Merge branch 'main' into add_accordion_pipelineps

Author: mashehu

.cache.tar.xz

@@ -0,0 +1 @@
+src/content @nf-core/docs

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+{
+    $schema: "https://docs.renovatebot.com/renovate-schema.json",
+    extends: ["github>nf-core/ops//.github/renovate/default.json5", "config:recommended", "schedule:monthly"]
+}

.github/renovate.json5

@@ -0,0 +1 @@
+Astro

.github/styles/config/vocabularies/Docs/accept.txt

@@ -0,0 +1,85 @@
+name: Open PR with tools API docs based on webhook call
+on:
+  workflow_dispatch:
+    inputs:
+      ref_name:
+        description: 'The name of the release branch'
+        required: true
+        default: 'dev'
+
+jobs:
+  api-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Checkout tools code
+        uses: actions/checkout@v4
+        with:
+          repository: 'nf-core/tools'
+          ref: ${{ inputs.ref_name }}
+          path: 'tools'
+
+      - name: setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: '20'
+
+      - name: Install dependencies
+        run: |
+          npm install remark unist-util-visit
+
+      # Install pre-commit
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
+
+      # install prettier plugins
+      - run: npm install --only=dev
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: install nf-core
+        run: |
+          cd tools
+          pip install --upgrade -r requirements-dev.txt -e .
+
+      - name: run API generation script
+        run: |
+          cd tools
+          bash docs/api/generate-api-docs.sh --release ${{ inputs.ref_name }}
+
+      - name: remove tools code
+        run: rm -rf tools
+
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
+
+      - name: Commit & push changes
+        id: commit-and-push
+        run: |
+          git config user.email "[email protected]"
+          git config user.name "nf-core-bot"
+          # restore package.json changes
+          git restore package.json
+          git restore package-lock.json
+          git add .
+          git status
+          git commit -m "[automated] Update nf-core/tools API docs for ${{ inputs.ref_name }}"
+
+      - name: Create PR
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update nf-core/tools API docs for ${{inputs.ref_name}}
+          title: Update nf-core/tools API docs for ${{inputs.ref_name}}
+          body: |
+            This PR updates the nf-core/tools API docs for ${{inputs.ref_name}}.
+            Please review the changes and merge if they look good.
+          branch: 'update-api-docs-${{inputs.ref_name}}'
+          delete-branch: true
+          base: 'main'
+          draft: false

.github/workflows/add-tools-api-docs.yml

@@ -1,9 +1,11 @@
 name: build json files and md-cache
 
 on:
-  schedule: # every day at 7am
-    - cron: '0 7 * * *'
+  schedule: # every day at 2am and 2pm
+    - cron: '0 2,14 * * *'
   workflow_dispatch:
+  repository_dispatch:
+    types: [update-website]
 
 jobs:
   build-component-json:
@@ -16,14 +18,14 @@ jobs:
         id: date
         run: echo "::set-output name=date::$(date +'%Y-%m-%d')"
       # Set up the main website repo
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           fetch-depth: 0 # Don't do a shallow clone
           token: ${{secrets.NF_CORE_BOT_AUTH_TOKEN}} # Needed for pushing back to the repo
 
       # install npm dependencies
       - name: Set up node.js
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
         with:
           node-version: 20
           cache: 'npm'
@@ -88,7 +90,7 @@ jobs:
       # Create a PR if there are too many lines changed
       - name: Create PR with changes
         if: ${{ steps.check_lines.outputs.changes }}
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@153407881ec5c347639a548ade7d8ad1d6740e38 # v5
         with:
           token: ${{ secrets.CREATE_PR_TOKEN }}
           commit-message: 'chore: update pipeline.json and component.json'

.github/workflows/build-json-files-and-md-cache.yml

@@ -13,10 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
       # Action runs on the issue comment, so we don't get the PR by default
       # Use the gh cli to check out the PR
       - name: Checkout Pull Request
@@ -25,14 +32,64 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@v3
-      - uses: pre-commit/[email protected]
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+        with:
+          python-version: 3.11
+
+      # install prettier plugins
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
+        with:
+          node-version: 20
+      - run: npm install --only=dev
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        id: pre-commit
+        run: pre-commit run --all-files
+        continue-on-error: true
+
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.pre-commit.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: '+1'
 
       - name: Commit & push changes
-        if: steps.prettier_status.outputs.result == 'fail'
+        id: commit-and-push
+        if: steps.pre-commit.outcome == 'failure'
         run: |
           git config user.email "[email protected]"
           git config user.name "nf-core-bot"
           git config push.default upstream
+          git add .
           git status
-          git diff --quiet || (git commit -am "[automated] Fix linting with Prettier" && git push)
+          git commit -m "[automated] Fix code linting"
+          git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@23ff15729ef2fc348714a3bb66d2f655ca9066f2 # v3
+        with:
+          issue-number: ${{ github.event.issue.number }}
+          body: |
+            @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
+            See [CI log](https://github.com/nf-core/website/actions/runs/${{ github.run_id }}) for more details.

.github/workflows/fix-linting.yml

@@ -0,0 +1,23 @@
+name: Lint code
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
+        with:
+          node-version: 20
+      - run: npm install --only=dev
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507 # v3.0.0
+  vale:
+    name: runner / vale
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: errata-ai/vale-action@reviewdog

.github/workflows/linting.yml

@@ -12,8 +12,8 @@ jobs:
     timeout-minutes: 30
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/setup-node@b39b52d1213e96004bfcb1c61a8a6fa8ab84f3e8 # v4
         with:
           node-version: 18
           cache: 'npm'
@@ -22,7 +22,7 @@ jobs:
       - name: Install Playwright Browsers
         run: npx playwright install --with-deps
       - name: Waiting for 200 from the Netlify Preview
-        uses: jakepartusch/[email protected]
+        uses: jakepartusch/wait-for-netlify-action@f1e137043864b9ab9034ae3a5adc1c108e3f1a48 # v1.4
         id: waitFor200
         with:
           site_name: 'nf-core'
@@ -31,7 +31,7 @@ jobs:
         run: npx playwright test
         env:
           PLAYWRIGHT_TEST_BASE_URL: 'https://deploy-preview-${{github.event.pull_request.number}}--nf-core.netlify.app'
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4
         if: always()
         with:
           name: playwright-report