⚡️ Move docs to docs/ and add Makefile back

microsoft · Jul 27, 2022 · 1c7b7d0 · 1c7b7d0
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,11 +9,11 @@ build:
  python: miniconda3-4.7
 
 sphinx:
- configuration: sphinx-docs/source/conf.py
+ configuration: docs/source/conf.py
 
 python:
  install:
- - requirements: sphinx-docs/requirements.txt
+ - requirements: docs/requirements.txt
 
 conda:
  environment: environment.yml
diff --git a/docs/Makefile b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = source
+BUILDDIR = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/README.md b/docs/README.md
@@ -0,0 +1,12 @@
+# Building docs for InnerEye-DeepLearning
+
+1. First, make sure you have all the packages necessary for InnerEye.
+1. Install pip dependencies from sphinx-docs/requirements.txt:
+
+```shell
+pip install -r requirements.txt
+```
+
+1. Run `make html` from the `docs` folder. This will create html files under docs/build/html.
+1. From the `docs/build/html` folder, run `python -m http.server 8080` to host the docs locally.
+1. From your browser, navigate to `http:https://localhost:8080` to view the documentation.
diff --git a/docs/build/doctrees/docs/CHANGELOG.doctree b/docs/build/doctrees/docs/CHANGELOG.doctree
diff --git a/docs/build/doctrees/docs/WSL.doctree b/docs/build/doctrees/docs/WSL.doctree
diff --git a/docs/build/doctrees/docs/bring_your_own_model.doctree b/docs/build/doctrees/docs/bring_your_own_model.doctree
diff --git a/docs/build/doctrees/docs/building_models.doctree b/docs/build/doctrees/docs/building_models.doctree
diff --git a/docs/build/doctrees/docs/contributing.doctree b/docs/build/doctrees/docs/contributing.doctree
diff --git a/docs/build/doctrees/docs/creating_dataset.doctree b/docs/build/doctrees/docs/creating_dataset.doctree
diff --git a/docs/build/doctrees/docs/debugging_and_monitoring.doctree b/docs/build/doctrees/docs/debugging_and_monitoring.doctree
diff --git a/docs/build/doctrees/docs/deploy_on_aml.doctree b/docs/build/doctrees/docs/deploy_on_aml.doctree
diff --git a/docs/build/doctrees/docs/environment.doctree b/docs/build/doctrees/docs/environment.doctree
diff --git a/docs/build/doctrees/docs/fastmri.doctree b/docs/build/doctrees/docs/fastmri.doctree
diff --git a/docs/build/doctrees/docs/hello_world_model.doctree b/docs/build/doctrees/docs/hello_world_model.doctree
diff --git a/docs/build/doctrees/docs/hippocampus_model.doctree b/docs/build/doctrees/docs/hippocampus_model.doctree
diff --git a/docs/build/doctrees/docs/innereye_as_submodule.doctree b/docs/build/doctrees/docs/innereye_as_submodule.doctree
diff --git a/docs/build/doctrees/docs/innereye_deeplearning.doctree b/docs/build/doctrees/docs/innereye_deeplearning.doctree
diff --git a/docs/build/doctrees/docs/model_diagnostics.doctree b/docs/build/doctrees/docs/model_diagnostics.doctree
diff --git a/docs/build/doctrees/docs/move_model.doctree b/docs/build/doctrees/docs/move_model.doctree
diff --git a/docs/build/doctrees/docs/pull_requests.doctree b/docs/build/doctrees/docs/pull_requests.doctree
diff --git a/docs/build/doctrees/docs/releases.doctree b/docs/build/doctrees/docs/releases.doctree
diff --git a/docs/build/doctrees/docs/sample_tasks.doctree b/docs/build/doctrees/docs/sample_tasks.doctree
diff --git a/docs/build/doctrees/docs/self_supervised_models.doctree b/docs/build/doctrees/docs/self_supervised_models.doctree
diff --git a/docs/build/doctrees/docs/setting_up_aml.doctree b/docs/build/doctrees/docs/setting_up_aml.doctree
diff --git a/docs/build/doctrees/docs/testing.doctree b/docs/build/doctrees/docs/testing.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/rst/api/ML/augmentations.doctree b/docs/build/doctrees/rst/api/ML/augmentations.doctree
diff --git a/docs/build/doctrees/rst/api/ML/configs.doctree b/docs/build/doctrees/rst/api/ML/configs.doctree
diff --git a/docs/build/doctrees/rst/api/ML/index.doctree b/docs/build/doctrees/rst/api/ML/index.doctree
diff --git a/docs/build/doctrees/rst/api/ML/photometric_normalization.doctree b/docs/build/doctrees/rst/api/ML/photometric_normalization.doctree
diff --git a/docs/build/doctrees/rst/api/ML/pipelines.doctree b/docs/build/doctrees/rst/api/ML/pipelines.doctree
diff --git a/docs/build/doctrees/rst/api/ML/runner.doctree b/docs/build/doctrees/rst/api/ML/runner.doctree
diff --git a/docs/build/doctrees/rst/api/index.doctree b/docs/build/doctrees/rst/api/index.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 900492d52b06307a7fb0eddba23873a7
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/...nx-docs/source/docs/images/deployment.png → docs/build/html/_images/deployment.png b/...nx-docs/source/docs/images/deployment.png → docs/build/html/_images/deployment.png
diff --git a/...ges/screenshot_azureml_patch_sampling.png → ...ges/screenshot_azureml_patch_sampling.png b/...ges/screenshot_azureml_patch_sampling.png → ...ges/screenshot_azureml_patch_sampling.png
diff --git a/docs/build/html/_modules/InnerEye/ML/augmentations/augmentation_for_segmentation_utils.html b/docs/build/html/_modules/InnerEye/ML/augmentations/augmentation_for_segmentation_utils.html
diff --git a/docs/build/html/_modules/InnerEye/ML/augmentations/image_transforms.html b/docs/build/html/_modules/InnerEye/ML/augmentations/image_transforms.html
diff --git a/docs/build/html/_modules/InnerEye/ML/augmentations/transform_pipeline.html b/docs/build/html/_modules/InnerEye/ML/augmentations/transform_pipeline.html
diff --git a/docs/build/html/_modules/InnerEye/ML/config.html b/docs/build/html/_modules/InnerEye/ML/config.html
diff --git a/docs/build/html/_modules/InnerEye/ML/photometric_normalization.html b/docs/build/html/_modules/InnerEye/ML/photometric_normalization.html
diff --git a/docs/build/html/_modules/InnerEye/ML/pipelines/ensemble.html b/docs/build/html/_modules/InnerEye/ML/pipelines/ensemble.html
diff --git a/docs/build/html/_modules/InnerEye/ML/pipelines/inference.html b/docs/build/html/_modules/InnerEye/ML/pipelines/inference.html
diff --git a/docs/build/html/_modules/InnerEye/ML/pipelines/scalar_inference.html b/docs/build/html/_modules/InnerEye/ML/pipelines/scalar_inference.html
diff --git a/docs/build/html/_modules/InnerEye/ML/runner.html b/docs/build/html/_modules/InnerEye/ML/runner.html
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+ <meta charset="utf-8" />
+ <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+ <title>Overview: module code &mdash; InnerEye-DeepLearning 1.0.0 documentation</title>
+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+ <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+ <!--[if lt IE 9]>
+ <script src="../_static/js/html5shiv.min.js"></script>
+ <![endif]-->
+
+ <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
+ <script src="../_static/jquery.js"></script>
+ <script src="../_static/underscore.js"></script>
+ <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
+ <script src="../_static/doctools.js"></script>
+ <script src="../_static/js/theme.js"></script>
+ <link rel="index" title="Index" href="../genindex.html" />
+ <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+ <div class="wy-grid-for-nav">
+ <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+ <div class="wy-side-scroll">
+ <div class="wy-side-nav-search" >
+ <a href="../index.html" class="icon icon-home"> InnerEye-DeepLearning
+ </a>
+<div role="search">
+ <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+ <input type="text" name="q" placeholder="Search docs" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+ </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+ <ul>
+<li class="toctree-l1"><a class="reference internal" href="../docs/innereye_deeplearning.html">InnerEye-DeepLearning</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/WSL.html">How to use the Windows Subsystem for Linux (WSL2) for development</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/environment.html">Set up InnerEye-DeepLearning</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/setting_up_aml.html">How to setup Azure Machine Learning for InnerEye</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/creating_dataset.html">Dataset Creation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/building_models.html">Building Models</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/sample_tasks.html">Sample Tasks</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/debugging_and_monitoring.html">Debugging and Monitoring Jobs</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Further reading for contributors</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../docs/pull_requests.html">Suggested Workflow for Pull Requests</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/testing.html">Pytest and testing on CPU and GPU machines</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/contributing.html">Contributing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/hello_world_model.html">Training a Hello World segmentation model</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/deploy_on_aml.html">Model Deployment</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/bring_your_own_model.html">Bring Your Own PyTorch Lightning Model</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/fastmri.html">Working with FastMRI models</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/innereye_as_submodule.html">Using the InnerEye code as a git submodule of your project</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/model_diagnostics.html">Model Diagnostics</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/move_model.html">Move a model to other workspace</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/releases.html">Releases</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/self_supervised_models.html">Training of self-supervised models</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../docs/CHANGELOG.html">Changelog</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">API documentation (🚧 Work In Progress 🚧)</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../rst/api/ML/index.html">Machine learning</a></li>
+</ul>
+
+ </div>
+ </div>
+ </nav>
+
+ <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+ <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+ <a href="../index.html">InnerEye-DeepLearning</a>
+ </nav>
+
+ <div class="wy-nav-content">
+ <div class="rst-content">
+ <div role="navigation" aria-label="Page navigation">
+ <ul class="wy-breadcrumbs">
+ <li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
+ <li>Overview: module code</li>
+ <li class="wy-breadcrumbs-aside">
+ </li>
+ </ul>
+ <hr/>
+</div>
+ <div role="main" class="document" itemscope="itemscope" itemtype="http:https://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <h1>All modules for which code is available</h1>
+<ul><li><a href="InnerEye/ML/augmentations/augmentation_for_segmentation_utils.html">InnerEye.ML.augmentations.augmentation_for_segmentation_utils</a></li>
+<li><a href="InnerEye/ML/augmentations/image_transforms.html">InnerEye.ML.augmentations.image_transforms</a></li>
+<li><a href="InnerEye/ML/augmentations/transform_pipeline.html">InnerEye.ML.augmentations.transform_pipeline</a></li>
+<li><a href="InnerEye/ML/config.html">InnerEye.ML.config</a></li>
+<li><a href="InnerEye/ML/photometric_normalization.html">InnerEye.ML.photometric_normalization</a></li>
+<li><a href="InnerEye/ML/pipelines/ensemble.html">InnerEye.ML.pipelines.ensemble</a></li>
+<li><a href="InnerEye/ML/pipelines/inference.html">InnerEye.ML.pipelines.inference</a></li>
+<li><a href="InnerEye/ML/pipelines/scalar_inference.html">InnerEye.ML.pipelines.scalar_inference</a></li>
+<li><a href="InnerEye/ML/runner.html">InnerEye.ML.runner</a></li>
+</ul>
+
+ </div>
+ </div>
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