Resolve merge conflict

lina-kim · Jul 22, 2024 · 02e0695 · 02e0695
2 parents 65be714 + a4c00bb
commit 02e0695
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diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
@@ -47,6 +47,7 @@ jobs:
         run: bundle exec jekyll build 
         env:
           JEKYLL_ENV: production
+          PAGES_REPO_NWO: bokulich-lab/nf-ducken
       - name: Upload artifact
         # Automatically uploads an artifact from the './_site' directory by default
         uses: actions/upload-pages-artifact@v3
@@ -55,10 +56,15 @@ jobs:
   deploy:
     environment:
       name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
+      url: ${{ steps.chnage-page-url.outputs.new_page_url }}
     runs-on: ubuntu-latest
     needs: build
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4
+        with:
+          publish_dir: docs/_site
+      - name: Override page_url
+        id: change-page-url
+        run: echo "new_page_url=${{ steps.deployment.outpus.page_url }}docs/" >> $GITHUB_OUTPUT
diff --git a/Gemfile b/Gemfile
@@ -7,12 +7,14 @@ source "https://rubygems.org"
 #
 # This will help ensure the proper Jekyll version is running.
 # Happy Jekylling!
-gem "jekyll", "~> 4.3.3"
+#gem "jekyll", "~> 3.9.5"
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
-gem "minima", "~> 2.5"
+gem "minima", "~> 2.5.1"
 # 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
+gem "github-pages", "~> 231", group: :jekyll_plugins
+gem "jekyll-github-metadata"
+
 # If you have any plugins, put them here!
 group :jekyll_plugins do
   gem "jekyll-feed", "~> 0.12"

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,45 +1,210 @@
 GEM
   remote: https://rubygems.org/
   specs:
+    activesupport (7.1.3.3)
+      base64
+      bigdecimal
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      connection_pool (>= 2.2.5)
+      drb
+      i18n (>= 1.6, < 2)
+      minitest (>= 5.1)
+      mutex_m
+      tzinfo (~> 2.0)
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
+    base64 (0.2.0)
+    bigdecimal (3.1.8)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.12.2)
     colorator (1.1.0)
+    commonmarker (0.23.10)
     concurrent-ruby (1.2.3)
+    connection_pool (2.4.1)
+    dnsruby (1.72.1)
+      simpleidn (~> 0.2.1)
+    drb (2.2.1)
     em-websocket (0.5.3)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
     eventmachine (1.2.7)
+    execjs (2.9.1)
+    faraday (2.9.0)
+      faraday-net_http (>= 2.0, < 3.2)
+    faraday-net_http (3.1.0)
+      net-http
     ffi (1.16.3)
     forwardable-extended (2.6.0)
-    google-protobuf (4.26.1-x86_64-darwin)
-      rake (>= 13)
+    gemoji (4.1.0)
+    github-pages (231)
+      github-pages-health-check (= 1.18.2)
+      jekyll (= 3.9.5)
+      jekyll-avatar (= 0.8.0)
+      jekyll-coffeescript (= 1.2.2)
+      jekyll-commonmark-ghpages (= 0.4.0)
+      jekyll-default-layout (= 0.1.5)
+      jekyll-feed (= 0.17.0)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.16.1)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.13.0)
+      kramdown (= 2.4.0)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.4)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.13.6, < 2.0)
+      rouge (= 3.30.0)
+      terminal-table (~> 1.4)
+    github-pages-health-check (1.18.2)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (>= 4, < 8)
+      public_suffix (>= 3.0, < 6.0)
+      typhoeus (~> 1.3)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
     http_parser.rb (0.8.0)
-    i18n (1.14.4)
+    i18n (1.14.5)
       concurrent-ruby (~> 1.0)
-    jekyll (4.3.3)
+    jekyll (3.9.5)
       addressable (~> 2.4)
       colorator (~> 1.0)
       em-websocket (~> 0.5)
-      i18n (~> 1.0)
-      jekyll-sass-converter (>= 2.0, < 4.0)
+      i18n (>= 0.7, < 2)
+      jekyll-sass-converter (~> 1.0)
       jekyll-watch (~> 2.0)
-      kramdown (~> 2.3, >= 2.3.1)
-      kramdown-parser-gfm (~> 1.0)
+      kramdown (>= 1.17, < 3)
       liquid (~> 4.0)
-      mercenary (>= 0.3.6, < 0.5)
+      mercenary (~> 0.3.3)
       pathutil (~> 0.9)
-      rouge (>= 3.0, < 5.0)
+      rouge (>= 1.7, < 4)
       safe_yaml (~> 1.0)
-      terminal-table (>= 1.8, < 4.0)
-      webrick (~> 1.7)
+    jekyll-avatar (0.8.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.2.2)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.12)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.4.0)
+      commonmarker (~> 0.23.7)
+      jekyll (~> 3.9.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 5.0)
+    jekyll-default-layout (0.1.5)
+      jekyll (>= 3.0, < 5.0)
     jekyll-feed (0.17.0)
       jekyll (>= 3.7, < 5.0)
-    jekyll-sass-converter (3.0.0)
-      sass-embedded (~> 1.54)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.16.1)
+      jekyll (>= 3.4, < 5.0)
+      octokit (>= 4, < 7, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
     jekyll-seo-tag (2.8.0)
       jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
     jekyll-watch (2.2.1)
       listen (~> 3.0)
+    jemoji (0.13.0)
+      gemoji (>= 3, < 5)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
     kramdown (2.4.0)
       rexml
     kramdown-parser-gfm (1.1.0)
@@ -48,38 +213,75 @@ GEM
     listen (3.9.0)
       rb-fsevent (~> 0.10, >= 0.10.3)
       rb-inotify (~> 0.9, >= 0.9.10)
-    mercenary (0.4.0)
+    mercenary (0.3.6)
     minima (2.5.1)
       jekyll (>= 3.5, < 5.0)
       jekyll-feed (~> 0.9)
       jekyll-seo-tag (~> 2.1)
+    minitest (5.23.1)
+    mutex_m (0.2.0)
+    net-http (0.4.1)
+      uri
+    nokogiri (1.16.5-aarch64-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.5-arm-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.5-arm64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.5-x86-linux)
+      racc (~> 1.4)
+    nokogiri (1.16.5-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.5-x86_64-linux)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     public_suffix (5.0.5)
-    rake (13.2.1)
+    racc (1.8.0)
     rb-fsevent (0.11.2)
-    rb-inotify (0.10.1)
+    rb-inotify (0.11.1)
       ffi (~> 1.0)
     rexml (3.2.8)
       strscan (>= 3.0.9)
-    rouge (4.2.1)
+    rouge (3.30.0)
+    rubyzip (2.3.2)
     safe_yaml (1.0.5)
-    sass-embedded (1.75.0-x86_64-darwin)
-      google-protobuf (>= 3.25, < 5.0)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.2)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    simpleidn (0.2.3)
     strscan (3.1.0)
-    terminal-table (3.0.2)
-      unicode-display_width (>= 1.1.1, < 3)
-    unicode-display_width (2.5.0)
-    webrick (1.8.1)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    typhoeus (1.4.1)
+      ethon (>= 0.9.0)
+    tzinfo (2.0.6)
+      concurrent-ruby (~> 1.0)
+    unicode-display_width (1.8.0)
+    uri (0.13.0)
 
 PLATFORMS
+  aarch64-linux
+  arm-linux
+  arm64-darwin
+  x86-linux
   x86_64-darwin
+  x86_64-linux
 
 DEPENDENCIES
+  github-pages (~> 231)
   http_parser.rb (~> 0.6.0)
-  jekyll (~> 4.3.3)
   jekyll-feed (~> 0.12)
-  minima (~> 2.5)
+  jekyll-github-metadata
+  minima (~> 2.5.1)
   tzinfo (>= 1, < 3)
   tzinfo-data
   wdm (~> 0.1.1)

diff --git a/docs/_config.yml b/docs/_config.yml
@@ -2,18 +2,20 @@
 
 title: nf-ducken Documentation
 email: [email protected]
+repository: bokulich-lab/nf-ducken
 description: >- # this means to ignore newlines until "baseurl:" 
  nf-ducken is a scalable platform for microbiome bioinformatics analysis using QIIME 2 and Nextflow.
-baseurl: /docs 
-destination: _site/
-url: https://bokulich-lab.github.io/nf-ducken # the base hostname & protocol for your site, e.g. http://example.com
+baseurl: /nf-ducken/docs/
+url: "https://bokulich-lab.github.io" # the base hostname & protocol for your site, e.g. http://example.com
+destination: docs/_site/
 twitter_username: linathekim
 github_username:  bokulich-lab
 
 # Build settings
 theme: minima
 plugins:
   - jekyll-feed
+  - jekyll-github-metadata
 
 # Exclude from processing.
 # The following items will not be processed, by default.