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Updating the SDK to use newer and updated dependencies, namely Holosc…
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…an SDK (#481)

* Updated the SDK to use Holoscan SDK v1.0, and tested apps and Notebooks

Signed-off-by: M Q <[email protected]>

* Doc updates

Signed-off-by: M Q <[email protected]>

* Fix typo

Signed-off-by: M Q <[email protected]>

* Add Holoscan license file

Signed-off-by: M Q <[email protected]>

* Add release note and editorial changes

Signed-off-by: M Q <[email protected]>

* Update readme

Signed-off-by: M Q <[email protected]>

* Add missing packages in the example in the Readme

Signed-off-by: M Q <[email protected]>

* Add new package to make gen_docs work even just in Python 3.8 env

Signed-off-by: M Q <[email protected]>

* Updated user guide

Signed-off-by: M Q <[email protected]>

* Rerun the notebook to clear some warnings

Signed-off-by: M Q <[email protected]>

* rerun notebook

Signed-off-by: M Q <[email protected]>

* touch the file

Signed-off-by: M Q <[email protected]>

* touch the file

Signed-off-by: M Q <[email protected]>

* fix formatting complaints

Signed-off-by: M Q <[email protected]>

* ignore the complaint

Signed-off-by: M Q <[email protected]>

* touch file

Signed-off-by: M Q <[email protected]>

* touch the file

Signed-off-by: M Q <[email protected]>

* Successfully run after getting new clara-viz fix for Python 3.10+

Signed-off-by: M Q <[email protected]>

* specififies OS and CUDA requirements in the release note

Signed-off-by: M Q <[email protected]>

* Adding a note for doc building succeeding with Python3.8 only

Signed-off-by: M Q <[email protected]>

* Update docs and Notebooks

Signed-off-by: M Q <[email protected]>

* Explicitly specifying GPU and CUDA12 req.

Signed-off-by: M Q <[email protected]>

* Explicitly specifying GPU and CUDA12 req in README.

Signed-off-by: M Q <[email protected]>

* Add ref to MONAI guide per review commnents

Signed-off-by: M Q <[email protected]>

---------

Signed-off-by: M Q <[email protected]>
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4 changes: 2 additions & 2 deletions CODE_OF_CONDUCT.md
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Expand Up @@ -67,8 +67,8 @@ members of the project's leadership.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 2.1,
available at https://www.contributor-covenant.org/version/2/1/code_of_conduct

[homepage]: https://www.contributor-covenant.org

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21 changes: 14 additions & 7 deletions CONTRIBUTING.md
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Expand Up @@ -19,6 +19,8 @@

Welcome to Project MONAI Deploy App SDK! We're excited you're here and want to contribute. This documentation is intended for individuals and institutions interested in contributing to MONAI Deploy App SDK. MONAI Deploy App SDK is an open-source project and, as such, its success relies on its community of contributors willing to keep improving it. Your contribution will be a valued addition to the code base; we simply ask that you read this page and understand our contribution process, whether you are a seasoned open-source contributor or whether you are a first-time contributor.

Please also refer to [MONAI Contributing Guide](https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md) for general information as well as MONAI Core specifics.

### Communicate with us

We are happy to talk with you about your needs for MONAI Deploy App SDK and your ideas for contributing to the project. One way to do this is to create an issue discussing your thoughts. It might be that a very similar feature is under development or already exists, so an issue is a great starting point. If you are looking for an issue to resolve that will help Project MONAI Deploy App SDK, see the [*good first issue*](https://github.com/Project-MONAI/monai-deploy-app-sdk/labels/good%20first%20issue) and [*Contribution wanted*](https://github.com/Project-MONAI/monai-deploy-app-sdk/labels/Contribution%20wanted) labels.
Expand Down Expand Up @@ -74,7 +76,7 @@ Before submitting a pull request, we recommend that all linting should pass, by
License information: all source code files should start with this paragraph:

```python
# Copyright 2021 MONAI Consortium
# Copyright 2021-2024 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
Expand Down Expand Up @@ -135,6 +137,10 @@ MONAI Deploy App SDK's code coverage report is available at [CodeCov](https://co

#### Building the documentation

:::{note}
Please note that the documentation builds successfully in Python 3.8 environment, but fails with Python 3.10.
:::

MONAI's documentation is located at `docs/`.

```bash
Expand Down Expand Up @@ -241,21 +247,22 @@ For string definition, [f-string](https://www.python.org/dev/peps/pep-0498/) is

### Submitting pull requests

TBD
Please see this [general guidance](https://github.com/gabrieldemarmiesse/getting_started_open_source)

## The code reviewing process

TBD
Please see this [general guidance](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/about-pull-request-reviews)

### Reviewing pull requests

TBD
At least one contributor of the project needs to approve a pull request.

## Admin tasks

TBD
The contributors with Admin role in the project handle admin tasks.

### Release a new version

[github ci]: https://github.com/Project-MONAI/monai-deploy-app-sdk/actions
[monai-deploy-app-sdk issue list]: https://github.com/Project-MONAI/monai-deploy-app-sdk/issues
[github ci](https://github.com/Project-MONAI/monai-deploy-app-sdk/actions)

[monai-deploy-app-sdk issue list](https://github.com/Project-MONAI/monai-deploy-app-sdk/issues)
12 changes: 9 additions & 3 deletions README.md
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Expand Up @@ -22,7 +22,7 @@ MONAI Deploy App SDK offers a framework and associated tools to design, develop

## User Guide

User guide is available at [docs.monai.io](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/).
User guide is available at [docs.monai.io](https://docs.monai.io/projects/monai-deploy-app-sdk/en/stable/).

## Installation

Expand All @@ -32,9 +32,15 @@ To install [the current release](https://pypi.org/project/monai-deploy-app-sdk/)
pip install monai-deploy-app-sdk # '--pre' to install a pre-release version.
```

Please also note the following system requirements:
- Ubuntu 22.04 on X86-64 is required, as this is the only X86 platform that the underlying Holoscan SDK has been tested to support as of now.
- [CUDA 12](https://developer.nvidia.com/cuda-12-0-0-download-archive) is required along with a supported NVIDIA GPU with at least 8GB of video RAM. If AI inference is not used in the example application and a GPU is not installed, at least [CUDA 12 runtime](https://pypi.org/project/nvidia-cuda-runtime-cu12/) is required, as this is one of the requirements of Holoscan SDK, in addition, the `LIB_LIBRARY_PATH` must be set to include the installed shared library, e.g. in a Python 3.8 env, ```export LD_LIBRARY_PATH=`pwd`/.venv/lib/python3.8/site-packages/nvidia/cuda_runtime/lib:$LD_LIBRARY_PATH```



## Getting Started

Getting started guide is available at [here](https://docs.monai.io/projects/monai-deploy-app-sdk/en/latest/getting_started/index.html).
Getting started guide is available at [here](https://docs.monai.io/projects/monai-deploy-app-sdk/en/stable/getting_started/index.html).

```bash
pip install monai-deploy-app-sdk # '--pre' to install a pre-release version.
Expand All @@ -44,7 +50,7 @@ git clone https://github.com/Project-MONAI/monai-deploy-app-sdk.git
cd monai-deploy-app-sdk

# Install necessary dependencies for simple_imaging_app
pip install scikit-image
pip install matplotlib Pillow scikit-image

# Execute the app locally
python examples/apps/simple_imaging_app/app.py -i examples/apps/simple_imaging_app/brain_mr_input.jpg -o output
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202 changes: 202 additions & 0 deletions THIRD_PARTY_NOTICES/holoscan_Apache2.0_LICENSE.txt
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@@ -0,0 +1,202 @@

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3 changes: 2 additions & 1 deletion docs/requirements.txt
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Expand Up @@ -36,4 +36,5 @@ sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
sphinxcontrib-mermaid==0.7.1
sphinxcontrib-mermaid==0.7.1
lxml_html_clean
2 changes: 1 addition & 1 deletion docs/source/conf.py
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Expand Up @@ -41,7 +41,7 @@

# -- Project information -----------------------------------------------------
project = "MONAI Deploy App SDK"
copyright = "2021 MONAI Consortium"
copyright = "2021-2024 MONAI Consortium"
author = "MONAI Contributors"

# The full version, including alpha/beta/rc tags
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10 changes: 4 additions & 6 deletions docs/source/getting_started/installing_app_sdk.md
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Expand Up @@ -15,16 +15,14 @@ pip install --upgrade monai-deploy-app-sdk
```

:::{note}
For packaging your application, [MONAI Application Packager](/developing_with_sdk/packaging_app) and [MONAI Application Runner (MAR)](/developing_with_sdk/executing_packaged_app_locally) requires NVIDIA Docker (NVIDIA Container Toolkit) installed:
For packaging and running your application using [MONAI Application Packager](/developing_with_sdk/packaging_app) and [MONAI Application Runner (MAR)](/developing_with_sdk/executing_packaged_app_locally), [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/install-guide.html) needs to be installed.

<https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html#docker>
For version 1.0.0, `nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu` is used by [MONAI Application Packager](/developing_with_sdk/packaging_app) as base image for X86-64 in Linux system, though this will change with versions.

Currently, `nvcr.io/nvidia/clara-holoscan/holoscan:v0.6.0-dgpu` base Docker image is used by [MONAI Application Packager](/developing_with_sdk/packaging_app) by default for X86-64 in Linux system.

The base image size is large so please pull the image in advance to save time. Note that the container image tag in the following example, e.g. v0.6.0, corresponds to the SDK version.
The base image size is large, so it is recommended to pull the image in advance to save time. Note that the container image tag in the following example, e.g. `v1.0.3`, corresponds to the underlying Holoscan SDK version.

```bash
docker pull nvcr.io/nvidia/clara-holoscan/holoscan:v0.6.0-dgpu
docker pull nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu
```

:::
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