From 5d68e1cd5f0c72e78ce940ea201e8cdd20a171db Mon Sep 17 00:00:00 2001 From: Gigon Bae Date: Thu, 9 Sep 2021 10:27:12 -0700 Subject: [PATCH 1/2] Use consistent name - MONAI Deploy App SDK Signed-off-by: Gigon Bae --- .github/ISSUE_TEMPLATE/bug_report.md | 4 ++-- .github/ISSUE_TEMPLATE/feature_request.md | 4 ++-- CONTRIBUTING.md | 14 +++++++------- README.md | 6 +++--- docs/source/conf.py | 2 +- docs/srs.md | 8 ++++---- .../operators/monai_seg_inference_operator.py | 2 +- monai/deploy/utils/importutil.py | 2 +- monai/deploy/utils/version.py | 6 +++--- 9 files changed, 24 insertions(+), 24 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 1e6d093d..709be185 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -1,6 +1,6 @@ --- name: Bug report -about: Create a bug report to help us improve MONAI Deploy Application SDK +about: Create a bug report to help us improve MONAI Deploy App SDK title: "[BUG] " labels: bug assignees: '' @@ -26,7 +26,7 @@ A clear and concise description of what you expected to happen. - OS/Platform: - Python Version: -- Method of MONAI Deploy Application SDK install: [pip, conda, Docker, or from source] +- Method of MONAI Deploy App SDK install: [pip, conda, Docker, or from source] - SDK Version: **Additional context** diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index d9e46135..8880f6ce 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,6 +1,6 @@ --- name: Feature request -about: Suggest an idea for MONAI Deploy Application SDK +about: Suggest an idea for MONAI Deploy App SDK title: "[FEA] " labels: enhancement assignees: '' @@ -9,7 +9,7 @@ assignees: '' **Is your feature request related to a problem? Please describe.** **Describe the solution you'd like** diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 867864b4..7a01086f 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -17,11 +17,11 @@ ## Introduction -Welcome to Project MONAI Deploy Application SDK (MONAI 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 App SDK. MONAI 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. +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. ### Communicate with us -We are happy to talk with you about your needs for MONAI 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 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. +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. ## The contribution process @@ -29,11 +29,11 @@ _Pull request early_ We encourage you to create pull requests early. It helps us track the contributions under development, whether they are ready to be merged or not. Change your pull request's title, to begin with `[WIP]` and/or [create a draft pull request](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests#draft-pull-requests) until it is ready for formal review. -Please note that, as per PyTorch, MONAI App SDK uses American English spelling. This means classes and variables should be: normali**z**e, visuali**z**e, colo~~u~~r, etc. +Please note that, as per PyTorch, MONAI Deploy App SDK uses American English spelling. This means classes and variables should be: normali**z**e, visuali**z**e, colo~~u~~r, etc. ### Preparing pull requests -To ensure the code quality, MONAI App SDK relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort)), +To ensure the code quality, MONAI Deploy App SDK relies on several linting tools ([flake8 and its plugins](https://gitlab.com/pycqa/flake8), [black](https://github.com/psf/black), [isort](https://github.com/timothycrosley/isort)), static type analysis tools ([mypy](https://github.com/python/mypy), [pytype](https://github.com/google/pytype)), as well as a set of unit/integration/system tests. This section highlights all the necessary preparation steps required before sending a pull request. @@ -87,7 +87,7 @@ If you intend for any variables/functions/classes to be available outside of the #### Unit testing -MONAI App SDK tests are located under `tests/` (it has `unit`/`integration`/`performance`/`system` subfolders.) +MONAI Deploy App SDK tests are located under `tests/` (it has `unit`/`integration`/`performance`/`system` subfolders.) - The unit test's file name currently follows `test_[module_name].py` or `test_[module_name]_dist.py`. - The `test_[module_name]_dist.py` subset of unit tests requires a distributed environment to verify the module with distributed GPU-based computation. @@ -120,10 +120,10 @@ or (for new features that would not break existing functionality): _If it's not tested, it's broken_ All new functionality should be accompanied by an appropriate set of tests. -MONAI App SDK functionality has plenty of unit tests from which you can draw inspiration, +MONAI Deploy App SDK functionality has plenty of unit tests from which you can draw inspiration, and you can reach out to us if you are unsure of how to proceed with testing. -MONAI APP SDK's code coverage report is available at [CodeCov](https://codecov.io/gh/Project-MONAI/monai-deploy-app-sdk). +MONAI Deploy App SDK's code coverage report is available at [CodeCov](https://codecov.io/gh/Project-MONAI/monai-deploy-app-sdk). #### Building the documentation diff --git a/README.md b/README.md index 7810a568..f1f654e7 100644 --- a/README.md +++ b/README.md @@ -2,9 +2,9 @@ project-monai

-# MONAI Deploy Application SDK +# MONAI Deploy App SDK -MONAI Deploy Application SDK offers a framework and associated tools to design, verify and analyze the performance of AI-driven applications in the healthcare domain. +MONAI Deploy App SDK offers a framework and associated tools to design, verify and analyze the performance of AI-driven applications in the healthcare domain. ## Features @@ -64,7 +64,7 @@ For local development, please execute the following command: This will set up the development environment, installing necessary packages. -For guidance on making a contribution to MONAI Deploy Application SDK, see the [contributing guidelines](CONTRIBUTING.md). +For guidance on making a contribution to MONAI Deploy App SDK, see the [contributing guidelines](CONTRIBUTING.md). ## Community diff --git a/docs/source/conf.py b/docs/source/conf.py index b24c9e56..368efa77 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -20,7 +20,7 @@ # -- Project information ----------------------------------------------------- -project = "MONAI Deploy Application SDK" +project = "MONAI Deploy App SDK" copyright = "2021 MONAI Consortium" author = "MONAI Contributors" diff --git a/docs/srs.md b/docs/srs.md index 3b00ecba..c03c731f 100644 --- a/docs/srs.md +++ b/docs/srs.md @@ -1,4 +1,4 @@ -# MONAI Deploy Application SDK +# MONAI Deploy App SDK ## Introduction @@ -29,7 +29,7 @@ For each requirement, the following attributes have been specified: * **Requirement Body**: This is the text of the requirement which describes the goal and purpose behind the requirement * **Background**: Provides necessary background to understand the context of the requirements * **Verification Strategy**: A high-level plan on how to test this requirement at a system level -* **Target Release**: Specifies which release of the MONAI App SDK this requirement is targeted for +* **Target Release**: Specifies which release of the MONAI Deploy App SDK this requirement is targeted for --- @@ -93,7 +93,7 @@ The SDK shall enable dependencies among upstream and downstream operators in an ### Background -Most healthcare application workflows involve multiple stages. Application developers need a way to organize functional units of AI-based inference apps. A DAG (Directed Acyclic Graph) is the core concept of MONAI App SDK, collecting Operators together, organized with dependencies and relationships to specify how they should run. +Most healthcare application workflows involve multiple stages. Application developers need a way to organize functional units of AI-based inference apps. A DAG (Directed Acyclic Graph) is the core concept of MONAI Deploy App SDK, collecting Operators together, organized with dependencies and relationships to specify how they should run. ### Verification Strategy @@ -311,7 +311,7 @@ The SDK shall allow integration of a Clara Train generated Medical Model ARchive ### Background -MMAR defines the standard structure for storing artifacts (files) needed and produced by the model development workflow (training, validation, inference, etc.). The MMAR includes all the information about the model including configurations and scripts to provide a workspace to perform different model development tasks. In the context of the MONAI App SDK, the relevant usage of the MMAR is for the purpose of inference. +MMAR defines the standard structure for storing artifacts (files) needed and produced by the model development workflow (training, validation, inference, etc.). The MMAR includes all the information about the model including configurations and scripts to provide a workspace to perform different model development tasks. In the context of the MONAI Deploy App SDK, the relevant usage of the MMAR is for the purpose of inference. ### Verification Strategy diff --git a/monai/deploy/operators/monai_seg_inference_operator.py b/monai/deploy/operators/monai_seg_inference_operator.py index 3b259a65..864b158b 100644 --- a/monai/deploy/operators/monai_seg_inference_operator.py +++ b/monai/deploy/operators/monai_seg_inference_operator.py @@ -267,7 +267,7 @@ def _get_meta_dict(self, img: Image) -> Dict: Get the meta data of the image and convert to dict type. Args: - img: an Monai App Sdk Image object. + img: a MONAI Deploy App SDK Image object. """ img_meta_dict = img.metadata() meta_dict = {key: img_meta_dict[key] for key in img_meta_dict.keys()} diff --git a/monai/deploy/utils/importutil.py b/monai/deploy/utils/importutil.py index ee439ec4..47de77b4 100644 --- a/monai/deploy/utils/importutil.py +++ b/monai/deploy/utils/importutil.py @@ -44,7 +44,7 @@ def get_docstring(cls: Type) -> str: def is_subclass(cls: Type, class_or_tuple: Union[str, Tuple[str]]) -> bool: - """Check if the given type is a subclass of a MONAI App SDK class. + """Check if the given type is a subclass of a MONAI Deploy App SDK class. Args: cls (Type): A class to check. diff --git a/monai/deploy/utils/version.py b/monai/deploy/utils/version.py index a6a8eb25..688e1d5f 100644 --- a/monai/deploy/utils/version.py +++ b/monai/deploy/utils/version.py @@ -64,7 +64,7 @@ def get_sdk_semver(): """Convert a version string to a semver string. - MONAI App SDK is a python package and its version is based on PEP-0440 + MONAI Deploy App SDK is a python package and its version is based on PEP-0440 (https://www.python.org/dev/peps/pep-0440/). e.g., 0.1.0a1, 1.0.0a2.dev456, 1.0+abc.5, 0.1.0a1+0.g8444606.dirty @@ -74,9 +74,9 @@ def get_sdk_semver(): [N!]N(.N)*[{a|b|rc}N][.postN][.devN] MONAI Application Package (MAP) requires a semver string to be used in. - The semver string is used to identify the version of the MONAI App SDK package. + The semver string is used to identify the version of the MONAI Deploy App SDK package. - This method converts the MONAI App SDK package version string to a semver string. + This method converts the MONAI Deploy App SDK package version string to a semver string. This uses a regular expression from the following link to parse the version string. From 40cfff63b8d6d5d7bc7f11dfa88822d554a87037 Mon Sep 17 00:00:00 2001 From: Gigon Bae Date: Thu, 9 Sep 2021 10:34:12 -0700 Subject: [PATCH 2/2] Fix typos in README.md and CONTRIBUTING.md Signed-off-by: Gigon Bae --- CONTRIBUTING.md | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7a01086f..4256fd77 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -152,7 +152,7 @@ Before submitting a pull request, it is recommended to: - [MyST with Sphinx](https://myst-parser.readthedocs.io/en/v0.15.2_a/sphinx/index.html) - check the auto-generated documentation (by browsing the generated documents after executing `./run gen_docs_dev`) - build HTML documentation locally (`./run gen_docs`) -- execute `./run gen_docs_dev` to clean temporary and final documents. +- execute `./run clean_docs` to clean temporary and final documents. #### Automatic code formatting diff --git a/README.md b/README.md index f1f654e7..e95497b2 100644 --- a/README.md +++ b/README.md @@ -64,7 +64,7 @@ For local development, please execute the following command: This will set up the development environment, installing necessary packages. -For guidance on making a contribution to MONAI Deploy App SDK, see the [contributing guidelines](CONTRIBUTING.md). +For guidance on making a contribution to MONAI Deploy App SDK, see the [contributing guidelines](https://github.com/Project-MONAI/monai-deploy-app-sdk/blob/main/CONTRIBUTING.md). ## Community