feat: Initialize documentation

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