Updates auto generated documentation with theme and basic support

JSybrandt · Apr 29, 2020 · 7e35ce7 · 7e35ce7
1 parent 080b0a6
commit 7e35ce7
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Showing 11 changed files with 40 additions and 23 deletions.
diff --git a/docs/.gitignore b/docs/.gitignore
@@ -0,0 +1,2 @@
+_api
+_build
diff --git a/docs/Makefile b/docs/Makefile
@@ -16,5 +16,17 @@ help:
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
+%: Makefile autodoc
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+autodoc:
+	rm -rf _api
+	mkdir -p _api
+	sphinx-apidoc \
+		--implicit-namespaces \
+		--separate \
+		--force \
+		-H Agatha \
+		-d 2 \
+		-o _api \
+		../agatha
diff --git a/docs/_static/sidebar_logo.png b/docs/_static/sidebar_logo.png
diff --git a/docs/_templates/.include b/docs/_templates/.include
diff --git a/docs/agatha.rst b/docs/agatha.rst
diff --git a/docs/conf.py b/docs/conf.py
@@ -35,6 +35,7 @@
     "sphinx.ext.autodoc",  # Make documentation from source
     "sphinx.ext.napoleon",  # Read docs in Google format
     "sphinx_autodoc_typehints",  # Allow automatic documentation to see hints
+    "sphinx_rtd_theme",  # Provides theme
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -47,8 +48,8 @@
     '_build',
     'Thumbs.db',
     '.DS_Store',
-    'test*',
-    '**__pycache__**',
+    'api/test*',
+    'api/*_pb2.rst',
 ]
 
 # Enable txt and md files
@@ -63,9 +64,11 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "sphinx_rtd_theme"
 
 # 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_logo = "_static/sidebar_logo.png"
diff --git a/docs/help/toc.rst b/docs/help/toc.rst
@@ -0,0 +1,7 @@
+Help
+====
+
+.. toctree::
+   :maxdepth: 1
+
+   train_agatha
diff --git a/docs/help/train_agatha.md b/docs/help/train_agatha.md
@@ -0,0 +1,6 @@
+How to train the Agatha Deep-Learning Model
+-------------------------------------------
+
+
+This is a quick tutorial on how to train the Agatha deep-learning model.
+Hopefully, this will be relatively painless to write...
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,7 +3,9 @@ Agatha: Biomedical Hypothesis Generation
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+
+   help/toc
+   api/modules
 
 
 
@@ -12,4 +14,3 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
diff --git a/docs/modules.rst b/docs/modules.rst
diff --git a/requirements.txt b/requirements.txt
@@ -87,3 +87,6 @@ recommonmark
 
 # Allow sphinx to see type hints
 sphinx-autodoc-typehints
+
+# Theme
+sphinx-rtd-theme