change theme

docs/Gemfile

@@ -9,7 +9,7 @@ source "https://rubygems.org"
 # Happy Jekylling!
 #gem "jekyll", "~> 4.3.2"
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
-gem "minima", "~> 2.5"
+#gem "minima", "~> 2.5"
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.
 # gem "github-pages", group: :jekyll_plugins
@@ -34,3 +34,5 @@ gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
 gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
 
 gem "webrick", "~> 1.8"
+gem "just-the-docs"
+gem 'jekyll-redirect-from'

docs/Gemfile.lock

@@ -207,6 +207,11 @@ GEM
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0, < 5.0)
+    just-the-docs (0.7.0)
+      jekyll (>= 3.8.5)
+      jekyll-include-cache
+      jekyll-seo-tag (>= 2.0)
+      rake (>= 12.3.1)
     kramdown (2.3.2)
       rexml
     kramdown-parser-gfm (1.1.0)
@@ -231,6 +236,7 @@ GEM
       forwardable-extended (~> 2.6)
     public_suffix (4.0.7)
     racc (1.7.2)
+    rake (13.1.0)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
@@ -271,7 +277,8 @@ DEPENDENCIES
   github-pages (~> 228)
   http_parser.rb (~> 0.6.0)
   jekyll-feed (~> 0.12)
-  minima (~> 2.5)
+  jekyll-redirect-from
+  just-the-docs
   tzinfo (>= 1, < 3)
   tzinfo-data
   wdm (~> 0.1.1)

docs/_config.yml

@@ -18,20 +18,45 @@
 # You can create any custom variable you would like, and they will be accessible
 # in the templates via {{ site.myvariable }}.
 
-title: Chrastil Lab Documentation on GitHub Page
+title: Chrastil Lab Documentation
 email: [email protected]
 description: >- # this means to ignore newlines until "baseurl:"
   Welcome to the Chrastil Lab Code Documentation Repository on GitHub! This repository serves as the central hub for organizing and sharing the coding documentation related to the research and projects conducted by the Chrastil Lab.
 baseurl: "/" # the subpath of your site, e.g. /blog
 #domain: "chrastillab.github.io" # the base hostname & protocol for your site, e.g. http://example.com
 url: "http://chrastillab.github.io/" # the base hostname & protocol for your site, e.g. http://example.com
-twitter_username: jekyllrb
-github_username: spatialneuroscience
+#twitter_username: jekyllrb
+#github_username: chrastillab
 
 # Build settings
-theme: minima
+theme: just-the-docs
 plugins:
   - jekyll-feed
+  - jekyll-redirect-from
+
+logo: "/assets/images/logo.png"
+favicon_ico: "/assets/images/brainnn.png"
+mermaid:
+  version: "9.1.3"
+
+aux_links:
+  "Chrastil Lab Github":
+    - "//github.com/chrastillab"
+  "Spatial Neuroscience Github":
+    - "//github.com/chrastillab"
+
+aux_links_new_tab: true
+
+collections:
+  misc:
+    permalink: "/:collection/:path/"
+    output: true
+
+just_the_docs:
+  collections:
+    misc:
+      name: Miscellaneous
+
 
 # Exclude from processing.
 # The following items will not be processed, by default.

docs/_misc/github_page/first-time-setup.md

@@ -0,0 +1,34 @@
+---
+layout: default
+title: How to setup a github page site with Jekyll like this site
+nav_order: 1
+parent: GitHub Page
+---
+# Perquisite (For Windows Users)
+
+1. Installing Ruby with Bundler
+	1. Go to [Ruby Installer Download](https://rubyinstaller.org/downloads/)
+	2. Download the latest release **with** DevKit (DevKits allows the installation of jekyll)
+			- At the end of the installation, check the box to install `MSYS2 and MINGW`
+	3. Open a command shell to check ruby is installed `ruby --vesion`
+		- If command is not found or recognized, check that the `PATH` environment variables contains path to ruby executable and restart command shell
+	4. Then, run `gem install jekyll bundler`
+	5. Sip coffee (2-5 minutes depends on your computer specs)
+
+2. Follow [Detailed GitHub Official Tutorial](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/creating-a-github-pages-site-with-jekyll)
+	1. Ensure you've commented out  the line that starts with `gem "jekyll"` in `Gemfile`
+	2. Ensure you've added `gem "github-pages", "~> GITHUB-PAGES-VERSION", group: :jekyll_plugins` and replace the version accordingly
+
+## The `_config.yml`
+```yml
+title: Chrastil Lab Documentation on GitHub Page
+email: [email protected]
+description: Welcome to the Chrastil Lab Code Documentation Repository on GitHub! This repository serves as the central hub for organizing and sharing the coding documentation related to the research and projects conducted by the Chrastil Lab.
+baseurl: "/" 
+url: "http://chrastillab.github.io/" 
+github_username: spatialneuroscience, chrastillab
+# Build settings
+theme: minima
+plugins:
+  - jekyll-feed
+```

docs/_misc/github_page/index.md

@@ -0,0 +1,6 @@
+---
+layout: default
+title: GitHub Page
+nav_order: 1
+has_children: true
+---

docs/about.md

@@ -0,0 +1,30 @@
+---
+layout: page
+title: About
+permalink: /
+redirect_from:
+    - /about
+---
+
+🔬 About Chrastil Lab:
+Chrastil Lab is a dynamic and innovative research group dedicated to advancing the field of cognitive neuroscience. Our work focuses on understanding the intricate mechanisms of human memory, navigation, and spatial cognition. We utilize cutting-edge technologies and data analysis techniques to unravel the mysteries of the human brain.
+
+👨‍💻 What You'll Find Here:
+In this repository, you'll discover a wealth of coding resources, scripts, and documentation that power our research. Whether you're a member of our lab, a collaborator, or a curious coder from the community, this is the place to access and contribute to our codebase. Here's what you can expect to find:
+
+Code Documentation: Detailed documentation for the algorithms, models, and tools we've developed. These documents provide insights into the rationale behind the code, usage guidelines, and explanations of key functions.
+
+Research Code: The actual code implementations of our research projects. You can explore, clone, and fork these repositories to replicate our experiments or adapt them for your own work.
+
+Tutorials and Guides: Step-by-step tutorials and guides to help you get started with our codebase. Whether you're new to our lab or a seasoned member, these resources will facilitate your journey.
+
+Issue Tracking: Report bugs, suggest improvements, or contribute to ongoing discussions about our code. Your input is valuable in maintaining the quality of our projects.
+
+Contributions: We encourage contributions from our lab members and the open-source community. If you have code, scripts, or documentation to add, feel free to submit pull requests and collaborate with us.
+
+🌟 Get Involved:
+We believe in the power of collaboration and open science. Whether you're a researcher, a coder, or someone interested in our work, we welcome your participation and feedback. Explore our repositories, join discussions, and help us advance our understanding of the brain and cognition through code.
+
+Stay connected with us:
+
+[Lab Website](https://faculty.sites.uci.edu/spatialneuro/)

docs/index.markdown → docs/index.md.bak

@@ -4,3 +4,4 @@
 
 layout: home
 ---
+

docs/tips/index.md

@@ -0,0 +1,8 @@
+---
+layout: default
+title: Tips
+nav_order: 2
+has_children: true
+---
+
+

docs/tips/sample-tip.md

@@ -0,0 +1,8 @@
+---
+layout: default
+title: Sample Tip
+nav_order: 2
+parent: Tips
+---
+
+Tip 1