Add Elixir toolkit theme to CoDex

.github/workflows/deploy_jekyll.yml

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+name: Deploy Jekyll site to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: [ "main" ]
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Setup Ruby
+        uses: ruby/[email protected]
+        with:
+          ruby-version: '3.3'
+          bundler-cache: true
+          cache-version: 0
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Install dependencies
+        run: |
+          bundle install
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: |
+          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
+        env:
+          PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_ENV: production
+          JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
+      - name: Upload artifact
+        # Automatically uploads an artifact from the './_site' directory by default
+        uses: actions/upload-pages-artifact@v2
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.github/workflows/lint_jekyll.yaml

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+name: Lint Jekyll site
+
+on: [push, pull_request]
+
+jobs:
+  check-internal-links:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: docs
+    steps:
+      - uses: actions/checkout@v3
+      - uses: ruby/[email protected]
+        with:
+          ruby-version: '3.3'
+          bundler-cache: true
+          cache-version: 0
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Install dependencies
+        run: |
+          bundle install
+      - name: Build with Jekyll
+        # Outputs to the './_site' directory by default
+        run: |
+          bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}" --strict_front_matter 
+        env:
+          PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_ENV: production
+          JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
+      #- name: Validate HTML and check links
+      #  run: |
+      #    bundle exec htmlproofer \
+      #      --allow_missing_href=true \
+      #      --ignore-urls "/.*localhost.*/","/.*gitter\.im.*/" \
+      #      --enforce-https=false  \
+      #      --disable-external=true \
+      #      --ignore_empty_alt=true \
+      #      --ignore_missing_alt=true \
+      #      --check-internal-hash=false \
+      #      ./_site

.gitignore

@@ -1,4 +1,5 @@
 .DS_Store
 __pycache__
 results/test*
-results/*/test*
+results/*/test*
+docs/_site

docs/Gemfile

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+source "https://rubygems.org"
+
+# GitHub pages dependencies
+gem 'github-pages', group: :jekyll_plugins
+
+# Webrick needed for Ruby v3.0+ compatibility
+gem "webrick"
+gem "html-proofer"

docs/_config.yml

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+title: Galaxy CoDex
+# This appears in the html browser tab for the site title (seen mostly by search engines, not users)
+
+topnav_title: CoDex
+# Optional: this appears on the top navigation bar next to the main_logo.svg icon
+
+description: "Galaxy Communities Dock (Galaxy Codex) is a catalog of Galaxy resources (i.e. tools, training, workflows) that can be filtered for any community."
+# Metadata description of the website
+
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
+
+theme_variables:
+  # biocommons blue
+  theme_color: 205a86
+  datatables: 
+    searchbuilder: True
+  topnav:
+    brand_logo: assets/img/galaxy_project_logo_square.png
+
+exclude:
+  - README.md
+  - CODE_OF_CONDUCT.md
+  - publications/*
+  - vendor
+
+defaults:
+  -
+    scope:
+      path: "pages"
+      type: "pages"
+    values:
+      permalink: /:basename
+      layout: "page"
+      sidebar: main
+  -
+    scope:
+      path: "index.md"
+      type: "pages"
+    values:
+      permalink: /:basename
+      layout: "page"
+      sidebar: main
+
+plugins:
+  - jemoji
+  - jekyll-sitemap
+  - jekyll-github-metadata
+  - webrick
+  - elixir-toolkit-theme-plugins

docs/_data/CONTRIBUTORS.yml

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+
+############################
+### List of contributors ###
+############################
+
+### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+
+#############################################################################################################################################
+### add maintainers/contributors below and use their name in the contributors metadata section on each page they have contributed towards ###
+#############################################################################################################################################
+
+# an example contributor is included below
+# example roles include "lead", "first-author", "author", "editor", "workflow-tester"
+
+Johan Gustafsson:
+    git: supernord
+    orcid: 0000-0002-2977-5032
+    affiliation: Australian BioCommons / University of Melbourne

docs/_data/affiliations.yml

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+############################
+### List of affiliations ###
+############################
+
+### see https://github.com/ELIXIR-Belgium/elixir-toolkit-theme
+
+#########################################################################################################
+### add affiliations below and use the name(s) in the relevant metadata sections or code on each page ###
+#########################################################################################################
+
+### add new affiliations below as needed
+
+#- name: Australian BioCommons
+#  image_url: /assets/img/biocommons_logo.png
+#  expose: true
+#  type: infrastructure
+#  url: https://www.biocommons.org.au/

docs/_data/footer.yml

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+# see https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/main/_data/footer.yml
+#copyright: ''
+#extra_line: Add other relevant information here!
+#columns:
+#  - type: links
+#    width: 3

docs/_data/sidebars/main.yml

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+subitems:
+  - title: About
+    url: /about
+  - title: Publications and online information
+    url: /project
+  - title: How-to contribute
+    url: /contributing
+

docs/_data/tool_and_resource_list.yml

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+- name: How to improve the annotation of Galaxy resources?
+  type: Hub post
+  description: Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources.
+  url: https://galaxyproject.org/news/2024-04-microgalaxy-hackathon/
+- name: GCC 2024 Training
+  type: Hub post
+  description: Collecting, Organizing, and Broadcasting Galaxy Tools for a Dedicated Scientific Community (using the Galaxy Tool Metadata Extractor Workflow).
+  url: https://galaxyproject.org/events/gcc2024/training/tool-finding/
+- name: Project 25 - ELIXIR BioHackathon in Barcelona
+  type: Hub post
+  description: Project 25 - Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities.
+  url: https://galaxyproject.org/news/2023-11-06-biohackathon/#project-25-increasing-the-findability-visibility-and-impact-of-galaxy-tools-for-specialised-scientific-communities
+- name: Project 25 GitHub - BioHackathon Europe projects 2023
+  type: Repository
+  description: Project 25 - Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities.
+  url: https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/25
+- name: microGalaxy SIG - microbial data analysis resources in Galaxy
+  type: Project using CoDex
+  description: Microbiology research involving microbiomes, meta*omics, and targeted microbial data analysis requires advanced programming skills, specialized tools, and significant computing power. Autonomous handling of these tasks can impede researchers’ progress. The microGalaxy Scientific Interest Group (SIG) is here to help! The microGalaxy SIG maintains the Galaxy Community Hub page and a dedicated microbial Galaxy subdomain - <https://microgalaxy.usegalaxy.eu>.
+  url: https://doi.org/10.7490/f1000research.1119768.1
+- name: ELIXIR Research Software Ecosystem (RSEc)
+  type: Project using CoDex
+  description: The ELIXIR Research Software Ecosystem (RSEc) is a project that centralizes and curates high-quality metadata for computational biology software tools, providing a unified resource for researchers.
+  url: https://research-software-ecosystem.github.io
+- name: microGalaxy Technical Paper 2024 Preparation
+  type: Paper
+  description: This repository includes all the scripts written to produce figures in the paper along with the resulting figures.
+  url: https://github.com/usegalaxy-eu/microgalaxy_technical_paper_2024
+- name: Creation of an interactive Galaxy tools table for your community.
+  type: GTN tutorial
+  description: Create a community reviewed table for Galaxy tools within a specific scientific domain, and embed an interactive table in a community page.
+  url: https://gxy.io/GTN:T00426
+- name: Adding and updating best practice metadata for Galaxy tools using the bio.tools registry
+  type: GTN tutorial
+  description: Identify Galaxy tools without a bio.tools entry, create a bio.tools entry, update a bio.tools entry, add EDAM ontology terms to a bio.tools entry, and link a Galaxy tool to its corresponding bio.tools entry.
+  url: https://gxy.io/GTN:T00421