From 76657e6a56a0b3615d4ab32f86c20840dba98be9 Mon Sep 17 00:00:00 2001 From: amjjbonvin Date: Sat, 18 Nov 2023 15:33:41 +0100 Subject: [PATCH] Updated publication list and installation instructions --- .gitignore | 13 +---- Gemfile | 39 +++++++++++++-- README.md | 51 ++++++++++++++----- _config.yml | 114 ++++++++++++++++++++---------------------- publications/index.md | 4 +- 5 files changed, 132 insertions(+), 89 deletions(-) diff --git a/.gitignore b/.gitignore index 110d8a6c..f40fbd8b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,14 +1,5 @@ _site .sass-cache -.DS_Store -Gemfile.lock -*.sublime-project -*.sublime-workspace -codekit-config.json -node_modules -_asset_bundler_cache -images/molecules-raw -.bundle +.jekyll-cache .jekyll-metadata -.markdownlint.json -ruby/ +vendor diff --git a/Gemfile b/Gemfile index 2903fa5c..0d7fbc62 100644 --- a/Gemfile +++ b/Gemfile @@ -1,6 +1,35 @@ -source 'https://rubygems.org' +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 +# If you have any plugins, put them here! +group :jekyll_plugins do + gem "jekyll-feed", "~> 0.12" +end -gem 'jekyll' -gem "jekyll-sitemap" -gem 'octopress', '~> 3.0.0.rc.12' -gem 'github-pages' +# 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", "~> 1.8" diff --git a/README.md b/README.md index 291c0f87..7951b4cc 100644 --- a/README.md +++ b/README.md @@ -8,29 +8,56 @@ web page](http://mmistakes.github.io/minimal-mistakes/theme-setup/). 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/). -### Installation Instructions (updt. Feb. 2016) +### Installation Instructions (updt. Nov. 2023) + +Following the instructions from: https://github.com/BillRaymond/install-jekyll-apple-silicon/blob/main/README.md + +And using homebrew + + +1. Install ruby3.0 -1. Install [RVM](https://rvm.io) (optional, to manage your Ruby installations) -```bash -\curl -sSL https://get.rvm.io | bash -s stable --ruby -rvm install ruby-2.6.3 -rvm --default use ruby-2.6.3 +``` +brew install ruby@3.0 ``` -2. Install Bundler -```bash -gem install bundler +2. Add path to ruby3.0 in .bashrc (or .bash_provile) + +export PATH="/opt/homebrew/opt/ruby@3.0/bin/:$PATH" + +3. Restart your terminal and make sure you are now using ruby3.0 + +``` +ruby -v +``` + +4. Install Jekyll and Bundler + +``` +gem install --user-install bundler jekyll ``` -3. Clone the haddocking.github.io repository and install all dependency Gems with Bundler +5. Add the path to the gems to in .bashrc (or .bash_provile) + +export PATH="~/.local/share/gem/ruby/3.0.0/bin:$PATH" + + +6. Clone the haddocking.github.io repository and install all dependency Gems with 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 ``` -4. Adapt the settings in _config.yml accordingly +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 @@ -52,7 +79,7 @@ To preview changes, which you should always do before committing anything or mak $ python _utilities/create_new_article.py 'A Random Post' ``` -4. For updating jeckyll and bundle +8. For updating jeckyll and bundle ```bash $ gem update jekyll diff --git a/_config.yml b/_config.yml index a59e9d48..ef7ba7c1 100644 --- a/_config.yml +++ b/_config.yml @@ -1,61 +1,55 @@ -# For general help on the options -# # http://jekyllrb.com/docs/configuration/ - -# Site wide configuration - -title: Bonvin Lab -locale: en_US -url: https://www.bonvinlab.org -#url: http://127.0.0.1:4000/ - -# RSS Feed configuration -name: Bonvin Lab -description: Webpage of the computational structural biology lab of Alexandre Bonvin -rss: true - -# Jekyll configuration -permalink: /:categories/:title/ -post_dir: false -markdown: kramdown -sass: - sass_dir: _sass - style: compressed +# 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: Your awesome title +email: your-email@example.com +description: >- # this means to ignore newlines until "baseurl:" + Write an awesome description for your new site here. You can edit this + line in _config.yml. It will appear in your document head meta (for + Google search results) and in your feed.xml site description. +baseurl: "" # the subpath of your site, e.g. /blog +url: "" # the base hostname & protocol for your site, e.g. http://example.com +twitter_username: jekyllrb +github_username: jekyll + +# Build settings +theme: minima plugins: - - jekyll-sitemap - - jekyll-coffeescript - - jekyll-paginate - -kramdown: - auto_ids: true - footnote_nr: 1 - entity_output: as_char - toc_levels: 1..6 - -# Github Specific Settings that *cannot* be changed -# To ensure proper reproducibility -# https://help.github.com/articles/configuring-jekyll/ -gist: - noscript: false -github: [metadata] -highlighter: rouge -incremental: false -lsi: false -safe: true - -# Site owner -owner: - name: Alexandre Bonvin - avatar: bio-haddock.png - bio: "Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level." - email: a.m.j.j.bonvin@uu.nl - youtube: haddocking - google: - analytics: G-RNH61RX63Z - verify: - ad-client: - ad-slot: - github: haddocking - -include: [".htaccess"] -#exclude: [vendor, ruby] -exclude: ["lib", "config.rb", "Capfile", "config", "log", "Rakefile", "Rakefile.rb", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules", "Gemfile", "Gemfile.lock", "LICENSE", "README.md", "_utilities"] + - 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/publications/index.md b/publications/index.md index a6f6bb7d..f065245a 100644 --- a/publications/index.md +++ b/publications/index.md @@ -6,9 +6,11 @@ image: --- ## 2023 +* M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and **A.M.J.J. Bonvin**. [Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking](https://doi.org/10.1101/2023.11.17.567543). _BioRxiv_ 10.1101/2023.11.17.567543 (2023). + * M. Giulini, R.V. Honorato, J.L. Rivera, **A.M.J.J. Bonvin**. [ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information](https://doi.org/10.1101/2023.07.10.548477). _BioRxiv_ 2023.07.10.548477 (2023). -* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1101/2023.06.22.546080). _BioRxiv_ 2023.06.22.546080 (2023). +* X. Xu, **A.M.J.J. Bonvin**. [DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model](https://doi.org/10.1101/2023.06.22.546080). _BioRxiv_ 10.1101/2023.06.22.546080 (2023). * **A.M.J.J. Bonvin**. [Empowering Global Collaboration in Structural Biology and Life Sciences](https://zenodo.org/record/8135315). DOI:10.5281/zenodo.8135315 (2023).