Skip to content

Commit

Permalink
adding new notes
Browse files Browse the repository at this point in the history
  • Loading branch information
greasycat committed Nov 2, 2023
1 parent 9f26d3b commit 8c94fc6
Show file tree
Hide file tree
Showing 7 changed files with 161 additions and 18 deletions.
92 changes: 85 additions & 7 deletions _misc/github_page/first-time-setup.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,31 +4,109 @@ title: How to setup a github page site with Jekyll like this site
nav_order: 1
parent: GitHub Page
---
# Perquisite (For Windows Users)
# What is Jekyll

Jekyll is a popular open-source static site generator (SSG) written in Ruby. It's designed to simplify the process of creating and maintaining websites, particularly blogs and simple websites. Jekyll takes your content, written in plain text or in Markdown, and combines it with templates to generate static HTML pages.



# 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`
4. 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`
### A sample `_config.yml`
```yml
title: Chrastil Lab Documentation on GitHub Page
# Title of the website
title: Chrastil Lab Documentation

# Email (can be removed)
email: [email protected]

# Some decription
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.

# Do not change unless you're not using gh page
baseurl: "/"
url: "http://chrastillab.github.io/"
github_username: spatialneuroscience, chrastillab
# Build settings

# The link to the website
url: "http://chrastillab.github.io/"

# A theme-related variable to put a github link on the footer
github_username: spatialneuroscience

# Choose a Theme
theme: minima

# Plugins
plugins:
  - jekyll-feed
```

# Changing the theme
Jekyll has a lively community that creates various themes for different needs. This makes it simple to discover a theme you prefer and use it for your own project. For our current lab documentation site, I chose the [Just The Docs](https://just-the-docs.com/) theme. It's a straightforward theme that's great for organizing content effectively.

### Installing the theme

1. Add a new line `gem "just-the-docs"` to `Gemfile`
2. Editing the `_config.yml`

### Changing `_config.yml` (read the comments)

```yml
# Changing from minima to just-the-docs
theme: just-the-docs

# The logo image on the top left
logo: "/assets/images/logo.png"

# The icon on the browser tab
favicon_ico: "/assets/images/brainnn.png"

# An engine to plot diagrams
mermaid:
version: "9.1.3"

# Links to be displayed on the top navigation bar
aux_links:
"Chrastil Lab Github":
- "//github.com/chrastillab"
"Spatial Neuroscience Github":
- "//github.com/chrastillab"

# Make sure when people click on the link, it will opne a new page
aux_links_new_tab: true

# Defining Custom collection that can be shown on left sidebar
collections:
misc:
permalink: "/:collection/:path/"
output: true

# Pass the collection information to the theme variable
just_the_docs:
collections:
misc:
name: Miscellaneous
```
3. Run `bundle install`
4. Run `bundle exec jekyll serve` to test the changes
5. Git push your changes

There're a lot more customizations that could be enabled but we will omit them here. Check out the [configuration](https://just-the-docs.com/docs/configuration/) yourself!

# Theme not properly showing on Github Pages

Open the github repo -> Settings -> Pages -> Build and Deployment -> Github Action
- Search for a github action called `Jekyll` created by Github Action
- Click configure and don't change anything, the workflow should automatically build and depoly the site (if you put your source code in a subfolder, you should move them to the root folder or finding another GitHub Action)
44 changes: 43 additions & 1 deletion _misc/github_page/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,4 +3,46 @@ layout: default
title: GitHub Page
nav_order: 1
has_children: true
---
---

# GitHub Page?


GitHub Pages is a web hosting service provided by GitHub for hosting static websites. It allows users to easily publish and share web content, such as documentation, personal blogs, project websites, and more. GitHub Pages is tightly integrated with Git and GitHub repositories, making it a popular choice for developers and teams to showcase their work online.

## Key Features

- **Free Hosting**: GitHub Pages is offered for free, making it accessible to individual developers, open-source projects, and organizations with budget constraints.

- **Static Websites**: GitHub Pages hosts static websites, which are composed of HTML, CSS, JavaScript, and other static assets. This approach ensures fast page loading times and improved security.

- **GitHub Integration**: GitHub Pages is tightly integrated with GitHub repositories. You can easily publish a website directly from a repository by following specific naming conventions for branches and directories.

- **Custom Domains**: Users can associate custom domain names with their GitHub Pages sites, allowing for branded and memorable web addresses (e.g., www.yourdomain.com).

- **Automated Builds**: GitHub Pages supports automatic generation of websites using static site generators like Jekyll. This enables easy content updates with each repository commit.

- **Project Sites**: In addition to user and organization pages, GitHub Pages can be used to host project-specific sites. These project sites are associated with a particular repository.

## Use Cases

- **Documentation**: Many software projects use GitHub Pages to host documentation, making it readily accessible to users and contributors.

- **Blogs**: GitHub Pages provides a platform for bloggers to create and host personal or project-related blogs using Markdown or HTML.

- **Portfolios**: Developers and designers often use GitHub Pages to showcase their portfolios, demonstrating their skills and past work.

- **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.
17 changes: 8 additions & 9 deletions about.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,24 +7,23 @@ redirect_from:
---

🔬 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.
- 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.
**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.
**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.
**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.

🌟 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:

[The Repository of this documentation](https://github.com/ChrastilLab/chrastillab.github.io)

[Lab Website](https://faculty.sites.uci.edu/spatialneuro/)
6 changes: 6 additions & 0 deletions server_management/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
---
layout: default
title: Server Management
nav_order: 2
has_children: true
---
11 changes: 11 additions & 0 deletions server_management/user_management/adding-ssh-key.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
---
layout: default
title: Using SSH key to login
nav_order: 2
parent: User Management
grand_parent: Server Management
---

# Tired of typing password every time you login onto Hopper?
# Use SSH Keys!

7 changes: 7 additions & 0 deletions server_management/user_management/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
---
layout: default
title: User Management
nav_order: 1
parent: Server Management
has_children: true
---
2 changes: 1 addition & 1 deletion tips/index.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
---
layout: default
title: Tips
nav_order: 2
nav_order: 3
has_children: true
---

Expand Down

0 comments on commit 8c94fc6

Please sign in to comment.