diff --git a/.bundle/config b/.bundle/config new file mode 100644 index 00000000..23692288 --- /dev/null +++ b/.bundle/config @@ -0,0 +1,2 @@ +--- +BUNDLE_PATH: "vendor/bundle" diff --git a/Gemfile b/Gemfile index ff2c3428..453ecc8e 100644 --- a/Gemfile +++ b/Gemfile @@ -1,33 +1,20 @@ 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 "jekyll", "~> 4.2" + 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 -# 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] + +gem "webrick", "~> 1.9" diff --git a/Gemfile.lock b/Gemfile.lock new file mode 100644 index 00000000..707db659 --- /dev/null +++ b/Gemfile.lock @@ -0,0 +1,176 @@ +GEM + remote: https://rubygems.org/ + specs: + addressable (2.8.7) + public_suffix (>= 2.0.2, < 7.0) + base64 (0.3.0) + bigdecimal (3.2.2) + colorator (1.1.0) + concurrent-ruby (1.3.5) + csv (3.3.5) + em-websocket (0.5.3) + eventmachine (>= 0.12.9) + http_parser.rb (~> 0) + eventmachine (1.2.7) + ffi (1.17.2) + ffi (1.17.2-aarch64-linux-gnu) + ffi (1.17.2-aarch64-linux-musl) + ffi (1.17.2-arm-linux-gnu) + ffi (1.17.2-arm-linux-musl) + ffi (1.17.2-arm64-darwin) + ffi (1.17.2-x86-linux-gnu) + ffi (1.17.2-x86-linux-musl) + ffi (1.17.2-x86_64-darwin) + ffi (1.17.2-x86_64-linux-gnu) + ffi (1.17.2-x86_64-linux-musl) + forwardable-extended (2.6.0) + google-protobuf (4.31.1) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-aarch64-linux-gnu) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-aarch64-linux-musl) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-arm64-darwin) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-x86-linux-gnu) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-x86-linux-musl) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-x86_64-darwin) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-x86_64-linux-gnu) + bigdecimal + rake (>= 13) + google-protobuf (4.31.1-x86_64-linux-musl) + bigdecimal + rake (>= 13) + http_parser.rb (0.8.0) + i18n (1.14.7) + concurrent-ruby (~> 1.0) + jekyll (4.4.1) + addressable (~> 2.4) + base64 (~> 0.2) + colorator (~> 1.0) + csv (~> 3.0) + em-websocket (~> 0.5) + i18n (~> 1.0) + jekyll-sass-converter (>= 2.0, < 4.0) + jekyll-watch (~> 2.0) + json (~> 2.6) + kramdown (~> 2.3, >= 2.3.1) + kramdown-parser-gfm (~> 1.0) + liquid (~> 4.0) + mercenary (~> 0.3, >= 0.3.6) + pathutil (~> 0.9) + rouge (>= 3.0, < 5.0) + safe_yaml (~> 1.0) + terminal-table (>= 1.8, < 4.0) + webrick (~> 1.7) + jekyll-feed (0.17.0) + jekyll (>= 3.7, < 5.0) + jekyll-sass-converter (3.1.0) + sass-embedded (~> 1.75) + jekyll-seo-tag (2.8.0) + jekyll (>= 3.8, < 5.0) + jekyll-watch (2.2.1) + listen (~> 3.0) + json (2.12.2) + kramdown (2.5.1) + rexml (>= 3.3.9) + kramdown-parser-gfm (1.1.0) + kramdown (~> 2.0) + liquid (4.0.4) + listen (3.9.0) + rb-fsevent (~> 0.10, >= 0.10.3) + rb-inotify (~> 0.9, >= 0.9.10) + mercenary (0.4.0) + minima (2.5.2) + jekyll (>= 3.5, < 5.0) + jekyll-feed (~> 0.9) + jekyll-seo-tag (~> 2.1) + pathutil (0.16.2) + forwardable-extended (~> 2.6) + public_suffix (6.0.2) + rake (13.3.0) + rb-fsevent (0.11.2) + rb-inotify (0.11.1) + ffi (~> 1.0) + rexml (3.4.1) + rouge (4.5.2) + safe_yaml (1.0.5) + sass-embedded (1.89.2) + google-protobuf (~> 4.31) + rake (>= 13) + sass-embedded (1.89.2-aarch64-linux-android) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-aarch64-linux-gnu) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-aarch64-linux-musl) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-arm-linux-androideabi) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-arm-linux-gnueabihf) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-arm-linux-musleabihf) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-arm64-darwin) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-riscv64-linux-android) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-riscv64-linux-gnu) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-riscv64-linux-musl) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-x86_64-darwin) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-x86_64-linux-android) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-x86_64-linux-gnu) + google-protobuf (~> 4.31) + sass-embedded (1.89.2-x86_64-linux-musl) + google-protobuf (~> 4.31) + terminal-table (3.0.2) + unicode-display_width (>= 1.1.1, < 3) + unicode-display_width (2.6.0) + webrick (1.9.1) + +PLATFORMS + aarch64-linux-android + aarch64-linux-gnu + aarch64-linux-musl + arm-linux-androideabi + arm-linux-gnu + arm-linux-gnueabihf + arm-linux-musl + arm-linux-musleabihf + arm64-darwin + riscv64-linux-android + riscv64-linux-gnu + riscv64-linux-musl + ruby + x86-linux-gnu + x86-linux-musl + x86_64-darwin + x86_64-linux-android + x86_64-linux-gnu + x86_64-linux-musl + +DEPENDENCIES + http_parser.rb (~> 0.6.0) + jekyll (~> 4.2) + jekyll-feed (~> 0.12) + minima (~> 2.5) + tzinfo (>= 1, < 3) + tzinfo-data + wdm (~> 0.1.1) + webrick (~> 1.9) + +BUNDLED WITH + 2.6.9 diff --git a/README.md b/README.md index 7951b4cc..40e0dd82 100644 --- a/README.md +++ b/README.md @@ -1,86 +1,62 @@ -# Bonvin Lab webpage based on the Jekyll template [Minimal Mistakes](http://mmistakes.github.io/minimal-mistakes) +# BonvinLab webpage -See a [live version of this website](http://haddocking.github.io/) hosted on GitHub. -For more information on the template and folder organization, visit the [original author's -web page](http://mmistakes.github.io/minimal-mistakes/theme-setup/). +> Go to [bonvinlab.org](https://bonvinlab.org) for +> the latest version of the BonvinLab website. -## Getting Started +## Adding to the page -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/). +### Install dependencies -### Installation Instructions (updt. Nov. 2023) +#### Ruby -Following the instructions from: https://github.com/BillRaymond/install-jekyll-apple-silicon/blob/main/README.md - -And using homebrew - - -1. Install ruby3.0 +Install Ruby following your system's instructions. +```text +brew install ruby ``` -brew install ruby@3.0 -``` - -2. Add path to ruby3.0 in .bashrc (or .bash_provile) - -export PATH="/opt/homebrew/opt/ruby@3.0/bin/:$PATH" - -3. Restart your terminal and make sure you are now using ruby3.0 +```text +sudo apt install ruby-full ``` -ruby -v + +```text +sudo pacman -S ruby ruby-erb ``` -4. Install Jekyll and Bundler +#### Clone this repository -``` -gem install --user-install bundler jekyll +```bash +git clone --depth 1 https://github.com/haddocking/haddocking.github.io.git bonvinlab-website +cd bonvinlab-website ``` -5. Add the path to the gems to in .bashrc (or .bash_provile) +#### Install website dependencies -export PATH="~/.local/share/gem/ruby/3.0.0/bin:$PATH" +These are Ruby packages (gems) required to run the website. +First, install Ruby's dependency manager `bundler` and `jekyll` +```bash +# Change the ruby version if you are not using `3.4.0` +export PATH="$HOME/.local/share/gem/ruby/3.4.0/bin:$PATH" +gem install --user-install bundler jekyll +``` -6. Clone the haddocking.github.io repository and install all dependency Gems with Bundler +Now install the required website dependencies (gems) using Bundler. ```bash -git clone https://github.com/haddocking/haddocking.github.io.git haddocking-website -cd haddocking-website -bundle init -bundle add jekyll --version "~>4.2" bundle config set --local path 'vendor/bundle' bundle install -bundle exec jekyll new --force --skip-bundle . -bundle add webrick -bundle install bundle update ``` -7. Adapt the settings in _config.yml accordingly -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. - -```yaml -url: "" # Empty string will render the page successfully locally. Do not commit it to the main repository! -incremental: true # This will be disabled by Github, but is useful for testing changes locally! -``` - -### Running the website locally +### Running the site locally -To preview changes, which you should always do before committing anything or making any pull requests, run the web server locally using the following: +Serve it locally by running: -```bash --login - $ bundle exec jekyll serve -``` - -### Small utility to create a new post automatically. Quick and dirty replacement of `octopress new post` - -```python - $ python _utilities/create_new_article.py 'A Random Post' +```bash +bundle exec jekyll serve ``` -8. For updating jeckyll and bundle +It should now be served on [http://127.0.0.1:4000](http://127.0.0.1:4000) -```bash - $ gem update jekyll - $ gem update bundle +Go ahead and edit/add what you need! To see the rendered version, refresh the page.