diff --git a/docs/.gitignore b/docs/.gitignore new file mode 100644 index 0000000..f40fbd8 --- /dev/null +++ b/docs/.gitignore @@ -0,0 +1,5 @@ +_site +.sass-cache +.jekyll-cache +.jekyll-metadata +vendor diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..086a5c9 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,25 @@ +--- +permalink: /404.html +layout: default +--- + + + +
+

404

+ +

Page not found :(

+

The requested page could not be found.

+
diff --git a/docs/Gemfile b/docs/Gemfile new file mode 100644 index 0000000..90acbd0 --- /dev/null +++ b/docs/Gemfile @@ -0,0 +1,34 @@ +source "https://rubygems.org" +# Hello! This is where you manage which Jekyll version is used to run. +# When you want to use a different version, change it below, save the +# file and run `bundle install`. Run Jekyll with `bundle exec`, like so: +# +# bundle exec jekyll serve +# +# 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" +end + +# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem +# and associated library. +platforms :mingw, :x64_mingw, :mswin, :jruby do + gem "tzinfo", ">= 1", "< 3" + gem "tzinfo-data" +end + +# Performance-booster for watching directories on Windows +gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin] + +# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem +# do not have a Java counterpart. +gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby] diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock new file mode 100644 index 0000000..213c4da --- /dev/null +++ b/docs/Gemfile.lock @@ -0,0 +1,279 @@ +GEM + remote: https://rubygems.org/ + specs: + activesupport (7.1.1) + base64 + bigdecimal + concurrent-ruby (~> 1.0, >= 1.0.2) + connection_pool (>= 2.2.5) + drb + i18n (>= 1.6, < 2) + minitest (>= 5.1) + mutex_m + tzinfo (~> 2.0) + addressable (2.8.5) + public_suffix (>= 2.0.2, < 6.0) + base64 (0.1.1) + bigdecimal (3.1.4) + coffee-script (2.4.1) + coffee-script-source + execjs + coffee-script-source (1.11.1) + colorator (1.1.0) + commonmarker (0.23.10) + concurrent-ruby (1.2.2) + connection_pool (2.4.1) + dnsruby (1.70.0) + simpleidn (~> 0.2.1) + drb (2.1.1) + ruby2_keywords + em-websocket (0.5.3) + eventmachine (>= 0.12.9) + http_parser.rb (~> 0) + ethon (0.16.0) + ffi (>= 1.15.0) + eventmachine (1.2.7) + execjs (2.9.1) + faraday (2.7.11) + base64 + faraday-net_http (>= 2.0, < 3.1) + ruby2_keywords (>= 0.0.4) + faraday-net_http (3.0.2) + ffi (1.16.3-x64-mingw-ucrt) + forwardable-extended (2.6.0) + gemoji (3.0.1) + github-pages (228) + github-pages-health-check (= 1.17.9) + jekyll (= 3.9.3) + jekyll-avatar (= 0.7.0) + jekyll-coffeescript (= 1.1.1) + jekyll-commonmark-ghpages (= 0.4.0) + jekyll-default-layout (= 0.1.4) + jekyll-feed (= 0.15.1) + jekyll-gist (= 1.5.0) + jekyll-github-metadata (= 2.13.0) + jekyll-include-cache (= 0.2.1) + jekyll-mentions (= 1.6.0) + jekyll-optional-front-matter (= 0.3.2) + jekyll-paginate (= 1.1.0) + jekyll-readme-index (= 0.3.0) + jekyll-redirect-from (= 0.16.0) + jekyll-relative-links (= 0.6.1) + jekyll-remote-theme (= 0.4.3) + jekyll-sass-converter (= 1.5.2) + jekyll-seo-tag (= 2.8.0) + jekyll-sitemap (= 1.4.0) + jekyll-swiss (= 1.0.0) + jekyll-theme-architect (= 0.2.0) + jekyll-theme-cayman (= 0.2.0) + jekyll-theme-dinky (= 0.2.0) + jekyll-theme-hacker (= 0.2.0) + jekyll-theme-leap-day (= 0.2.0) + jekyll-theme-merlot (= 0.2.0) + jekyll-theme-midnight (= 0.2.0) + jekyll-theme-minimal (= 0.2.0) + jekyll-theme-modernist (= 0.2.0) + jekyll-theme-primer (= 0.6.0) + jekyll-theme-slate (= 0.2.0) + jekyll-theme-tactile (= 0.2.0) + jekyll-theme-time-machine (= 0.2.0) + jekyll-titles-from-headings (= 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ruby2_keywords (0.0.5) + rubyzip (2.3.2) + safe_yaml (1.0.5) + sass (3.7.4) + sass-listen (~> 4.0.0) + sass-listen (4.0.0) + rb-fsevent (~> 0.9, >= 0.9.4) + rb-inotify (~> 0.9, >= 0.9.7) + sawyer (0.9.2) + addressable (>= 2.3.5) + faraday (>= 0.17.3, < 3) + simpleidn (0.2.1) + unf (~> 0.1.4) + terminal-table (1.8.0) + unicode-display_width (~> 1.1, >= 1.1.1) + typhoeus (1.4.0) + ethon (>= 0.9.0) + tzinfo (2.0.6) + concurrent-ruby (~> 1.0) + tzinfo-data (1.2023.3) + tzinfo (>= 1.0.0) + unf (0.1.4) + unf_ext + unf_ext (0.0.8.2) + unicode-display_width (1.8.0) + wdm (0.1.1) + +PLATFORMS + x64-mingw-ucrt + +DEPENDENCIES + github-pages (~> 228) + http_parser.rb (~> 0.6.0) + jekyll-feed (~> 0.12) + minima (~> 2.5) + tzinfo (>= 1, < 3) + tzinfo-data + wdm (~> 0.1.1) + +BUNDLED WITH + 2.4.21 diff --git a/docs/_config.yml b/docs/_config.yml new file mode 100644 index 0000000..63146c1 --- /dev/null +++ b/docs/_config.yml @@ -0,0 +1,54 @@ +# Welcome to Jekyll! +# +# This config file is meant for settings that affect your whole blog, values +# which you are expected to set up once and rarely edit after that. If you find +# yourself editing this file very often, consider using Jekyll's data files +# feature for the data you need to update frequently. +# +# For technical reasons, this file is *NOT* reloaded automatically when you use +# 'bundle exec jekyll serve'. If you change this file, please restart the server process. +# +# If you need help with YAML syntax, here are some quick references for you: +# https://learn-the-web.algonquindesign.ca/topics/markdown-yaml-cheat-sheet/#yaml +# https://learnxinyminutes.com/docs/yaml/ +# +# Site settings +# These are used to personalize your new site. If you look in the HTML files, +# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on. +# 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 +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: "/docs" # 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: "https://chrastillab.github.io" # the base hostname & protocol for your site, e.g. http://example.com +twitter_username: jekyllrb +github_username: spatialneuroscience + +# Build settings +theme: minima +plugins: + - jekyll-feed + +# Exclude from processing. +# The following items will not be processed, by default. +# Any item listed under the `exclude:` key here will be automatically added to +# the internal "default list". +# +# Excluded items can be processed by explicitly listing the directories or +# their entries' file path in the `include:` list. +# +# exclude: +# - .sass-cache/ +# - .jekyll-cache/ +# - gemfiles/ +# - Gemfile +# - Gemfile.lock +# - node_modules/ +# - vendor/bundle/ +# - vendor/cache/ +# - vendor/gems/ +# - vendor/ruby/ diff --git a/docs/_posts/2023-11-01-welcome-to-jekyll.markdown b/docs/_posts/2023-11-01-welcome-to-jekyll.markdown new file mode 100644 index 0000000..8ccab6f --- /dev/null +++ b/docs/_posts/2023-11-01-welcome-to-jekyll.markdown @@ -0,0 +1,29 @@ +--- +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 new file mode 100644 index 0000000..8b4e0b2 --- /dev/null +++ b/docs/about.markdown @@ -0,0 +1,18 @@ +--- +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/index.markdown b/docs/index.markdown new file mode 100644 index 0000000..0671507 --- /dev/null +++ b/docs/index.markdown @@ -0,0 +1,6 @@ +--- +# Feel free to add content and custom Front Matter to this file. +# To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults + +layout: home +---