DOC: Add scripts to RTD (#793)

InnerEye/Scripts/move_model.py

@@ -3,6 +3,7 @@
 # Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 # ------------------------------------------------------------------------------------------
 from argparse import ArgumentParser
+import argparse
 from pathlib import Path
 from typing import Tuple
 
@@ -99,7 +100,7 @@ def get_workspace(config: MoveModelConfig) -> Workspace:
  resource_group=config.resource_group)
 
 
-def main() -> None:
+def get_move_model_parser() -> argparse.ArgumentParser:
  parser = ArgumentParser()
  parser.add_argument("-a", "--action", type=str, required=True,
  help="Action (download or upload)")
@@ -114,6 +115,11 @@ def main() -> None:
  parser.add_argument("-m", "--model_id", type=str, required=True,
  help="The AzureML model ID")
 
+ return parser
+
+def main() -> None:
+
+ parser = get_move_model_parser()
  args = parser.parse_args()
  config = MoveModelConfig(workspace_name=args.workspace_name, subscription_id=args.subscription_id,
  resource_group=args.resource_group,

InnerEye/Scripts/submit_for_inference.py

@@ -3,6 +3,7 @@
 # Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
 # ------------------------------------------------------------------------------------------
 
+import argparse
 import logging
 import shutil
 import sys
@@ -213,6 +214,16 @@ def submit_for_inference(args: SubmitForInferenceConfig, azure_config: AzureConf
  return download_path
 
 
+def get_submit_for_inference_parser() -> argparse.ArgumentParser:
+ """This function is need to allow sphinx to access the arguments for documenation
+
+ :return: An example parser used for inference submission
+ """
+
+ inference_config = SubmitForInferenceConfig(should_validate=False)
+ return inference_config.create_argparser()
+
+
 def main(args: Optional[List[str]] = None, project_root: Optional[Path] = None) -> None:
  """
  Main function.

TestSubmodule/environment.yml

@@ -23,6 +23,8 @@ dependencies:
  - lame=3.100=h7b6447c_0
  - lcms2=2.12=h3be6417_0
  - ld_impl_linux-64=2.38=h1181459_1
+ - lerc=3.0=h295c915_0
+ - libdeflate=1.8=h7f8727e_5
  - libffi=3.3=he6710b0_2
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
@@ -31,7 +33,7 @@ dependencies:
  - libpng=1.6.37=hbc83047_0
  - libstdcxx-ng=11.2.0=h1234567_1
  - libtasn1=4.16.0=h27cfd23_0
- - libtiff=4.2.0=h2818925_1
+ - libtiff=4.4.0=hecacb30_0
  - libunistring=0.9.10=h27cfd23_0
  - libuv=1.40.0=h7b6447c_0
  - libvpx=1.7.0=h439df22_0
@@ -52,7 +54,7 @@ dependencies:
  - pytorch=1.10.0=py3.8_cuda11.3_cudnn8.2.0_0
  - pytorch-mutex=1.0=cuda
  - readline=8.1.2=h7f8727e_1
- - setuptools=61.2.0=py38h06a4308_0
+ - setuptools=63.4.1=py38h06a4308_0
  - sqlite=3.39.2=h5082296_0
  - tk=8.6.12=h1ccaba5_0
  - torchvision=0.11.1=py38_cu113
@@ -111,17 +113,17 @@ dependencies:
  - bleach==5.0.1
  - cachetools==4.2.4
  - cffi==1.15.1
- - charset-normalizer==2.1.0
+ - charset-normalizer==2.1.1
  - click==8.1.3
  - cloudpickle==1.6.0
  - colorama==0.4.5
  - commonmark==0.9.1
  - conda-merge==0.1.5
  - contextlib2==21.6.0
- - coverage==6.4.3
+ - coverage==6.4.4
  - cryptography==3.3.2
  - cycler==0.11.0
- - databricks-cli==0.17.1
+ - databricks-cli==0.17.3
  - dataclasses-json==0.5.2
  - debugpy==1.6.3
  - defusedxml==0.7.1
@@ -146,7 +148,7 @@ dependencies:
  - google-auth==1.35.0
  - google-auth-oauthlib==0.4.6
  - gputil==1.4.0
- - greenlet==1.1.2
+ - greenlet==1.1.3
  - grpcio==1.47.0
  - gunicorn==20.1.0
  - h5py==2.10.0
@@ -163,21 +165,21 @@ dependencies:
  - ipykernel==6.15.1
  - ipython==7.31.1
  - ipython-genutils==0.2.0
- - ipywidgets==7.7.1
+ - ipywidgets==8.0.1
  - isodate==0.6.1
  - itsdangerous==2.1.2
  - jeepney==0.8.0
  - jinja2==3.0.2
  - jmespath==0.10.0
  - joblib==0.16.0
  - jsonpickle==2.2.0
- - jsonschema==4.9.1
+ - jsonschema==4.14.0
  - jupyter==1.0.0
  - jupyter-client==6.1.5
  - jupyter-console==6.4.4
  - jupyter-core==4.11.1
  - jupyterlab-pygments==0.2.2
- - jupyterlab-widgets==1.1.1
+ - jupyterlab-widgets==3.0.2
  - kiwisolver==1.4.4
  - lightning-bolts==0.4.0
  - llvmlite==0.34.0
@@ -186,13 +188,13 @@ dependencies:
  - markdown==3.4.1
  - markdown-it-py==2.1.0
  - markupsafe==2.1.1
- - marshmallow==3.17.0
+ - marshmallow==3.17.1
  - marshmallow-enum==1.5.1
  - matplotlib==3.3.0
  - mccabe==0.6.1
  - mdit-py-plugins==0.3.0
  - mdurl==0.1.2
- - mistune==0.8.4
+ - mistune==2.0.4
  - mlflow==1.23.1
  - mlflow-skinny==1.28.0
  - monai==0.6.0
@@ -205,12 +207,12 @@ dependencies:
  - mypy==0.910
  - mypy-extensions==0.4.3
  - myst-parser==0.18.0
- - nbclient==0.6.6
- - nbconvert==6.5.3
+ - nbclient==0.6.7
+ - nbconvert==7.0.0
  - nbformat==5.4.0
  - ndg-httpsclient==0.5.1
  - nest-asyncio==1.5.5
- - networkx==2.8.5
+ - networkx==2.8.6
  - nibabel==4.0.1
  - notebook==6.4.12
  - numba==0.51.2
@@ -259,7 +261,7 @@ dependencies:
  - pywavelets==1.3.0
  - pyyaml==6.0
  - pyzmq==23.2.1
- - qtconsole==5.3.1
+ - qtconsole==5.3.2
  - qtpy==2.2.0
  - querystring-parser==1.2.4
  - requests==2.28.1
@@ -282,6 +284,7 @@ dependencies:
  - snowballstemmer==2.2.0
  - soupsieve==2.3.2.post1
  - sphinx==5.0.2
+ - sphinx-argparse==0.3.1
  - sphinx-basic-ng==0.0.1a12
  - sphinx-rtd-theme==1.0.0
  - sphinxcontrib-applehelp==1.0.2
@@ -310,13 +313,13 @@ dependencies:
  - torchmetrics==0.6.0
  - tornado==6.2
  - tqdm==4.64.0
- - typing-inspect==0.7.1
+ - typing-inspect==0.8.0
  - umap-learn==0.5.2
  - urllib3==1.26.7
  - webencodings==0.5.1
- - websocket-client==1.3.3
+ - websocket-client==1.4.0
  - werkzeug==2.2.2
- - widgetsnbextension==3.6.1
+ - widgetsnbextension==4.0.2
  - wrapt==1.14.1
  - yacs==0.1.8
  - yarl==1.8.1

docs/source/conf.py

@@ -26,29 +26,30 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'InnerEye-DeepLearning'
-copyright = 'Microsoft Corporation'
-author = 'Microsoft'
+project = "InnerEye-DeepLearning"
+copyright = "Microsoft Corporation"
+author = "Microsoft"
 
 # The full version, including alpha/beta/rc tags
-release = '0.4'
+release = "0.4"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# extensions coming with Sphinx (named "sphinx.ext.*") or your custom
 # ones.
 extensions = [
- 'sphinx.ext.autodoc',
- 'sphinx.ext.autosummary',
- 'sphinx_rtd_theme',
- 'myst_parser',
- 'sphinx.ext.viewcode',
+ "sphinx.ext.autodoc",
+ "sphinx.ext.autosummary",
+ "sphinx_rtd_theme",
+ "myst_parser",
+ "sphinx.ext.viewcode",
+ "sphinxarg.ext",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -61,23 +62,23 @@
 # The theme to use for HTML and HTML Help pages. See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'furo'
+html_theme = "furo"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-# html_static_path = ['_static']
+# html_static_path = ["_static"]
 
 source_suffix = {
- '.rst': 'restructuredtext',
- '.md': 'markdown',
+ ".rst": "restructuredtext",
+ ".md": "markdown",
 }
 
 # Autodoc options
 
 autodoc_default_options = {
- 'members': True,
- 'undoc-members': True,
+ "members": True,
+ "undoc-members": True,
 }
 
 

docs/source/index.rst

@@ -39,7 +39,7 @@ InnerEye-DeepLearning Documentation
  md/CHANGELOG.md
 
 .. toctree::
- :caption: API documentation (🚧 Work In Progress 🚧)
+ :caption: API documentation
  :maxdepth: 2
 
  rst/api/index

docs/source/rst/api/Scripts/move_model.rst

@@ -0,0 +1,6 @@
+Move model
+===========
+
+.. argparse::
+ :ref: InnerEye.Scripts.move_model.get_move_model_parser
+ :prog: move_model.py

docs/source/rst/api/Scripts/runner.rst

@@ -0,0 +1,8 @@
+Runner
+======
+
+This script is the entry point for running all InnerEye jobs, both locally and in AzureML. See the user guides for example usage.
+
+.. argparse::
+ :ref: InnerEye.Azure.azure_runner.create_runner_parser
+ :prog: runner.py

docs/source/rst/api/Scripts/scripts.rst

@@ -0,0 +1,11 @@
+Scripts
+=======
+
+Please see links below for details on the available arguments for each of the primary InnerEye scripts.
+
+.. toctree::
+ :maxdepth: 1
+
+ runner
+ submit_for_inference
+ move_model

docs/source/rst/api/Scripts/submit_for_inference.rst

@@ -0,0 +1,8 @@
+Submit for Inference
+====================
+
+This script is used to submit a single image for inference against a trained model.
+
+.. argparse::
+ :ref: InnerEye.Scripts.submit_for_inference.get_submit_for_inference_parser
+ :prog: submit_for_inference.py

docs/source/rst/api/index.rst

@@ -1,3 +1,4 @@
 .. toctree::
 
  ML/ML
+ Scripts/scripts