Cleaning file structure

Adding to conf.py for the API documentation, deleted unneeded files, updated the README, and added to conf.py for notebook to html conversions.

Author: mg-andrews

docs/README.md

@@ -1,18 +1,19 @@
 
-# Locally Rendering Sphinx
+# Documentation Site Using Sphinx
 
 Guide to rendering the documentation site using Sphinx. 
 
 This document includes:
-- The coderdata/docs directory structure
-- Sphinx commands
-- Guide to updating the documentation site 
-- Helpful sphinx features
+- [The Sphinx local directory structure](#local-directory-structure)
+- [Sphinx commands](#sphinx-commands)
+- [Guide to updating the documentation site](#updating-the-documentation-site)
+- [Helpful sphinx features](#helpful-sphinx-features)
+- [Site Deployment](#deploying-the-documentation-site-using-github-actions)
 
 
-## Directory Structure
+## Local Directory Structure
 
-![Directory Structure](sphinx_dir_struct.png?raw=true)
+![Directory Structure](local_struct.jpg?raw=true)
 
 ## Sphinx Commands
 
@@ -28,7 +29,7 @@ Included in `coderdata/docs/requirements.txt`. Extra installations that enable v
 
 ### Build
 
-To build the Sphinx documentation locally, navigate to the `docs` directory and run the `sphinx-build` command. This command processes the content files from the `source` directory and generates the rendered HTML output in the `build` directory.
+To build the Sphinx documentation locally, navigate to the `docs/` directory and run the `sphinx-build` command. This command processes the content files from the `docs/source/` directory and generates the rendered HTML output in the `docs/build/` directory.
 
 ```sh
 $ cd ../coderdata/docs
@@ -49,43 +50,43 @@ $ python -m sphinx.cmd.quickstart
 ```
 Questions will follow this command and when it prompts if you'd like to separate the source and build directories select yes. 
 
-## Updating Documentation Site 
+## Updating the Documentation Site 
 
-The `conf.py` file is the central configuration file for Sphinx and it determines the behavior and appearance of the generated documentation. Specifically it configures extensions, defines metadata, controls output settings, and customizes sphinx behavior. The `index.rst` file is the starting page for the Sphinx documentation build process. It acts as the root file, linking all other pages and defining the document hierarchy. All other .md and .rst files are added and internally referenced within the index page or within the sidebar. 
+The `conf.py` file is the central configuration file for Sphinx and it determines the behavior and appearance of the generated documentation. Specifically it configures extensions, defines metadata, controls output settings, and customizes sphinx behavior. The `index.rst` file is the starting page for the Sphinx documentation build process. It acts as the root file, linking all other pages and defining the document hierarchy. All other .md and .rst files are added and internally referenced within the index page and/or within the sidebar. 
 
 ### Pages
 
-To update pages navigate to `docs/source`, all .rst and .md files live here. Here a reference of the main pages used for the documentation site. 
+To update pages navigate to `docs/source/`, all .rst and .md files live here. Here a reference of the main pages used for the documentation site. 
 
-|  Main Pages      | File Name                                                               | Content                        |
+| Page             | File Name                                                               | Content                        |
 | -----------------| ----------------------------------------------------------------------- | ------------------------------ |
 | Home Page        | index.rst                                                               | Introduction and Install       |
 | Usage            | usage.md                                                                | API and CLI                    |
 | API Reference    | APIreference.rst                                                        | Sphinx autogenerated docstrings|
-| Datasets Included| datasets_included.rst                                                   | Datasets overview table        |
-| Tutorials        | tutorials.rst                                                           | Deep Learning Tutorial         |
-| How To Contribute| contribution_guide.rst *includes contribution.md and add_code_guide.md* | Contribution Guide             |
+| Datasets         | datasets_included.rst                                                   | Datasets overview table        |
+| Tutorial         | tutorials.rst                                                           | Deep Learning Tutorial         |
+| Contributing     | contribution_guide.rst *includes contribution.md and add_code_guide.md* | Contribution Guide             |
 
-Note: When adding pages, reStructuredText files are the most sphinx friendly and allow for use of helpful sphinx features. However, Markdown files can be used and will render properly when the myst-parser extension is used. 
+**Note:** When adding pages, reStructuredText files are the most sphinx friendly and allow for use of helpful directives. However, Markdown files can be used and will render properly when the myst-parser extension is used. 
 
 ### Images and Graphics
 
-To add any new images they will live in `docs/source/_static`. The coderdata_header.png and home_page_graphic.png were made using [canva](https://www.canva.com/). The designs are shared with team members so that they can easily be edited if needed!
+To add any new images they will live in `docs/source/_static/`. The coderdata_header.png was made using [canva](https://www.canva.com/) and coderdata_1 was made using biorender.
 
 ### Site Theme and Design
 
-The original sphinx theme used is 'sphinxdoc', however, to change certain aspects an additional file custom.css was included to override the sphinxdoc theme. To update the custom theme navigate to `docs/source/_static/custom.css`. Changes to the sidebar can be made in `docs/source/_templates/my_custom_sidebar.html`. Any other custom templates will be added to `docs/source/_templates`.
+The original sphinx theme used is 'sphinxdoc', however, to change certain aspects I created `custom.css` to override the sphinxdoc theme. To update the custom theme navigate to `docs/source/_static/custom.css`. Changes to the sidebar can be made in `docs/source/_templates/my_custom_sidebar.html`. Any other custom templates will be added to `docs/source/_templates/`.
 
-Note: The sphinxdoc theme is automatically generated during the build command into `docs/build/html/_static/sphinxdoc.css`. It is regenerated everytime sphinx build runs so changes to the theme must be made in custom.css. 
+**Note:** The sphinxdoc theme is auto-generated during the build command into `docs/build/html/_static/sphinxdoc.css`. It is regenerated everytime sphinx build runs so changes must be made in custom.css. 
 
 
 ## Helpful Sphinx Features
 
 ### Site Links
 
-- [Sphinx Documentation](https://www.sphinx-doc.org/en/master/index.html)
-- [Sphinxdoc Sample](https://sphinx-themes.org/sample-sites/default-sphinxdoc/)
-- [Full List of Directives in Sphinx](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#rst-directives)
+- [sphinx-doc.org](https://www.sphinx-doc.org/en/master/index.html)
+- [sphinx.org/sample-sites](https://sphinx-themes.org/sample-sites/default-sphinxdoc/)
+- [sphinx.org/directives](https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html#rst-directives)
 
 
 ### Directives and Examples Used in CoderData Documentation
@@ -115,4 +116,19 @@ To include content from another file. Example shows how to render a markdown fil
 		:align: center
 		:scale: 100%
 ```
+## Deploying the Documentation Site Using Github Actions
 
+### Directory Structure for Deployment with Relevant Branches
+
+![Directory Structure](deploy_struct.jpg?raw=true)
+
+### Site Deployment
+
+- We added `sphinx.yml` to the `.github/workflows/` directory in the `documentation-staging` branch.
+
+- Then in `documentation-staging` we included all the source directory files that are needed to build the documentation. (These are all the same files that are needed to build the documentation locally, the only addition is `requirements.txt`). 
+**Note:** If you have been building the documentation locally and then are moving to commit to the staging branch there is no need to include any files from `docs/build/` directory.
+
+- Once a push is made from `documentation-staging` the workflow is triggered.
+
+- The built html files are then deployed to the root of the `gh-pages` branch. The included files in the branch are shown in the graphic above.