feat: Initialize documentation (#85)

Start of documentation, mostly copied the core dependencies and plugins
from med-imagetools

- Set up initial documentation structure using MkDocs, including
configuration and integration of Markdown files for the README and
CHANGELOG.

this "core" would be the base of the main vs 2.0 branch 


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
	- Added badges for project health and status in the README.
- Expanded installation instructions with a new environment setup
method.
	- Introduced a section for serving documentation locally.

- **Documentation**
- Enhanced clarity and structure of the README, including command-line
options and contributing guidelines.
	- Updated inclusion method for CHANGELOG and README in documentation.
- Introduced a new configuration file for MkDocs documentation,
improving navigation and usability.

- **Bug Fixes**
- Corrected formatting for bash commands in the README to enhance
readability.

- **Chores**
	- Updated project version and dependencies in the configuration files.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

README.md

@@ -1,4 +1,5 @@
 # READII
+<!--intro-start-->
 [![codecov](https://codecov.io/gh/bhklab/readii/graph/badge.svg?token=obsN5dhXPx)](https://codecov.io/gh/bhklab/readii)
 [![CI-CD](https://github.com/bhklab/readii/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/bhklab/readii/actions/workflows/ci-cd.yml)
 [![CodeFactor](https://www.codefactor.io/repository/github/bhklab/readii/badge)](https://www.codefactor.io/repository/github/bhklab/readii)
@@ -23,6 +24,7 @@ $ pip install readii
 ```
 
 ### (recommended) Create new `pixi` environment for a project
+
 ```bash
 mkdir my_project
 cd my_project
@@ -31,13 +33,15 @@ pixi add --pypi readii
 ```
 
 ### (recommended) Create new conda virtual environment
-```
+
+```bash
 conda create -n readii python=3.9
 conda activate readii
 pip install readii
 ```
 
 ## Usage
+
 `readii` is a tool to perform radiomic feature extraction on DICOM CT images with region of interest (ROI) segmentations as either DICOM SEG or RTSTRUCT.
 
 ```bash
@@ -51,28 +55,31 @@ $ readii [INPUT DIRECTORY] [OUTPUT DIRECTORY] \
 
 ### Negative control options
 
-Negative controls are applied to one of three masks: 
+Negative controls are applied to one of three masks:
+
 1. full = voxels in the entire image
 2. roi = just voxels within the specified region of interest (ROI) in the segmentation
 3. non_roi = all voxels except the ROI.
 
 The three transformations are:
+
 1. shuffle = shuffle all voxels in the specified mask
 2. randomized = randomly generate new values within the original range within the specified mask
 3. randomized_sampled = randomly sample original values with replacement to get new values within the specified mask
 
-
 ## Contributing
 
 Please use the following angular commit message format:
-```
+
+```text
 <type>(optional scope): short summary in present tense
 
 (optional body: explains motivation for the change)
 
 (optional footer: note BREAKING CHANGES here, and issues to be closed)
 
 ```
+
 `<type>` refers to the kind of change made and is usually one of:
 
 - `feat`: A new feature.
@@ -88,10 +95,14 @@ Please use the following angular commit message format:
 
 Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
 
+### Serve Documentation Locally
+
+```bash
+pixi run -e docs doc-serve
+```
+
 ## License
 
 `readii` was created by Katy Scott. It is licensed under the terms of the MIT license.
 
-## Credits
-
-`readii` was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter).
+<!--intro-end-->

docs/changelog.md

@@ -1,2 +1,5 @@
-```{include} ../CHANGELOG.md
-```
+
+{%
+  include-markdown "../CHANGELOG.md"
+  rewrite-relative-urls=false
+%}

docs/index.md

@@ -1,13 +1,8 @@
-```{include} ../README.md
-```
+# READII (Radiomic Extraction and Analysis for DICOM Images)
 
-```{toctree}
-:maxdepth: 1
-:hidden:
-
-example.ipynb
-changelog.md
-contributing.md
-conduct.md
-autoapi/index
-```
+{%
+  include-markdown "../README.md"
+  start="<!--intro-start-->"
+  end="<!--intro-end-->"
+  rewrite-relative-urls=false
+%}

mkdocs.yaml

@@ -0,0 +1,53 @@
+site_name: READII
+repo_url: https://github.com/bhklab/readii
+repo_name: readii
+site_description: Package documentation for readii
+site_author: bhklab
+
+watch: [docs, src, mkdocs.yaml]
+# The directory where the documentation files are located
+docs_dir: docs
+
+# The directory where the documentation is built (add to .gitignore if changed)
+site_dir: site
+
+# Set a list of CSS files (relative to docs_dir) to be included by the theme
+# typically as <link> tags.
+extra_css: []
+
+# This is the branch where the documentation will pushed to using
+# 'mkdocs gh-deploy' and from where it will be served by GitHub Pages.
+remote_branch: gh-pages
+
+# Address when using 'mkdocs serve', format is 'address:port'
+dev_addr: 127.0.0.1:8001
+
+# The layout of the navigation links
+nav:
+  - Home: index.md
+  - Changelog: changelog.md
+
+plugins:
+  - awesome-pages                     # simplifies configuring page titles and their order
+  - search                            # necessary for search functionality to work
+  - git-authors                       # adds authors to pages using git history
+  - include-markdown                  # allows for including Markdown files into another Markdown file
+
+theme: 
+  name: material
+  features:
+    - announce.dismiss
+    - content.action.edit
+    - content.action.view
+    - content.code.annotate
+    - content.code.copy
+    - content.tooltips
+    - navigation.footer
+    - navigation.indexes
+    - navigation.sections
+    - navigation.tabs
+    - navigation.tabs.sticky
+    - navigation.top
+    - search.highlight
+    - search.suggest
+    - toc.follow