editing a few pages

ChrastilLab · Nov 2, 2023 · ad6e826 · ad6e826
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commit ad6e826
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Showing 14 changed files with 368 additions and 151 deletions.
diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,5 @@ _site
 .jekyll-cache
 .jekyll-metadata
 vendor
+.obsidian
+obsidian-templates
diff --git a/Gemfile b/Gemfile
@@ -8,17 +8,10 @@ source "https://rubygems.org"
 # This will help ensure the proper Jekyll version is running.
 # 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"
-# 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
-# gem "github-pages", "~> 228", group: :jekyll_plugins
-# If you have any plugins, put them here!
-# group :jekyll_plugins do
-  # gem "jekyll-feed", "~> 0.12"
 gem 'jekyll-redirect-from'
-# end
+gem 'jekyll-relative-links'
+gem 'jekyll-sitemap'
+gem 'jekyll-seo-tag'
 
 # Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
 # and associated library.
@@ -35,4 +28,5 @@ 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 "just-the-docs"
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -9,11 +9,9 @@ GEM
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
     eventmachine (1.2.7)
-    ffi (1.16.3)
     ffi (1.16.3-x64-mingw-ucrt)
     forwardable-extended (2.6.0)
     google-protobuf (3.25.0-x64-mingw-ucrt)
-    google-protobuf (3.25.0-x86_64-linux)
     http_parser.rb (0.8.0)
     i18n (1.14.1)
       concurrent-ruby (~> 1.0)
@@ -37,10 +35,14 @@ GEM
       jekyll (>= 3.7, < 5.0)
     jekyll-redirect-from (0.16.0)
       jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.7.0)
+      jekyll (>= 3.3, < 5.0)
     jekyll-sass-converter (3.0.0)
       sass-embedded (~> 1.54)
     jekyll-seo-tag (2.8.0)
       jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
     just-the-docs (0.7.0)
@@ -69,8 +71,6 @@ GEM
     safe_yaml (1.0.5)
     sass-embedded (1.69.5-x64-mingw-ucrt)
       google-protobuf (~> 3.23)
-    sass-embedded (1.69.5-x86_64-linux-gnu)
-      google-protobuf (~> 3.23)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     tzinfo (2.0.6)
@@ -83,12 +83,14 @@ GEM
 
 PLATFORMS
   x64-mingw-ucrt
-  x86_64-linux
 
 DEPENDENCIES
   http_parser.rb (~> 0.6.0)
   jekyll (~> 4.3.2)
   jekyll-redirect-from
+  jekyll-relative-links
+  jekyll-seo-tag
+  jekyll-sitemap
   just-the-docs
   tzinfo (>= 1, < 3)
   tzinfo-data

diff --git a/README.md b/README.md
@@ -0,0 +1,71 @@
+# README for GitHub Documentation Page
+
+Welcome to the documentation page for our GitHub repository! This repository contains documentation and information related to our project. If you would like to contribute or edit the documentation, please follow the instructions below.
+
+## Accessing the Documentation Locally
+
+To view and edit the documentation locally on your computer, you will need to set up a local development environment using Jekyll, which is a popular static site generator. Follow the steps below to get started:
+
+### Prerequisites
+
+What you need
+- Ruby
+- RubyGem
+- Bundler
+
+1. Read the offical installtion guide [Jekyll offical Installation Guide](https://jekyllrb.com/docs/installation/). It will guide your installtion of Ruby and RubyGem step-by-step
+-  If **Bundler** is not installed: Install Bundler by running `gem install bundler` in your terminal.
+
+### Setting Up the Local Environment
+
+1. Clone this repository to your local machine using the following command:
+
+   ```
+   git clone https://github.com/chrastillab/chrastillab.github.io
+   ```
+
+2. Navigate to the repository's root directory:
+
+   ```
+   cd chrastillab.github.io
+   ```
+
+3. Install the required dependencies using Bundler:
+
+   ```
+   bundle install
+   ```
+
+### Viewing the Documentation
+
+1. Once the dependencies are installed, you can start a local development server by running the following command:
+
+   ```
+   bundle exec jekyll serve
+   ```
+
+2. Open your web browser and visit the following URL:
+
+   [http://127.0.0.1:4000](http://127.0.0.1:4000)
+
+   You should see the documentation website running locally.
+
+### Editing the Documentation
+
+1. To make changes to the documentation, navigate to the appropriate Markdown files in the repository's directory structure.
+
+2. Edit the Markdown files using your preferred text editor.
+
+3. Save your changes.
+
+4. Refresh the documentation website in your browser to see your edits.
+
+### Contributing
+
+If you'd like to contribute to the documentation, please fork this repository, make your changes, and then submit a pull request. We welcome contributions from the community!
+
+For more information on how to contribute to this repository, please refer to [Add your own documentation](http://chrastillab.github.io/github_page/)
+
+Thank you for your interest in improving our documentation! If you have any questions or encounter any issues, please feel free to open an issue on this repository or contact us through our official channels.
+
+Happy documenting! 📚
diff --git a/_config.yml b/_config.yml
@@ -5,22 +5,20 @@
 # in the templates via {{ site.myvariable }}.
 
 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: chrastillab
 
-# Build settings
-theme: just-the-docs
 plugins:
   - jekyll-redirect-from
+  - jekyll-relative-links
+  - jekyll-sitemap
+  - jekyll-seo-tag
+
+# Build settings
+theme: just-the-docs
 
 logo: "/assets/images/logo.png"
-favicon_ico: "/assets/images/brainnn.png"
+favicon_ico: "/assets/images/brainnn.ico"
 mermaid:
   version: "9.1.3"
 
@@ -56,6 +54,8 @@ collections:
 
 just_the_docs:
   collections:
+    coding:
+      name: "Coding"
     server_management:
       name: "Server Management"
     misc:
@@ -69,4 +69,23 @@ compress_html:
 kramdown:
   syntax_highlighter_opts:
     block:
-      line_numbers: true
+      line_numbers: true
+
+# Callout settings
+callouts:
+  warning:
+    title: Warning
+    color: red
+  note:
+    title: Important
+    color: blue
+  highlight:
+    title: Highlight
+    color: yellow
+  new:
+    title: new
+    color: green
+
+exclude:
+  - .obsidian # I use obsidian to editing Markdown files, here I need to ignore the autogenerated obsidian folder
+  - obsidian-templates
diff --git a/_misc/github_page/first-time-setup.md b/_misc/github_page/first-time-setup.md
diff --git a/assets/images/github_page/adding-documentation/commit.png b/assets/images/github_page/adding-documentation/commit.png
diff --git a/assets/images/github_page/adding-documentation/fork.png b/assets/images/github_page/adding-documentation/fork.png
diff --git a/assets/images/github_page/adding-documentation/pull_request.png b/assets/images/github_page/adding-documentation/pull_request.png
diff --git a/assets/images/github_page/adding-documentation/review.png b/assets/images/github_page/adding-documentation/review.png
diff --git a/assets/images/github_page/adding-documentation/review_button.png b/assets/images/github_page/adding-documentation/review_button.png
diff --git a/github_page/adding-documentation.md b/github_page/adding-documentation.md
@@ -0,0 +1,22 @@
+---
+layout: default
+title: Adding your own documentation
+nav_order: 1
+parent: Write Your Own Documentation!
+---
+
+# How to add your own documentation to this site
+
+## Step 1: Fork
+![forking](/assets/images/github_page/adding-documentation/fork.png)
+
+## Step 2: Adding, Editing, Deleting Markdown files on your own forked repository
+![commit](/assets/images/github_page/adding-documentation/commit.png)
+
+## Step 3: Create a pull requests after you've reviewed your changes
+![pull request](/assets/images/github_page/adding-documentation/pull_request.png)
+
+# If you're a reviewer
+![review button](/assets/images/github_page/adding-documentation/review_button.png)
+![review](/assets/images/github_page/adding-documentation/review.png)
+- Now you can merge it !!!
diff --git a/_misc/github_page/index.md → github_page/index.md b/_misc/github_page/index.md → github_page/index.md
@@ -1,6 +1,6 @@
 ---
 layout: default
-title: GitHub Page
+title: Write Your Own Documentation!
 nav_order: 1
 has_children: true
 ---
@@ -34,15 +34,4 @@ GitHub Pages is a web hosting service provided by GitHub for hosting static webs
 
 - **Project Websites**: Open-source projects often maintain dedicated websites using GitHub Pages to provide information, news, and downloads.
 
-- **Team Pages**: Organizations can use GitHub Pages to share information about their teams, projects, and goals.
-
-## Getting Started
-
-To create a GitHub Pages site, you typically need to:
-1. Create a GitHub repository.
-2. Name the repository following specific conventions (e.g., `<username>.github.io` for user pages).
-3. Add your HTML, CSS, and other assets to the repository.
-4. Enable GitHub Pages in your repository's settings.
-5. Optionally, configure a custom domain.
-
-GitHub Pages simplifies the process of hosting web content, making it a valuable tool for developers to share their projects and ideas with a global audience.
+- **Team Pages**: Organizations can use GitHub Pages to share information about their teams, projects, and goals.