Updates to documentation

Updates to conf.py, added the tutorial notebook, and added packages to requirements.txt.

Author: mg-andrews

docs/README.md

@@ -1,8 +1,6 @@
 
 # Documentation Site Using Sphinx
 
-Guide to rendering the documentation site using Sphinx. 
-
 This document includes:
 - [The Sphinx local directory structure](#local-directory-structure)
 - [Sphinx commands](#sphinx-commands)
@@ -56,22 +54,22 @@ The `conf.py` file is the central configuration file for Sphinx and it determine
 
 ### 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 is a reference of the main pages used for the documentation site. The tutorial page consists if the docsite_tutorial.ipynb converted to an html. The notebook lives in `docs/source/_notebooks/` and is converted to an html during the build process based on code within `conf.py`.
 
 | 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         | datasets_included.rst                                                   | Datasets overview table        |
-| Tutorial         | tutorials.rst                                                           | Deep Learning Tutorial         |
+| API Reference    | APIreference.rst                                                        | Autogenerated documentation from docstrings|
+| Datasets         | datasets_included.rst                                                   | Datasets overview              |
+| Tutorial         | tutorials.rst *includes docsite_tutorial.ipynb*                         | 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 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 was made using [canva](https://www.canva.com/) and coderdata_1 was made using biorender.
+To add any new images they will live in `docs/source/_static/`. The coderdata_header.jpg was made using [canva](https://www.canva.com/) and coderdata_1.jpg was made using biorender.
 
 ### Site Theme and Design
 

docs/requirements.txt

@@ -3,6 +3,7 @@ myst-parser
 sphinx-design
 nbconvert
 nbsphinx
+notebook<7 
 sphinx_tabs
 numpy
 pandas

docs/source/APIreference.rst

@@ -4,7 +4,6 @@ API Reference
    :maxdepth: 2
 
 
-
 CoderData Object
 ^^^^^^^^^^^^^^^^
 
@@ -15,6 +14,13 @@ CoderData Object
 
 .. automodule:: coderdata.utils.utils
       :members: version, list_datasets
+      :undoc-members:
+      :show-inheritance:
+
+.. automodule:: coderdata.utils.stats
+      :members: summarize_response_metric, plot_response_metric, plot_2D_respones_metric
+      :undoc-members:
+      :show-inheritance:
 
 .. automodule:: coderdata.cli
    :members: info, check_folder
@@ -33,25 +39,3 @@ Dataset Object
    :members: load, format, train_test_validate, split_train_other, split_train_test_validate
    :undoc-members:
    :show-inheritance:
-
-.. Hidden
-.. ^^^^^^
-.. .. automodule:: coderdata.dataset.dataset
-   :members: _split_two_way, _create_classes, _balance_data, _filter, _determine_delimiter, _load_file
-   :undoc-members:
-   :show-inheritance:
-
-.. Build
-.. ^^^^^
-
-.. .. automodule:: build.build_dataset
-   :members: process_drugs, process_samples, process_omics, process_experiments, process_misc, process_genes, run_docker_cmd, process_docker, run_docker_validate_cmd, run_schema_checker
-   :undoc-members:
-   :show-inheritance:
-
-.. .. autoclass:: coderdata.build.build_dataset.process_genes
-
-.. .. automodule:: build.beatAML.GetBeatAML
-   :members: generate_samples_file
-   :undoc-members:
-   :show-inheritance: