chore: use yamlfmt for all yaml files (but not helm templates) (#2130)

### Summary - Add yamlfmt config to root - Recommend yamlfmt vscode extension This formatter with current config doesn't wrap long lines, which saves us a lot of lines. Install formatter with homebrew or: ``` go install github.com/google/yamlfmt/cmd/yamlfmt@latest ``` Blog writeup on the formatter: https://til.simonwillison.net/yaml/yamlfmt Alternative to #2124
loculus-project · Jun 17, 2024 · f7401b2 · f7401b2
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -40,9 +40,9 @@ updates:
       interval: monthly
     groups:
       minorAndPatch:
-          update-types:
-            - "minor"
-            - "patch"
+        update-types:
+          - "minor"
+          - "patch"
   - package-ecosystem: docker
     directories:
       - website
@@ -58,6 +58,6 @@ updates:
       interval: weekly
     groups:
       minorAndPatch:
-          update-types:
-            - "minor"
-            - "patch"
+        update-types:
+          - "minor"
+          - "patch"
diff --git a/.github/workflows/actions-usage.yml b/.github/workflows/actions-usage.yml
@@ -1,10 +1,8 @@
 name: Github Actions Usage Stats
-
 on:
   workflow_dispatch:
   schedule:
     - cron: "0 3 * * *" # Runs at 03:00 AM (UTC) every day
-
 jobs:
   gha-usage-minutes-report:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/backend-image.yml b/.github/workflows/backend-image.yml
@@ -1,5 +1,4 @@
 name: backend-image
-
 on:
   pull_request:
   push:
@@ -19,17 +18,14 @@ on:
         description: "Build for ARM as well"
         default: "false"
         required: true
-
 env:
   DOCKER_IMAGE_NAME: ghcr.io/loculus-project/backend
   BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
   BUILD_ARM: ${{ github.event.inputs.build_arm || inputs.build_arm || github.ref == 'refs/heads/main' }}
   sha: ${{ github.event.pull_request.head.sha || github.sha }}
-
 concurrency:
   group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-backend
   cancel-in-progress: true
-
 jobs:
   backend-image:
     name: Build Backend Docker Image # Don't change: Referenced by .github/workflows/update-argocd-metadata.yml
@@ -45,13 +41,11 @@ jobs:
       - name: Shorten sha
         run: echo "sha=${sha::7}" >> $GITHUB_ENV
       - uses: actions/checkout@v4
-
       - name: Generate files hash
         id: files-hash
         run: |
           DIR_HASH=$(echo -n ${{ hashFiles('backend/**', '.github/workflows/backend-image.yml') }})
           echo "DIR_HASH=$DIR_HASH${{ env.BUILD_ARM == 'true' && '-arm' || '' }}" >> $GITHUB_ENV
-
       - name: Setup Docker metadata
         id: dockerMetadata
         uses: docker/metadata-action@v5
@@ -69,32 +63,26 @@ jobs:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
-
       - name: Check if image exists
         id: check-image
         run: |
           EXISTS=$(docker manifest inspect ${{ env.DOCKER_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false")
           echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV
-
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
-
       - name: Set up JDK
         if: env.CACHE_HIT == 'false'
         uses: actions/setup-java@v4
         with:
           java-version: "21"
           distribution: "adopt"
-
       - name: Setup Gradle
         if: env.CACHE_HIT == 'false'
         uses: gradle/actions/setup-gradle@v3
-
       - name: Build Backend
         if: env.CACHE_HIT == 'false'
         working-directory: ./backend
         run: ./gradlew bootJar
-
       - name: Build and push image if input files changed
         if: env.CACHE_HIT == 'false'
         uses: docker/build-push-action@v5
@@ -105,7 +93,6 @@ jobs:
           cache-from: type=gha,scope=backend-${{ github.ref }}
           cache-to: type=gha,mode=max,scope=backend-${{ github.ref }}
           platforms: ${{ env.BUILD_ARM == 'true' && 'linux/amd64,linux/arm64' || 'linux/amd64' }}
-
       - name: Retag and push existing image if cache hit
         if: env.CACHE_HIT == 'true'
         run: |

diff --git a/.github/workflows/backend-tests.yml b/.github/workflows/backend-tests.yml
@@ -1,5 +1,4 @@
 name: backend-tests
-
 on:
   pull_request:
     paths:
@@ -9,11 +8,9 @@ on:
     branches:
       - main
   workflow_dispatch:
-
 concurrency:
   group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-backend-tests
   cancel-in-progress: true
-
 jobs:
   Tests:
     runs-on: codebuild-loculus-ci-${{ github.run_id }}-${{ github.run_attempt }}

diff --git a/.github/workflows/build-arm-images.yaml b/.github/workflows/build-arm-images.yaml
@@ -2,43 +2,35 @@
 
 on:
   workflow_dispatch:
-
 permissions:
   contents: read
   packages: write
   checks: read
-
 jobs:
   trigger-backend:
     uses: ./.github/workflows/backend-image.yml
     with:
       build_arm: true
-
   trigger-config-preprocessor:
     uses: ./.github/workflows/config-preprocessor-image.yml
     with:
       build_arm: true
-
   trigger-dummy-preprocessing:
     uses: ./.github/workflows/preprocessing-dummy-image.yml
     with:
       build_arm: true
-
   trigger-ingest:
     uses: ./.github/workflows/ingest-image.yml
     with:
       build_arm: true
-
   trigger-keycloakify:
     uses: ./.github/workflows/keycloakify-image.yml
     with:
       build_arm: true
-
   trigger-preprocessing-nextclade:
     uses: ./.github/workflows/preprocessing-nextclade-image.yml
     with:
       build_arm: true
-
   trigger-website:
     uses: ./.github/workflows/website-image.yml
     with:

diff --git a/.github/workflows/clean-cache-post-merge.yml b/.github/workflows/clean-cache-post-merge.yml
@@ -11,7 +11,6 @@ on:
         description: "Branch name"
         required: false
         default: ""
-
 jobs:
   cleanup:
     runs-on: ubuntu-latest
@@ -29,7 +28,6 @@ jobs:
           else
             echo "branch=${{ github.ref_name }}" >> $GITHUB_OUTPUT
           fi
-
       - name: Cleanup
         run: |
           gh extension install actions/gh-actions-cache

diff --git a/.github/workflows/config-preprocessor-image.yml b/.github/workflows/config-preprocessor-image.yml
@@ -1,5 +1,4 @@
 name: config-processor-image
-
 on:
   pull_request:
   push:
@@ -19,21 +18,17 @@ on:
         description: "Build for ARM as well"
         default: "false"
         required: true
-
 env:
   DOCKER_IMAGE_NAME: ghcr.io/loculus-project/config-processor
   BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
   BUILD_ARM: ${{ github.event.inputs.build_arm || inputs.build_arm || github.ref == 'refs/heads/main' }}
   sha: ${{ github.event.pull_request.head.sha || github.sha }}
-
 defaults:
   run:
     working-directory: ./kubernetes/config-processor
-
 concurrency:
   group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-config-processor-${{github.event.inputs.build_arm}}
   cancel-in-progress: true
-
 jobs:
   config-processor-image:
     name: Build config-processor Docker Image # Don't change: Referenced by .github/workflows/update-argocd-metadata.yml

diff --git a/.github/workflows/dependabot-validate.yml b/.github/workflows/dependabot-validate.yml
@@ -1,5 +1,4 @@
 name: dependabot validate
-
 on:
   pull_request:
     paths:

diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml
@@ -1,38 +1,30 @@
 name: Builds and deploy documentation
-
 on:
   workflow_dispatch:
   push:
     branches:
       - main
-
 jobs:
   build-and-deploy:
     permissions:
       contents: write
     runs-on: ubuntu-latest
     timeout-minutes: 15
-
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4
-
       - name: Set up Node.js
         uses: actions/setup-node@v4
         with:
           node-version-file: ./docs/.nvmrc
-
       - name: Navigate to docs directory
         run: cd docs
-
       - name: Install Dependencies
         run: npm install
         working-directory: ./docs
-
       - name: Build Project
         run: npm run build
         working-directory: ./docs
-
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v4
         with:

diff --git a/.github/workflows/docs-test.yml b/.github/workflows/docs-test.yml
@@ -1,5 +1,4 @@
 name: Docs Build Check
-
 on:
   pull_request:
     paths:
@@ -8,31 +7,24 @@ on:
   push:
     branches:
       - main
-
   workflow_dispatch:
-
 concurrency:
   group: ci-${{ github.ref == 'refs/heads/main' && github.run_id || github.ref }}-docs-build
   cancel-in-progress: true
-
 jobs:
   check-docs-build:
     runs-on: ubuntu-latest
     timeout-minutes: 15
-
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4
-
       - name: Set up Node.js
         uses: actions/setup-node@v4
         with:
           node-version-file: ./docs/.nvmrc
-
       - name: Install Dependencies
         run: npm install
         working-directory: ./docs
-
       - name: Check Build
         run: npm run build
         working-directory: ./docs