Merge branch 'main' of https://github.com/hexhowells/training-material …

…into music-update-tools

.devcontainer/README.md

@@ -0,0 +1 @@
+Devcontainer metadata reference: https://containers.dev/implementors/json_reference://containers.dev/implementors/json_reference/

.devcontainer/devcontainer.json

@@ -0,0 +1,28 @@
+{
+"forwardPorts": [4000],
+
+"portsAttributes": {
+  "4000": {
+    "label": "GTN preview",
+    "onAutoForward": "openPreview"
+  }
+},
+
+"onCreateCommand": "rm -rf /workspaces/.codespaces/shared/editors/jetbrains",
+
+"hostRequirements": {
+  "cpus": 4,
+  "memory": "16gb",
+  "storage": "32gb"
+},
+
+"customizations": {
+  "codespaces": {
+    "openFiles": [
+      ".devcontainer/welcome-message.txt"
+    ]
+  }
+}
+
+
+}

.devcontainer/welcome-message.txt

@@ -0,0 +1,11 @@
+👋 Welcome to GTN in CodeSpaces!
+
+🗃️ On the left, you see all the files in the GTN. Tutorials can be found inside
+the topics folder.
+
+🔍 To get a preview of the GTN website, run "make preview" (without the quotes)
+in the terminal (bottom panel of your screen)
+
+📝 For more information about using this environment, see our GTN tutorial:
+https://training.galaxyproject.org/topics/contributing/tutorials/running-codespaces/tutorial.html
+

.github/pull_request_template.md

@@ -1,9 +1,13 @@
---> Please remove all this text before submitting your PR, it's just a checklist to help you :) <--
+TODO: Describe your changes here..
 
-1. Give your pull request a **good title**
-    - e.g. "Fix typo in ansible-galaxy tutorial" or "Add new transcriptomics tutorial covering a new sequencing technology"
-2. Describe your changes in detail, list anything you still need some help with or things that are still TODO
-3. Check that your images are allowed to be re-hosted by the GTN!
-4. Still working on it? Make it a **Draft** pull request
-   - Once it is ready, choose **Ready for Review**
+<!-- Contributor Checklist
+
+1. Give your pull request a descriptive title
+2. Describe your changes in detail at the top of this text box
+3. List anything you still need some help with or things that are still TODO
+4. Check that your images are allowed to be re-hosted by the GTN!
+5. Not ready for review yet? Make it a **Draft** pull request
+   - Once you are done making changes, choose **Ready for Review**
    - Then the automated tests will run and we will know to review and merge it
+
+-->

.github/workflows/ci-main.yml

@@ -17,7 +17,7 @@ on:
       - 'news/**'
       - 'events/**'
       - CONTRIBUTORS.yaml
-      - FUNDERS.yaml
+      - GRANTS.yaml
       - ORGANISATIONS.yaml
 
 
@@ -28,6 +28,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 1
+          persist-credentials: false
 
       - uses: reviewdog/action-setup@v1
         with:
@@ -66,8 +67,8 @@ jobs:
 
       - 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
+          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 -fail-level=any
+          bundle exec ruby bin/lint.rb --format rdjson | reviewdog -filter-mode=file -reporter=github-pr-review -f=rdjsonl -fail-level=any
         env:
             REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: "[CI] Accessibility Linting"
+name: "[CI] GTN Build Testing"
 
 concurrency:
   group: ci-${{ github.head_ref }}
@@ -8,17 +8,6 @@ concurrency:
 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:
@@ -28,6 +17,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 1
+          persist-credentials: false
 
       # BEGIN Dependencies
       - uses: actions/setup-python@v5

.github/workflows/cron-commit-cache.yml

@@ -1,11 +1,14 @@
-name: "[Cron] Update Commit Cache"
+name: "[Cron] Update Commit Cache, PR Data"
 on:
   workflow_dispatch:
   schedule:
     - cron: '45 0 * * 1'
 jobs:
   runner-job:
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     # Only run on main repo on and PRs that match the main repo.
     if: |
       github.repository == 'galaxyproject/training-material' &&
@@ -15,6 +18,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 1000
+          persist-credentials: false
 
       # BEGIN Dependencies
       - uses: ruby/setup-ruby@v1
@@ -54,9 +58,16 @@ jobs:
         run: |
           bundle exec ruby bin/geocode.rb
 
+      - name: Update github metadata dataset
+        id: ghmeta
+        run: |
+          bundle exec ruby bin/collect-gh.rb
+        env:
+          GH_TOKEN: ${{ github.token }}
+
       - name: Create Pull Request
         # If it's not a Pull Request then commit any changes as a new PR.
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v7
         with:
           title: Update Cached Commit Data
           branch-suffix: timestamp

.github/workflows/deploy.yml

@@ -28,6 +28,7 @@ jobs:
           #  3rd Qu.: 94.0
           #  Max.   :282.0
           fetch-depth: 400
+          persist-credentials: false
 
       # BEGIN Dependencies
       - uses: actions/setup-python@v5
@@ -51,11 +52,12 @@ jobs:
             ${{ 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
+          sudo apt-get install -y build-essential libxi-dev libglu1-mesa-dev libglew-dev pkg-config graphviz # for node
           gem install bundler
           bundle config path vendor/bundle
           bundle install --jobs 4 --retry 3
-          npm install
+          rm -f package.json package-lock.json yarn.lock
+          npm install markdown-yaml-metadata-parser lunr
           bundle pristine ffi
       # END Dependencies
 
@@ -68,7 +70,7 @@ jobs:
           make annotate ACTIVATE_ENV=pwd
           curl -L https://docs.google.com/spreadsheets/d/1NfZhi5Jav7kl9zFCkeb7rIC2F8xW1isruv1TeO4WpNI/export\?format\=tsv | ruby bin/prepare_feedback.rb
           curl -L https://hexylena.github.io/toolshed-version-database/tool-meta.json > metadata/tool-meta.json
-          npm install
+          curl -L https://edamontology.org/EDAM.csv > metadata/EDAM.csv
           make rebuild-search-index ACTIVATE_ENV=pwd
           cat metadata/swagger.yaml | python bin/yaml2json.py > api/swagger.json
           rdoc bin _plugins/ --output gtn_rdoc