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Merge pull request #711 from haddocking/readme
simplify setup instructions
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‎.bundle/config‎

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---
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BUNDLE_PATH: "vendor/bundle"

‎Gemfile‎

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source "https://rubygems.org"
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# Hello! This is where you manage which Jekyll version is used to run.
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# When you want to use a different version, change it below, save the
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# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
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#
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# bundle exec jekyll serve
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#
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# This will help ensure the proper Jekyll version is running.
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# Happy Jekylling!
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gem "jekyll", "~> 4.3.2"
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# This is the default theme for new Jekyll sites. You may change this to anything you like.
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gem "jekyll", "~> 4.2"
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gem "minima", "~> 2.5"
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# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
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# uncomment the line below. To upgrade, run `bundle update github-pages`.
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# gem "github-pages", group: :jekyll_plugins
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# If you have any plugins, put them here!
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group :jekyll_plugins do
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gem "jekyll-feed", "~> 0.12"
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end
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# Windows and JRuby does not include zoneinfo files, so bundle the tzinfo-data gem
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# and associated library.
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platforms :mingw, :x64_mingw, :mswin, :jruby do
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gem "tzinfo", ">= 1", "< 3"
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gem "tzinfo-data"
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end
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# Performance-booster for watching directories on Windows
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gem "wdm", "~> 0.1.1", :platforms => [:mingw, :x64_mingw, :mswin]
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# Lock `http_parser.rb` gem to `v0.6.x` on JRuby builds since newer versions of the gem
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# do not have a Java counterpart.
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gem "http_parser.rb", "~> 0.6.0", :platforms => [:jruby]
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gem "webrick", "~> 1.9"

‎Gemfile.lock‎

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GEM
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remote: https://rubygems.org/
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specs:
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addressable (2.8.7)
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public_suffix (>= 2.0.2, < 7.0)
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base64 (0.3.0)
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bigdecimal (3.2.2)
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colorator (1.1.0)
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concurrent-ruby (1.3.5)
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csv (3.3.5)
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em-websocket (0.5.3)
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eventmachine (>= 0.12.9)
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http_parser.rb (~> 0)
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eventmachine (1.2.7)
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ffi (1.17.2)
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ffi (1.17.2-aarch64-linux-gnu)
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ffi (1.17.2-aarch64-linux-musl)
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ffi (1.17.2-arm-linux-gnu)
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ffi (1.17.2-arm-linux-musl)
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ffi (1.17.2-arm64-darwin)
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ffi (1.17.2-x86-linux-gnu)
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ffi (1.17.2-x86-linux-musl)
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ffi (1.17.2-x86_64-darwin)
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ffi (1.17.2-x86_64-linux-gnu)
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ffi (1.17.2-x86_64-linux-musl)
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forwardable-extended (2.6.0)
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google-protobuf (4.31.1)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-aarch64-linux-gnu)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-aarch64-linux-musl)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-arm64-darwin)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-x86-linux-gnu)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-x86-linux-musl)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-x86_64-darwin)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-x86_64-linux-gnu)
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bigdecimal
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rake (>= 13)
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google-protobuf (4.31.1-x86_64-linux-musl)
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bigdecimal
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rake (>= 13)
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http_parser.rb (0.8.0)
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i18n (1.14.7)
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concurrent-ruby (~> 1.0)
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jekyll (4.4.1)
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addressable (~> 2.4)
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base64 (~> 0.2)
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colorator (~> 1.0)
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csv (~> 3.0)
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em-websocket (~> 0.5)
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i18n (~> 1.0)
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jekyll-sass-converter (>= 2.0, < 4.0)
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jekyll-watch (~> 2.0)
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json (~> 2.6)
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kramdown (~> 2.3, >= 2.3.1)
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kramdown-parser-gfm (~> 1.0)
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liquid (~> 4.0)
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mercenary (~> 0.3, >= 0.3.6)
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pathutil (~> 0.9)
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rouge (>= 3.0, < 5.0)
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safe_yaml (~> 1.0)
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terminal-table (>= 1.8, < 4.0)
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webrick (~> 1.7)
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jekyll-feed (0.17.0)
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jekyll (>= 3.7, < 5.0)
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jekyll-sass-converter (3.1.0)
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sass-embedded (~> 1.75)
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jekyll-seo-tag (2.8.0)
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jekyll (>= 3.8, < 5.0)
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jekyll-watch (2.2.1)
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listen (~> 3.0)
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json (2.12.2)
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kramdown (2.5.1)
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rexml (>= 3.3.9)
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kramdown-parser-gfm (1.1.0)
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kramdown (~> 2.0)
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liquid (4.0.4)
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listen (3.9.0)
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rb-fsevent (~> 0.10, >= 0.10.3)
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rb-inotify (~> 0.9, >= 0.9.10)
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mercenary (0.4.0)
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minima (2.5.2)
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jekyll (>= 3.5, < 5.0)
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jekyll-feed (~> 0.9)
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jekyll-seo-tag (~> 2.1)
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pathutil (0.16.2)
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forwardable-extended (~> 2.6)
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public_suffix (6.0.2)
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rake (13.3.0)
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rb-fsevent (0.11.2)
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rb-inotify (0.11.1)
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ffi (~> 1.0)
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rexml (3.4.1)
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rouge (4.5.2)
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safe_yaml (1.0.5)
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sass-embedded (1.89.2)
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google-protobuf (~> 4.31)
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rake (>= 13)
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sass-embedded (1.89.2-aarch64-linux-android)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-aarch64-linux-gnu)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-aarch64-linux-musl)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-arm-linux-androideabi)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-arm-linux-gnueabihf)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-arm-linux-musleabihf)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-arm64-darwin)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-riscv64-linux-android)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-riscv64-linux-gnu)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-riscv64-linux-musl)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-x86_64-darwin)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-x86_64-linux-android)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-x86_64-linux-gnu)
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google-protobuf (~> 4.31)
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sass-embedded (1.89.2-x86_64-linux-musl)
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google-protobuf (~> 4.31)
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terminal-table (3.0.2)
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unicode-display_width (>= 1.1.1, < 3)
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unicode-display_width (2.6.0)
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webrick (1.9.1)
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PLATFORMS
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aarch64-linux-android
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aarch64-linux-gnu
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aarch64-linux-musl
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arm-linux-androideabi
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arm-linux-gnu
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arm-linux-gnueabihf
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arm-linux-musl
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arm-linux-musleabihf
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arm64-darwin
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riscv64-linux-android
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riscv64-linux-gnu
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riscv64-linux-musl
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ruby
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x86-linux-gnu
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x86-linux-musl
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x86_64-darwin
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x86_64-linux-android
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x86_64-linux-gnu
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x86_64-linux-musl
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DEPENDENCIES
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http_parser.rb (~> 0.6.0)
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jekyll (~> 4.2)
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jekyll-feed (~> 0.12)
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minima (~> 2.5)
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tzinfo (>= 1, < 3)
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tzinfo-data
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wdm (~> 0.1.1)
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webrick (~> 1.9)
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BUNDLED WITH
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2.6.9

‎README.md‎

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# Bonvin Lab webpage based on the Jekyll template [Minimal Mistakes](http://mmistakes.github.io/minimal-mistakes)
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# BonvinLab webpage
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See a [live version of this website](http://haddocking.github.io/) hosted on GitHub.
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For more information on the template and folder organization, visit the [original author's
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web page](http://mmistakes.github.io/minimal-mistakes/theme-setup/).
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> Go to [bonvinlab.org](https://bonvinlab.org) for
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> the latest version of the BonvinLab website.
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## Getting Started
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## Adding to the page
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To ensure whatever you create/change appears as faithfully as possible after pushing to the main repository, install the version of Ruby and the gems used by Github. See a list [here](https://pages.github.com/versions/).
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### Install dependencies
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### Installation Instructions (updt. Nov. 2023)
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#### Ruby
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Following the instructions from: https://github.com/BillRaymond/install-jekyll-apple-silicon/blob/main/README.md
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And using homebrew
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1. Install ruby3.0
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Install Ruby following your system's instructions.
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```text
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brew install ruby
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```
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brew install [email protected]
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```
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2. Add path to ruby3.0 in .bashrc (or .bash_provile)
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export PATH="/opt/homebrew/opt/[email protected]/bin/:$PATH"
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3. Restart your terminal and make sure you are now using ruby3.0
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```text
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sudo apt install ruby-full
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```
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ruby -v
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```text
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sudo pacman -S ruby ruby-erb
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```
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4. Install Jekyll and Bundler
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#### Clone this repository
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```
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gem install --user-install bundler jekyll
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```bash
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git clone --depth 1 https://github.com/haddocking/haddocking.github.io.git bonvinlab-website
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cd bonvinlab-website
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```
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5. Add the path to the gems to in .bashrc (or .bash_provile)
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#### Install website dependencies
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export PATH="~/.local/share/gem/ruby/3.0.0/bin:$PATH"
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These are Ruby packages (gems) required to run the website.
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First, install Ruby's dependency manager `bundler` and `jekyll`
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```bash
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# Change the ruby version if you are not using `3.4.0`
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export PATH="$HOME/.local/share/gem/ruby/3.4.0/bin:$PATH"
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gem install --user-install bundler jekyll
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```
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6. Clone the haddocking.github.io repository and install all dependency Gems with Bundler
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Now install the required website dependencies (gems) using Bundler.
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```bash
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git clone https://github.com/haddocking/haddocking.github.io.git haddocking-website
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cd haddocking-website
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bundle init
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bundle add jekyll --version "~>4.2"
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bundle config set --local path 'vendor/bundle'
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bundle install
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bundle exec jekyll new --force --skip-bundle .
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bundle add webrick
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bundle install
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bundle update
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```
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7. Adapt the settings in _config.yml accordingly
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In order for links to properly work, the `url` setting in must be set accordingly, otherwise you will be redirected to the live version. This sets all the `site.url` variable calls throughout _layouts/, _includes/, etc.
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```yaml
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url: "" # Empty string will render the page successfully locally. Do not commit it to the main repository!
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incremental: true # This will be disabled by Github, but is useful for testing changes locally!
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```
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### Running the website locally
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### Running the site locally
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To preview changes, which you should always do before committing anything or making any pull requests, run the web server locally using the following:
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Serve it locally by running:
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```bash --login
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$ bundle exec jekyll serve
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```
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### Small utility to create a new post automatically. Quick and dirty replacement of `octopress new post`
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```python
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$ python _utilities/create_new_article.py 'A Random Post'
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```bash
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bundle exec jekyll serve
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```
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8. For updating jeckyll and bundle
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It should now be served on [http://127.0.0.1:4000](http://127.0.0.1:4000)
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```bash
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$ gem update jekyll
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$ gem update bundle
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Go ahead and edit/add what you need! To see the rendered version, refresh the page.

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