merge master

CITATION.cff

@@ -0,0 +1,16 @@
+# YAML 1.2
+# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
+#
+---
+title: "MONAI: Medical Open Network for AI"
+abstract: "AI Toolkit for Healthcare Imaging"
+authors:
+ - name: "MONAI Consortium"
+date-released: 2020-03-28
+version: "0.6.0"
+doi: "10.5281/zenodo.4323058"
+license: "Apache-2.0"
+repository-code: "https://github.com/Project-MONAI/MONAI"
+cff-version: "1.1.0"
+message: "If you use this software, please cite it using these metadata."
+...

docs/_static/custom.css

@@ -1,2 +1,4 @@
 @import url('https://fonts.googleapis.com/css?family=Lekton:700|Roboto&display=swap');
-body{font-family:'Roboto',sans-serif;}.wy-side-nav-search>div.version{color:#222;}a:visited{color:#0285b0;}.wy-menu-vertical a:visited{color:#d9d9d9;}.wy-menu-vertical p.caption{color:#7cccc7;}
+body{font-family:'Roboto',sans-serif;}.wy-menu-vertical p.caption{color:#7cccc7;}
+*{font-variant-ligatures: none;}.autoclasstoc td {padding:0.2rem;line-height:normal;}
+dl.field-list>dt{word-break: normal}

docs/requirements.txt

@@ -9,8 +9,8 @@ scikit-image>=0.14.2
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0
-Sphinx==3.5.3
-sphinx-rtd-theme==0.5.2
+Sphinx
+pydata-sphinx-theme
 sphinxcontrib-applehelp
 sphinxcontrib-devhelp
 sphinxcontrib-htmlhelp

docs/source/api.rst

@@ -0,0 +1,20 @@
+:github_url: https://github.com/Project-MONAI/MONAI
+
+API Reference
+=============
+
+.. toctree::
+ :maxdepth: 1
+
+ apps
+ transforms
+ losses
+ networks
+ metrics
+ optimizers
+ data
+ engines
+ inferers
+ handlers
+ visualize
+ utils

docs/source/apps.rst

@@ -98,3 +98,15 @@ Clara MMARs
 .. autofunction:: compute_isolated_tumor_cells
 .. autoclass:: PathologyProbNMS
  :members:
+
+.. automodule:: monai.apps.pathology.transforms.stain.array
+.. autoclass:: ExtractHEStains
+ :members:
+.. autoclass:: NormalizeHEStains
+ :members:
+
+.. automodule:: monai.apps.pathology.transforms.stain.dictionary
+.. autoclass:: ExtractHEStainsd
+ :members:
+.. autoclass:: NormalizeHEStainsd
+ :members:

docs/source/conf.py

@@ -11,8 +11,8 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import os
-import sys
 import subprocess
+import sys
 
 sys.path.insert(0, os.path.abspath(".."))
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
@@ -68,12 +68,6 @@ def generate_apidocs(*args):
  )
 
 
-def setup(app):
- # Hook to allow for automatic generation of API docs
- # before doc deployment begins.
- app.connect("builder-inited", generate_apidocs)
-
-
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -94,8 +88,10 @@ def setup(app):
 
 autoclass_content = "both"
 add_module_names = True
+source_encoding = "utf-8"
 autosectionlabel_prefix_document = True
 napoleon_use_param = True
+napoleon_include_init_with_doc = True
 set_type_checking_flag = True
 
 # Add any paths that contain templates here, relative to this directory.
@@ -106,29 +102,54 @@ def setup(app):
 # The theme to use for HTML and HTML Help pages. See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = "pydata_sphinx_theme"
 # html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 html_theme_options = {
+ "external_links": [{"url": "https://github.com/Project-MONAI/tutorials", "name": "Tutorials"}],
+ "icon_links": [
+ {
+ "name": "GitHub",
+ "url": "https://github.com/project-monai/monai",
+ "icon": "fab fa-github-square",
+ },
+ {
+ "name": "Twitter",
+ "url": "https://twitter.com/projectmonai",
+ "icon": "fab fa-twitter-square",
+ },
+ ],
  "collapse_navigation": True,
- "display_version": True,
- "sticky_navigation": True, # Set to False to disable the sticky nav while scrolling.
- "logo_only": True, # if we have a html_logo below, this shows /only/ the logo with no title text
- "style_nav_header_background": "#FBFBFB",
+ "navigation_depth": 3,
+ "show_toc_level": 1,
+ "footer_items": ["copyright"],
+ "navbar_align": "content",
 }
 html_context = {
- "display_github": True,
  "github_user": "Project-MONAI",
  "github_repo": "MONAI",
  "github_version": "dev",
+ "doc_path": "docs/",
  "conf_py_path": "/docs/",
+ "VERSION": version,
 }
 html_scaled_image_link = False
 html_show_sourcelink = True
 html_favicon = "../images/favicon.ico"
 html_logo = "../images/MONAI-logo-color.png"
+html_sidebars = {"**": ["search-field", "sidebar-nav-bs"]}
+pygments_style = "sphinx"
 
 # 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_css_files = ["custom.css"]
+html_title = f"{project} {version} Documentation"
+
+# -- Auto-convert markdown pages to demo --------------------------------------
+
+
+def setup(app):
+ # Hook to allow for automatic generation of API docs
+ # before doc deployment begins.
+ app.connect("builder-inited", generate_apidocs)

docs/source/contrib.rst

@@ -0,0 +1,7 @@
+:github_url: https://github.com/Project-MONAI/MONAI
+
+Development
+===========
+
+For guidance on making a contribution to MONAI, see the `contributing guidelines
+<https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md>`_.

docs/source/data.rst

@@ -182,6 +182,10 @@ DistributedWeightedRandomSampler
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 .. autoclass:: monai.data.DistributedWeightedRandomSampler
 
+DatasetSummary
+~~~~~~~~~~~~~~
+.. autoclass:: monai.data.DatasetSummary
+
 Decathlon Datalist
 ~~~~~~~~~~~~~~~~~~
 .. autofunction:: monai.data.load_decathlon_datalist

docs/source/highlights.md

@@ -1,4 +1,4 @@
-# Modules overview
+# Modules Overview
 
 MONAI aims at supporting deep learning in medical image analysis at multiple granularities.
 This figure shows a typical example of the end-to-end workflow:

docs/source/index.rst

@@ -45,39 +45,26 @@ Technical documentation is available at `docs.monai.io <https://docs.monai.io>`_
  :maxdepth: 1
  :caption: Feature highlights
 
- whatsnew_0_6.md
- whatsnew_0_5.md
+ whatsnew
  highlights.md
 
 .. toctree::
  :maxdepth: 1
- :caption: APIs
-
- apps
- transforms
- losses
- networks
- metrics
- optimizers
- data
- engines
- inferers
- handlers
- visualize
- utils
+ :caption: API Reference
+
+ api
 
 .. toctree::
  :maxdepth: 1
  :caption: Installation
 
  installation
 
+.. toctree::
+ :maxdepth: 1
+ :caption: Contributing
 
-Contributing
-------------
-
-For guidance on making a contribution to MONAI, see the `contributing guidelines
-<https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md>`_.
+ contrib
 
 
 Links

docs/source/installation.md

@@ -1,4 +1,4 @@
-# Installation guide
+# Installation Guide
 
 ## Table of Contents
 1. [From PyPI](#from-pypi)