diff --git a/docs/Gemfile b/docs/Gemfile index 2f221b6..c6b9796 100644 --- a/docs/Gemfile +++ b/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' \ No newline at end of file diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock index 56ec302..413c4b1 100644 --- a/docs/Gemfile.lock +++ b/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) diff --git a/docs/_config.yml b/docs/_config.yml index 9247427..ed1023e 100644 --- a/docs/_config.yml +++ b/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: spatialneuroscience@uci.edu 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. diff --git a/docs/_misc/github_page/first-time-setup.md b/docs/_misc/github_page/first-time-setup.md new file mode 100644 index 0000000..21a2139 --- /dev/null +++ b/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: spatialneuroscience@uci.edu +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 +``` diff --git a/docs/_misc/github_page/index.md b/docs/_misc/github_page/index.md new file mode 100644 index 0000000..f07a1bc --- /dev/null +++ b/docs/_misc/github_page/index.md @@ -0,0 +1,6 @@ +--- +layout: default +title: GitHub Page +nav_order: 1 +has_children: true +--- \ No newline at end of file diff --git a/docs/_posts/2023-11-01-welcome-to-jekyll.markdown b/docs/_posts/2023-11-01-welcome-to-jekyll.markdown deleted file mode 100644 index 8ccab6f..0000000 --- a/docs/_posts/2023-11-01-welcome-to-jekyll.markdown +++ /dev/null @@ -1,29 +0,0 @@ ---- -layout: post -title: "Welcome to Jekyll!" -date: 2023-11-01 12:43:11 -0700 -categories: jekyll update ---- -You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated. - -Jekyll requires blog post files to be named according to the following format: - -`YEAR-MONTH-DAY-title.MARKUP` - -Where `YEAR` is a four-digit number, `MONTH` and `DAY` are both two-digit numbers, and `MARKUP` is the file extension representing the format used in the file. After that, include the necessary front matter. Take a look at the source for this post to get an idea about how it works. - -Jekyll also offers powerful support for code snippets: - -{% highlight ruby %} -def print_hi(name) - puts "Hi, #{name}" -end -print_hi('Tom') -#=> prints 'Hi, Tom' to STDOUT. -{% endhighlight %} - -Check out the [Jekyll docs][jekyll-docs] for more info on how to get the most out of Jekyll. File all bugs/feature requests at [Jekyll’s GitHub repo][jekyll-gh]. If you have questions, you can ask them on [Jekyll Talk][jekyll-talk]. - -[jekyll-docs]: https://jekyllrb.com/docs/home -[jekyll-gh]: https://github.com/jekyll/jekyll -[jekyll-talk]: https://talk.jekyllrb.com/ diff --git a/docs/about.markdown b/docs/about.markdown deleted file mode 100644 index 8b4e0b2..0000000 --- a/docs/about.markdown +++ /dev/null @@ -1,18 +0,0 @@ ---- -layout: page -title: About -permalink: /about/ ---- - -This is the base Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [jekyllrb.com](https://jekyllrb.com/) - -You can find the source code for Minima at GitHub: -[jekyll][jekyll-organization] / -[minima](https://github.com/jekyll/minima) - -You can find the source code for Jekyll at GitHub: -[jekyll][jekyll-organization] / -[jekyll](https://github.com/jekyll/jekyll) - - -[jekyll-organization]: https://github.com/jekyll diff --git a/docs/about.md b/docs/about.md new file mode 100644 index 0000000..31eb2ce --- /dev/null +++ b/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/) diff --git a/docs/assets/images/brainnn.ico b/docs/assets/images/brainnn.ico new file mode 100644 index 0000000..4f8294b Binary files /dev/null and b/docs/assets/images/brainnn.ico differ diff --git a/docs/assets/images/logo.png b/docs/assets/images/logo.png new file mode 100644 index 0000000..c75f811 Binary files /dev/null and b/docs/assets/images/logo.png differ diff --git a/docs/index.markdown b/docs/index.md.bak similarity index 99% rename from docs/index.markdown rename to docs/index.md.bak index 0671507..64a82a1 100644 --- a/docs/index.markdown +++ b/docs/index.md.bak @@ -4,3 +4,4 @@ layout: home --- + diff --git a/docs/landmarks/index.md b/docs/landmarks/index.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/tips/index.md b/docs/tips/index.md new file mode 100644 index 0000000..9141484 --- /dev/null +++ b/docs/tips/index.md @@ -0,0 +1,8 @@ +--- +layout: default +title: Tips +nav_order: 2 +has_children: true +--- + + diff --git a/docs/tips/sample-tip.md b/docs/tips/sample-tip.md new file mode 100644 index 0000000..f80b2d7 --- /dev/null +++ b/docs/tips/sample-tip.md @@ -0,0 +1,8 @@ +--- +layout: default +title: Sample Tip +nav_order: 2 +parent: Tips +--- + +Tip 1 \ No newline at end of file