Merge branch 'main' into analyze-unaligned-ncrna2

.dockerignore

@@ -1,4 +1,5 @@
 .git
+.cache
 .DS_Store
 .bundle
 _site
@@ -9,4 +10,5 @@ assets
 layouts
 staging
 templates
-vendor
+vendor
+videos

.dockstore.yml

@@ -0,0 +1,23 @@
+# Register workflows for Dockstore (https://dockstore.org/)
+version: 1.2
+workflows:
+  - name: intro-short
+    subclass: GALAXY
+    publish: true
+    primaryDescriptorPath: topics/introduction/tutorials/galaxy-intro-short/workflows/Galaxy-Workflow-galaxy-intro-short.ga
+  - name: intro-everyone
+    subclass: GALAXY
+    publish: true
+    primaryDescriptorPath: topics/introduction/tutorials/galaxy-intro-101-everyone/workflows/main_workflow.ga
+  - name: de-novo
+    subclass: GALAXY
+    publish: true
+    primaryDescriptorPath: topics/transcriptomics/tutorials/full-de-novo/workflows/main_workflow.ga
+  - name: dip
+    subclass: GALAXY
+    publish: true
+    primaryDescriptorPath: topics/variant-analysis/tutorials/dip/workflows/diploid.ga
+  - name: genome-annotation
+    subclass: GALAXY
+    publish: true
+    primaryDescriptorPath: topics/genome-annotation/tutorials/annotation-with-prokka/workflows/Galaxy-Workflow-Workflow_constructed_from_history__prokka-workflow_.ga

.github/labeler.yml

@@ -1,27 +1,67 @@
-topic:admin: topics/admin/**/*
-topic:assembly: topics/assembly/**/*
-topic:computational-chemistry: topics/computational-chemistry/**/*
-topic:contributing: topics/contributing/**/*
-topic:dev: topics/dev/**/*
-topic:ecology: topics/ecology/**/*
-topic:epigenetics: topics/epigenetics/**/*
-topic:galaxy-data-manipulation: topics/galaxy-data-manipulation/**/*
-topic:galaxy-ui: topics/galaxy-ui/**/*
-topic:genome-annotation: topics/genome-annotation/**/*
-topic:imaging: topics/imaging/**/*
-topic:instructors: topics/instructors/**/*
-topic:introduction: topics/introduction/**/*
-topic:metabolomics: topics/metabolomics/**/*
-topic:metagenomics: topics/metagenomics/**/*
-topic:proteomics: topics/proteomics/**/*
-topic:sequence-analysis: topics/sequence-analysis/**/*
-topic:statistics: topics/statistics/**/*
-topic:transcriptomics: topics/transcriptomics/**/*
-topic:variant-analysis: topics/variant-analysis/**/*
+faqs:
+  - faqs/**/*
+news:
+  - news/**/*
+
+# if any files touched outside of topics, faqs and news, label as template-and-tools
 template-and-tools:
-  - bin/**/*
-  - _includes/**/*
-  - _layouts/**/*
-  - _plugins/**/*
-  - assets/**/*
-  - ./*
+  - any: ['!topics/**/*', '!faqs/**/*', '!news/**/*']
+
+
+# topic labels
+admin:
+ - topics/admin/**/*
+ai4life:
+ - topics/ai4life/**/*
+assembly:
+  - topics/assembly/**/*
+climate:
+  - topics/climate/**/*
+computational-chemistry:
+  - topics/computational-chemistry/**/*
+contributing:
+  - topics/contributing/**/*
+data-science:
+  - topics/data-science/**/*
+dev:
+  - topics/dev/**/*
+ecology:
+  - topics/ecology/**/*
+epigenetics:
+  - topics/epigenetics/**/*
+evolution:
+  - topics/evolution/**/*
+fair:
+  - topics/fair/**/*
+galaxy-interface:
+  - topics/galaxy-interface/**/*
+genome-annotation:
+  - topics/genome-annotation/**/*
+imaging:
+  - topics/imaging/**/*
+instructors:
+  - topics/instructors/**/*
+introduction:
+  - topics/introduction/**/*
+metabolomics:
+  - topics/metabolomics/**/*
+metagenomics:
+  - topics/metagenomics/**/*
+proteomics:
+  - topics/proteomics/**/*
+sequence-analysis:
+  - topics/sequence-analysis/**/*
+single-cell:
+  - topics/single-cell/**/*
+statistics:
+  - topics/statistics/**/*
+synthetic-biolocy:
+  - topics/synthetic-biology/**/*
+teaching:
+  - topics/teaching/**/*
+transcriptomics:
+  - topics/transcriptomics/**/*
+variant-analysis:
+  - topics/variant-analysis/**/*
+visualisation:
+  - topics/visualisation/**/*

.github/pull_request_template.md

@@ -0,0 +1,24 @@
+# Thank you for contributing to the GTN! :yellow_heart:
+
+## Please check that:
+
+- [ ] Your pull request has a **good title**, e.g.
+    - "Fix typo in ansible-galaxy tutorial"
+    - "Add new transcriptomics tutorial covering a new sequencing technology"
+- [ ] Please **replace this entire pull request message** with a *description of your changes*, it will help us review your pull request faster
+- [ ] Check that your images are allowed to be re-hosted by the GTN
+
+Once these are done, you're ready to go!
+
+<details>
+    <summary>Consider sustainable computing with Draft Mode :green_heart:</summary>
+
+Is your pull request finished? 100% ready to be merged? Or do you want some time to work on it first (which we encourage! It's great to have visibility)
+
+If not, then please consider creating this pull request as a draft.
+
+Regular pull requests will trigger automated test runs when they are created
+and every time you update them.
+
+As a small contribution to sustainable computing, we skip the most energy intensive of these tests for pull requests marked as drafts. Once your pull request is ready to go, then you can click a button saying "Ready for Review" and the tests will be run!
+</details>

.github/workflows/ci-main.yml

@@ -0,0 +1,73 @@
+name: "[CI] GTN Tutorial Linting"
+
+concurrency:
+  group: ci-tutsli-${{ github.head_ref }}
+  cancel-in-progress: true
+
+on:
+  pull_request:
+    paths:
+      - 'Gemfile.lock'
+      - 'topics/**'
+      - '**/tutorial*.md'
+      - '**/slides.html'
+      - '**/slides/*.html'
+      - 'learning-pathways/*'
+      - 'faqs/**'
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      - uses: reviewdog/action-setup@v1
+        with:
+          reviewdog_version: latest
+
+      # BEGIN Dependencies
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+          architecture: 'x64'
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+      - uses: actions/cache@v2
+        with:
+          path: |
+            vendor/bundle
+          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}-
+          restore-keys: |
+            ${{ runner.os }}-gems-
+      - name: Install dependencies
+        run: |
+          gem install bundler rubocop
+          bundle config path vendor/bundle
+          bundle install --jobs 4 --retry 3
+          pip install pyyaml
+          bundle pristine ffi
+      # END Dependencies
+
+      - name: Check Frontmatter
+        run: |
+          make check-diffs ACTIVATE_ENV=pwd
+          make check-frontmatter ACTIVATE_ENV=pwd
+          make check-contributors ACTIVATE_ENV=pwd
+          python bin/mergeyaml.py --nondocker > /dev/null
+
+      - name: Check Tutorial Formatting
+        run: |
+          find topics/ -name tutorial.md | xargs -n 1 python bin/check-broken-boxes.py | reviewdog -efm="%f:%l: %m" -filter-mode=file -reporter=github-pr-review
+          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-on-error
+        env:
+            REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: rubocop
+        uses: reviewdog/action-rubocop@v2
+        with:
+          rubocop_version: gemfile
+          reporter: github-pr-review
+          fail_on_error: true

.github/workflows/ci.yml

@@ -0,0 +1,99 @@
+name: "[CI] Accessibility Linting"
+
+concurrency:
+  group: ci-${{ github.head_ref }}
+  cancel-in-progress: true
+
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#example-using-a-list-of-events
+on:
+  pull_request:
+    types: [opened, reopened, synchronize, ready_for_review]
+    paths:
+      - 'Gemfile.lock'
+      - '**/*.md'
+      - '**/*.html'
+      - '*.yml'
+      - '*.yaml'
+      - 'metadata/*'
+      - 'topics/*/images/*'
+      - '_plugins/*'
+      - '_plugins_dev/*'
+      - '**/*.bib'
+
+jobs:
+  build-site:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || !github.event.pull_request.draft
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 1
+
+      # BEGIN Dependencies
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
+          architecture: 'x64'
+      - uses: ruby/setup-ruby@v1
+        with:
+          ruby-version: "3.0"
+      - uses: actions/setup-node@v2
+        with:
+          node-version: '19'
+      - uses: actions/cache@v2
+        with:
+          path: |
+            vendor/bundle
+            ~/.npm
+          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}-node-${{ hashFiles('**/package-lock.json') }}
+          restore-keys: |
+            ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}-node-
+            ${{ runner.os }}-gems-
+      - name: Install dependencies
+        run: |
+          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config # for node
+          gem install bundler
+          bundle config path vendor/bundle
+          bundle install --jobs 4 --retry 3
+          npm install
+          bundle pristine ffi
+      # END Dependencies
+
+      - name: Build the site
+        run: bundle exec jekyll build --strict_front_matter -d _site/training-material --trace
+
+      - name: Validate all links, enforce alt text
+        run: |
+          bundle exec htmlproofer \
+            --ignore-urls "/.*localhost.*/","/.*vimeo\.com.*/","/.*gitter\.im.*/","/.*drmaa\.org.*/","/.*slides.html#.*/,/#embedded_jbrowse/","/.*videos.*.mp4.png/","/krona_(all|multisample).html/" \
+            --ignore-files "/.*krona.*\.html/","/.*\/files\/.*/","/.*\/node_modules\/.*/","/\/tutorials\/.*\/docker\//","/.*content.html/" \
+            --swap-urls "github.com/galaxyproject/training-material/tree/main:github.com/${GITHUB_REPOSITORY}/tree/${GITHUB_HEAD_REF}" \
+            --disable-external=true \
+            --enforce-https=false \
+            ./_site
+
+      - name: Ensure no unexpected encoded HTML in output
+        run: |
+          ! fgrep -R 'lt;blockquote' _site
+
+      - name: Run aXe accessibility testing on some representative URLs
+        run: |
+          node_modules/.bin/http-server _site/ &
+          # We can focus AND scroll these regions. I thus disable their violation warning.
+          # Twitter isn't our fault. Sorry.
+          node_modules/.bin/axe --disable scrollable-region-focusable --exclude '#twitter-widget-0' --chromedriver-path /usr/bin/chromedriver \
+            http://localhost:8080/training-material/ \
+            http://localhost:8080/training-material/hall-of-fame/ \
+            http://localhost:8080/training-material/hall-of-fame/hexylena/ \
+            http://localhost:8080/training-material/topics/introduction/ \
+            http://localhost:8080/training-material/topics/statistics/ \
+            http://localhost:8080/training-material/topics/genome-annotation/ \
+            http://localhost:8080/training-material/topics/admin/ \
+            http://localhost:8080/training-material/topics/dev/ \
+            http://localhost:8080/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html \
+            http://localhost:8080/training-material/topics/introduction/tutorials/galaxy-intro-short/workflows/ \
+            http://localhost:8080/training-material/topics/admin/tutorials/ansible-galaxy/tutorial.html
+
+      - name: Validate notebooks (If this fails, ask @hexylena to look at your notebook)
+        run: |
+          find _site | grep ipynb | xargs bundle exec ruby bin/check-valid-notebook.rb