DOC: Add scripts to RTD

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