Move to new way of tagging tools (#214)

* start with moving to new way * fix landingpage * introducing tools with ID * updating data analysis * less sass * update tools * update instance_of * some fixes * doc update * latest version of plugin * fix tool * latest version tools * move belgium to new way * Update _config.yml * update checklist url * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * Update contribute/tool-resource-update.md Co-authored-by: rafael buono <[email protected]> * implement suggestions --------- Co-authored-by: rafael buono <[email protected]>
elixir-europe · Aug 24, 2023 · 6bbbff9 · 6bbbff9
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diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -1,10 +1,10 @@
-
 name: Jekyll site CI
 
 on:
+  push:
   pull_request:
-    branches: [ main, master ]
-
+    branches: [ master, main ]
+  workflow_dispatch:
 
 permissions:
   contents: read
@@ -14,15 +14,14 @@ permissions:
 jobs:
   build:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout
         uses: actions/checkout@v3
         with:
           ref: ${{ github.event.inputs.branch }}
 
       - name: Setup Ruby
-        uses: ruby/setup-ruby@v1.127.0
+        uses: ruby/setup-ruby@v1
         with:
           ruby-version: '3.1'
           bundler-cache: true
@@ -53,8 +52,33 @@ jobs:
           bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
         env:
           PAGES_REPO_NWO: ${{ github.repository }}
+          JEKYLL_BUILD_BRANCH: ${{ github.ref_name }}
           JEKYLL_ENV: ${{ steps.name.outputs.jekyll_env }}
           JEKYLL_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JEKYLL_BASE_PATH: ${{ steps.pages.outputs.base_path }}
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v1
+
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: build
+
+    if: |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'push' && github.event.repository.default_branch == github.ref_name)
+
+    concurrency:
+      group: "pages"
+      cancel-in-progress: true
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v1
+
diff --git a/.github/workflows/tool_list_conversion.yml b/.github/workflows/tool_list_conversion.yml
@@ -1,11 +1,11 @@
 name: Validation of the tools and page metadata
-
 on:
   pull_request:
     branches: [ master, main ]
   schedule:
     - cron:  '0 13 * * 1'
   workflow_dispatch:
+
 jobs:
   validation:
     runs-on: ubuntu-latest
@@ -22,38 +22,47 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pyyaml requests python-frontmatter
+          pip install ruamel.yaml requests python-frontmatter
       - name: Run tool table 2 yaml
         run: | 
-          python var/conversions.py
+          python var/tools_validator.py
   
   registry-lookup:
     if: |
         github.repository_owner == 'elixir-europe' &&  github.event_name != 'pull_request'
   
     runs-on: ubuntu-latest
+
     strategy:
       matrix:
         python-version: [3.8]
+
     steps:
       - name: Checkout
         uses: actions/checkout@v3
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pyyaml requests python-frontmatter
-      - name: Run tool table 2 yaml
+          pip install ruamel.yaml requests python-frontmatter
+
+      - name: Run regsitry lookup for the tools file
         run: | 
-          python var/conversions.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
+          python var/tools_validator.py --reg --username ${{ secrets.FAIRSHARING_USERNAME }} --password "${{ secrets.FAIRSHARING_PASSWORD }}"
+
       - name: Fetch country names with corresponding iso
         run: |
           python var/country_list.py
+
       - name: Show differences
-        run: 'git diff --stat'
+        run: |
+          git diff --stat
+
       - name: Create Pull Request
         id: cpr
         uses: peter-evans/create-pull-request@v3
@@ -68,8 +77,6 @@ jobs:
           labels: |
             automatic PR
           reviewers: bedroesb
-          team-reviewers: |
-            maintainers
           branch: list_updates
           base: main
 

diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 _site/
 Gemfile.lock
+.jekyll-cache
 .jekyll-metadata
 .vscode/launch.json
diff --git a/Gemfile b/Gemfile
@@ -1,7 +1,17 @@
 source "https://rubygems.org"
 
-# GitHub pages dependencies
-gem 'github-pages', group: :jekyll_plugins
+gem "elixir-toolkit-theme-plugins", "~> 0.1.9"
+gem "webrick", "~> 1.7"
+gem "jekyll", "~> 4.3.1"
+gem "jemoji", "~> 0.13.0"
+gem "kramdown-parser-gfm", "~> 1.1"
+
+group :jekyll_plugins do
+  gem "jekyll-redirect-from", "~> 0.16.0"
+  gem "jekyll-sitemap", "~> 1.4"
+  gem "jekyll-github-metadata", "~> 2.15"
+  gem "jekyll-relative-links", "~> 0.6"
+  gem "jekyll-seo-tag", "~> 2.8"
+  gem "jekyll-remote-theme"
+end
 
-# Webrick needed for Ruby v3.0+ compatibility
-gem "webrick"
diff --git a/_config.yml b/_config.yml
@@ -4,7 +4,7 @@ title: Infectious Diseases Toolkit
 description: "Find tools and guidelines to help you access, analyse and share infectious disease data, and respond quickly to disease outbreaks."
 # Metadata description of the website
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@1.26.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@2.2.0
 
 gtag: G-TNT17YGXQ4
 
@@ -113,6 +113,8 @@ defaults:
       search_exclude: true
       no_robots: true
 plugins:
+  - elixir-toolkit-theme-plugins
   - jemoji
+  - jekyll-redirect-from
   - jekyll-sitemap
   - jekyll-github-metadata