simplify setup instructions

.bundle/config

@@ -0,0 +1,2 @@
+---
+BUNDLE_PATH: "vendor/bundle"

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"

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

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 [email protected]
-```
-
-2. Add path to ruby3.0 in .bashrc (or .bash_provile)
-
-export PATH="/opt/homebrew/opt/[email protected]/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.