloning repo and building MIS container [#214](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/214) by [@KavinKrishnan](https://github.com/KavinKrishnan)
+- Update notebooks with cloning repo and building MIS container [#215](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/215) by [@KavinKrishnan](https://github.com/KavinKrishnan)
+- Change the model name in the Spleen seg example dataset to model.ts [#222](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/222) by [@MMelQin](https://github.com/MMelQin)
+- Remove developer names/aliases from notebooks and documentation [#225](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/225) by [@KavinKrishnan](https://github.com/KavinKrishnan)
+- Fixed empty documentation on docs.monai [#233](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/233) by [@vikashg](https://github.com/vikashg)
+- Handle exception case with missing DICOM Rescale Intercept and Slope attributes [#236](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/236) by [@MMelQin](https://github.com/MMelQin)
+- Fix IPython detection routine [#237](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/237) by [@gigony](https://github.com/gigony)
+- Use Python 3.7 for JupyterLab [#241](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/241) by [@gigony](https://github.com/gigony)
+- Update gdown command and missing package [#246](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/246) by [@gigony](https://github.com/gigony)
+- Do not upgrade packages when packaging [#247](https://github.com/Project-MONAI/monai-deploy-app-sdk/pull/247) by [@gigony](https://github.com/gigony)
diff --git a/examples/apps/ai_livertumor_seg_app/livertumor_seg_operator.py b/examples/apps/ai_livertumor_seg_app/livertumor_seg_operator.py
@@ -34,7 +34,7 @@
 @md.input("image", Image, IOType.IN_MEMORY)
 @md.output("seg_image", Image, IOType.IN_MEMORY)
 @md.output("saved_images_folder", DataPath, IOType.DISK)
-@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "nibabel"])
+@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
 class LiverTumorSegOperator(Operator):
     """Performs liver and tumor segmentation using a DL model with an image converted from a DICOM CT series.
 

diff --git a/examples/apps/ai_spleen_seg_app/spleen_seg_operator.py b/examples/apps/ai_spleen_seg_app/spleen_seg_operator.py
@@ -34,7 +34,7 @@
 
 @md.input("image", Image, IOType.IN_MEMORY)
 @md.output("seg_image", Image, IOType.IN_MEMORY)
-@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "nibabel"])
+@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
 class SpleenSegOperator(Operator):
     """Performs Spleen segmentation with a 3D image converted from a DICOM CT series.
 

diff --git a/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py b/examples/apps/ai_unetr_seg_app/unetr_seg_operator.py
@@ -35,7 +35,7 @@
 @md.input("image", Image, IOType.IN_MEMORY)
 @md.output("seg_image", Image, IOType.IN_MEMORY)
 @md.output("saved_images_folder", DataPath, IOType.DISK)
-@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20", "nibabel"])
+@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21", "nibabel"])
 class UnetrSegOperator(Operator):
     """Performs multi-organ segmentation using UNETR model with an image converted from a DICOM CT series.
 

diff --git a/examples/apps/deply_app_on_aarch64_interim.md b/examples/apps/deply_app_on_aarch64_interim.md
@@ -31,7 +31,7 @@ Without using the MONAI Deploy App SDK Packager to automatically detect the depe
 monai>=0.6.0
 monai-deploy-app-sdk>=0.1.0
 nibabel
-numpy>=1.20
+numpy>=1.21
 pydicom>=1.4.2
 torch>=1.5
 ```

diff --git a/monai/deploy/operators/monai_seg_inference_operator.py b/monai/deploy/operators/monai_seg_inference_operator.py
@@ -43,7 +43,7 @@
 
 @md.input("image", Image, IOType.IN_MEMORY)
 @md.output("seg_image", Image, IOType.IN_MEMORY)
-@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.20"])
+@md.env(pip_packages=["monai==0.6.0", "torch>=1.5", "numpy>=1.21"])
 class MonaiSegInferenceOperator(InferenceOperator):
     """This segmentation operator uses MONAI transforms and Sliding Window Inference.
 

diff --git a/monai/deploy/packager/templates.py b/monai/deploy/packager/templates.py
@@ -12,7 +12,7 @@
 COMMON_FOOTPRINT = """
     USER root
 
-    RUN pip install --no-cache-dir --upgrade setuptools==57.4.0 pip==21.2.4 wheel==0.37.0 monai-deploy-app-sdk==0.2.0
+    RUN pip install --no-cache-dir --upgrade setuptools==57.4.0 pip==21.3.1 wheel==0.37.0 numpy>=1.21
 
     RUN mkdir -p /etc/monai/ \\
      && mkdir -p /opt/monai/ \\
@@ -34,9 +34,17 @@
      && rm -rf {executor_dir}/executor_pkg \\
      && chmod +x {executor_dir}/monai-exec
 
-    ENV PATH=/home/root/.local/bin:$PATH
+    ENV PATH=/root/.local/bin:$PATH
 
-    RUN pip install --no-cache-dir -r {map_requirements_path}
+    RUN pip install --no-cache-dir --user -r {map_requirements_path}
+
+    # Override monai-deploy-app-sdk module
+    COPY ./monai-deploy-app-sdk /root/.local/lib/python3.8/site-packages/monai/deploy/
+    RUN echo "User site package location: $(python3 -m site --user-site)" \\
+        && [ "$(python3 -m site --user-site)" != "/root/.local/lib/python3.8/site-packages" ] \\
+        && mkdir -p $(python3 -m site --user-site)/monai/deploy \\
+        && cp -r /root/.local/lib/python3.8/site-packages/monai/deploy/* $(python3 -m site --user-site)/monai/deploy/ \\
+        || true
 
     COPY ./map/app.json /etc/monai/
     COPY ./map/pkg.json /etc/monai/

diff --git a/notebooks/tutorials/03_segmentation_app.ipynb b/notebooks/tutorials/03_segmentation_app.ipynb
@@ -99,7 +99,7 @@
     "# Install MONAI and other necessary image processing packages for the application\n",
     "!python -c \"import monai\" || pip install -q \"monai\"\n",
     "!python -c \"import torch\" || pip install -q \"torch>=1.5\"\n",
-    "!python -c \"import numpy\" || pip install -q \"numpy>=1.20\"\n",
+    "!python -c \"import numpy\" || pip install -q \"numpy>=1.21\"\n",
     "!python -c \"import nibabel\" || pip install -q \"nibabel>=3.2.1\"\n",
     "!python -c \"import pydicom\" || pip install -q \"pydicom>=1.4.2\"\n",
     "!python -c \"import SimpleITK\" || pip install -q \"SimpleITK>=2.0.0\"\n",
@@ -747,7 +747,7 @@
    "source": [
     "@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
     "@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
-    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\"])\n",
+    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
     "class SpleenSegOperator(Operator):\n",
     "    \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
     "    \"\"\"\n",
@@ -1069,7 +1069,7 @@
     "\n",
     "@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
     "@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
-    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\", \"typeguard\"])\n",
+    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
     "class SpleenSegOperator(Operator):\n",
     "    \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
     "    \"\"\"\n",

diff --git a/notebooks/tutorials/05_full_tutorial.ipynb b/notebooks/tutorials/05_full_tutorial.ipynb
@@ -89,7 +89,7 @@
     "# Install MONAI and other necessary image processing packages for the application\n",
     "!python -c \"import monai\" || pip install -q \"monai\"\n",
     "!python -c \"import torch\" || pip install -q \"torch>=1.5\"\n",
-    "!python -c \"import numpy\" || pip install -q \"numpy>=1.20\"\n",
+    "!python -c \"import numpy\" || pip install -q \"numpy>=1.21\"\n",
     "!python -c \"import nibabel\" || pip install -q \"nibabel>=3.2.1\"\n",
     "!python -c \"import pydicom\" || pip install -q \"pydicom>=1.4.2\"\n",
     "!python -c \"import SimpleITK\" || pip install -q \"SimpleITK>=2.0.0\"\n",
@@ -739,7 +739,7 @@
    "source": [
     "@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
     "@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
-    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\"])\n",
+    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\"])\n",
     "class SpleenSegOperator(Operator):\n",
     "    \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
     "    \"\"\"\n",
@@ -1017,7 +1017,7 @@
     "\n",
     "@md.input(\"image\", Image, IOType.IN_MEMORY)\n",
     "@md.output(\"seg_image\", Image, IOType.IN_MEMORY)\n",
-    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.20\", \"nibabel\", \"typeguard\"])\n",
+    "@md.env(pip_packages=[\"monai==0.6.0\", \"torch>=1.5\", \"numpy>=1.21\", \"nibabel\", \"typeguard\"])\n",
     "class SpleenSegOperator(Operator):\n",
     "    \"\"\"Performs Spleen segmentation with a 3D image converted from a DICOM CT series.\n",
     "    \"\"\"\n",

diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-numpy>=1.17
+numpy>=1.21  # CVE-2021-33430
 networkx>=2.4
 colorama>=0.4.1
 typeguard>=2.12.1
diff --git a/setup.cfg b/setup.cfg
@@ -23,7 +23,7 @@ python_requires = >= 3.7
 # setup_requires =
 #     cucim
 install_requires =
-    numpy>=1.17
+    numpy>=1.21  # CVE-2021-33430
     networkx>=2.4
     colorama>=0.4.1
     typeguard>=2.12.1
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ @@
     ```{toctree}
     :maxdepth: 1
+    v0.2.1
     v0.2.0
     ```
@@ Expand Down @@