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Merge branch 'redesign2023' of https://github.com/nearform/bioconductor.org into nearform-redesign2023
2 parents 229b8e9 + 05b39bb commit a61bbe9

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‎.eslintignore

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assets/js/search.js
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assets/js/bioconductor.js
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assets/js/bioc_views.js

‎.eslintrc.json

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{
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"env": {
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"browser": true,
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"es2021": true,
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"es6": true,
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"node": true
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},
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"extends": "eslint:recommended",
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"parserOptions": {
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"ecmaVersion": "latest",
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"sourceType": "module"
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},
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"rules": {}
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}

‎.github/workflows/linter.yaml

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name: Run Linters
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on:
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pull_request:
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types: [opened, reopened, synchronize]
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jobs:
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build:
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if: github.event.pull_request.draft == false
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name: Run Linters
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: read
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statuses: write
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Lint Code Base
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uses: super-linter/super-linter/slim@v5
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env:
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LINTER_RULES_PATH: /
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VALIDATE_ALL_CODEBASE: false
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VALIDATE_GITHUB_ACTIONS: false
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VALIDATE_MARKDOWN: false
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VALIDATE_NATURAL_LANGUAGE: false
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VALIDATE_JSCPD: false
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VALIDATE_JSON: false
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VALIDATE_R: false
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VALIDATE_RUBY: false
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VALIDATE_JAVASCRIPT_STANDARD: false
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JAVASCRIPT_ES_CONFIG_FILE: .eslintrc.json
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DEFAULT_BRANCH: redesign2023
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/pr_close.yaml

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name: PR - Closed
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on:
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pull_request:
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types: [closed]
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jobs:
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dev-pr-close-s3:
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runs-on: ubuntu-latest
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environment: dev
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steps:
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- name: Empty Website Bucket
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run: |
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if aws s3api head-bucket --bucket pr-preview-bioconductor-pr${{github.event.number}} 2>/dev/null; then
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aws s3 rm s3://pr-preview-bioconductor-pr${{github.event.number}} --recursive
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echo "BUCKET_EXISTS=true" >> "$GITHUB_ENV"
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else
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echo "Bucket does not exist"
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echo "BUCKET_EXISTS=false" >> "$GITHUB_ENV"
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fi
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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AWS_REGION: "us-east-1"
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- name: Delete Website Bucket
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if: ${{env.BUCKET_EXISTS == 'true'}}
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uses: danburtenshaw/[email protected]
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with:
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bucket-prefix: "pr-preview-bioconductor"
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/pr_deploy.yaml

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name: Pr - Preview
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on:
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pull_request:
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types: [opened, reopened, synchronize]
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jobs:
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dev-pr-create-s3:
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if: github.event.pull_request.draft == false
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runs-on: ubuntu-latest
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environment: dev
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Restore Nanoc Cache
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id: cache-nanoc-tmp
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uses: actions/cache/restore@v3
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with:
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path: tmp
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key: ${{ runner.os }}-nanoc-tmp
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- name: Restore Site Output Cache
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id: cache-site-output
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uses: actions/cache/restore@v3
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with:
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path: output
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key: ${{ runner.os }}-site-output
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- name: Set up ruby
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uses: ruby/setup-ruby@ec02537da5712d66d4d50a0f33b7eb52773b5ed1
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with:
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ruby-version: "2.6.5"
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- name: Install dependencies
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run: bundle install --jobs 4 --retry 3
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- name: build website
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run: rake
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- name: Create Bucket
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run: |
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if aws s3api head-bucket --bucket pr-preview-bioconductor-pr${{github.event.number}} 2>/dev/null; then
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echo "Bucket already exists"
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else
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aws s3 mb s3://pr-preview-bioconductor-pr${{github.event.number}}
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aws s3api delete-public-access-block --bucket pr-preview-bioconductor-pr${{github.event.number}}
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aws s3api delete-bucket-ownership-controls --bucket pr-preview-bioconductor-pr${{github.event.number}}
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aws s3api put-bucket-website --bucket pr-preview-bioconductor-pr${{github.event.number}} \
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--website-configuration '{"IndexDocument":{"Suffix":"index.html"},"ErrorDocument":{"Key":"404.html"}}'
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fi
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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AWS_REGION: "us-east-1"
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- name: Deploy S3 Website
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uses: danburtenshaw/[email protected]
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with:
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bucket-prefix: "pr-preview-bioconductor"
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folder-to-copy: "./output"
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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kpi_metrics:
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needs: dev-pr-create-s3
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permissions:
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pull-requests: write
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name: All KPI metrics
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runs-on: ubuntu-latest
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steps:
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- name: checkout
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uses: actions/checkout@v3
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- name: Setup Node.js environment
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uses: actions/[email protected]
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with:
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node-version: 18
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- name: install psi and axe
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run: |
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npm install psi
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npm install @axe-core/cli
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- name: run desktop psi
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run: |
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echo "DESKTOP_PSI_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(node PageSpeed.js url=http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com,strategy=desktop,threshold=50,apiKey=none)" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: run mobile psi
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run: |
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echo "MOBILE_PSI_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(node PageSpeed.js url=http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com,strategy=mobile,threshold=50,apiKey=none)" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: add_comment_pageSpeed
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uses: mshick/add-pr-comment@v2
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with:
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message: |
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${{env.DESKTOP_PSI_RESULTS}}
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${{env.MOBILE_PSI_RESULTS}}
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message-id: psi
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- name: run axe accesibility test
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run: |
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echo "AXE_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(npx axe http://pr-preview-bioconductor-pr${{github.event.number}}.s3-website-us-east-1.amazonaws.com)" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: add_comment_axe
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uses: mshick/add-pr-comment@v2
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with:
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message: ${{env.AXE_RESULTS}}
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message-id: axe

‎.github/workflows/staging.yaml

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name: Deploy To staging
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on:
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push:
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branches:
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- redesign2023
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jobs:
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staging-deploy:
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concurrency: ci-${{ github.ref }}
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runs-on: ubuntu-latest
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environment: staging
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steps:
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- name: checkout
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uses: actions/checkout@v3
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- name: Use Nanoc Cache
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id: cache-nanoc-tmp
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uses: actions/cache@v3
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with:
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path: tmp
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key: ${{ runner.os }}-nanoc-tmp
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- name: Use Site Output Cache
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id: cache-site-output
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uses: actions/cache@v3
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with:
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path: output
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key: ${{ runner.os }}-site-output
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- name: Set up ruby
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uses: ruby/setup-ruby@ec02537da5712d66d4d50a0f33b7eb52773b5ed1
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with:
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ruby-version: "2.6.5"
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- name: Install dependencies
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run: bundle install --jobs 4 --retry 3
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- name: Build website
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run: rake
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- name: Deploy website to staging s3
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uses: Reggionick/[email protected]
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with:
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folder: output
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bucket: ${{secrets.S3_BUCKET}}
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bucket-region: us-east-1
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delete-removed: true
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env:
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AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
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AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
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kpi_metrics:
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needs: staging-deploy
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permissions:
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pull-requests: write
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name: All KPI metrics
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runs-on: ubuntu-latest
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steps:
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- name: checkout
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uses: actions/checkout@v3
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- name: Setup Node.js environment
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uses: actions/[email protected]
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with:
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node-version: 18
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- name: install psi and axe
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run: |
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npm install psi
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npm install @axe-core/cli
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- name: run desktop psi
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run: |
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echo "DESKTOP_PSI_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(node PageSpeed.js url=${{vars.STAGING_URL}},strategy=desktop,threshold=50,apiKey=none)" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: run mobile psi
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run: |
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echo "MOBILE_PSI_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(node PageSpeed.js url=${{vars.STAGING_URL}},strategy=mobile,threshold=50,apiKey=none)" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: run axe accesibility test
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run: |
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echo "AXE_RESULTS<<EOF" >> $GITHUB_ENV
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echo "$(npx axe ${{vars.STAGING_URL}})" >> $GITHUB_ENV
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echo "EOF" >> $GITHUB_ENV
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- name: send notification psi
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if: ${{ github.ref == 'refs/heads/redesign2023' }}
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uses: 8398a7/action-slack@v2
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with:
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status: ${{ job.status }}
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text: "${{env.DESKTOP_PSI_RESULTS}} \n ${{env.MOBILE_PSI_RESULTS}}"
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env:
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SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}
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- name: send notification axe
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if: ${{ github.ref == 'refs/heads/redesign2023' }}
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uses: 8398a7/action-slack@v2
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with:
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status: ${{ job.status }}
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text: "${{env.AXE_RESULTS}}"
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env:
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SLACK_WEBHOOK_URL: ${{secrets.SLACK_WEBHOOK}}

‎.gitignore

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workflows_tmp/
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content/help/workflows/*
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postgresql_password
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manifest/*
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manifest/*
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node_modules/
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package

‎.htmlhintrc

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{
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"doctype-first": false,
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"spec-char-escape": false,
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"head-script-disabled": true,
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"style-disabled": true,
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"attr-lowercase": true,
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"attr-no-duplications": true,
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"attr-no-unnecessary-whitespace": true,
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"attr-value-single-quotes": false,
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"attr-value-double-quotes": true,
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"attr-whitespace": true,
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"alt-require": true,
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"input-requires-lable": true,
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"tag-pair": false,
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"tagname-lowercase": true,
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"tagname-specialchars": true,
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"src-not-empty": true,
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"id-class-value": "dash",
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"inline-script-disabled": true,
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"inline-style-disabled": true
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}

‎.stylelintrc.json

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{
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"extends": ["stylelint-config-standard"]
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}

‎Dockerfile

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FROM ruby:2.6.5
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## System dependencies
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RUN apt-get update && apt install -y \
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rsync \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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RUN apt-get update && apt-get install -y \
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rsync \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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## Install gems
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COPY Gemfile /opt
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COPY Gemfile.lock /opt
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## Set the working directory to /opt/bioconductor.org
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WORKDIR /opt/bioconductor.org
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## Copy the remaining files from bioconductor.org/ to /opt/bioconductor.org
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COPY . .
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COPY Gemfile /tmp
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COPY Gemfile.lock /tmp
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WORKDIR /tmp
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## RUN bundle lock
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## Install bundle and dependencies
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RUN gem install bundler
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RUN bundle install --jobs=4 && bundle clean --force
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## Set up web server
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EXPOSE 3000
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## Create startup script
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RUN echo '#! /bin/bash \n\
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cd /bioconductor.org \n\
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rake \n\
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cd output \n\
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adsf\n' > .startup.sh \\
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RUN echo '#! /bin/bash' > .startup.sh \
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&& echo 'cd /opt/bioconductor.org' >> .startup.sh \
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&& echo 'rake' >> .startup.sh \
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&& echo 'cd output' >> .startup.sh \
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&& echo 'adsf' >> .startup.sh \
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&& chmod +x .startup.sh
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CMD ["./.startup.sh"]
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CMD ["/opt/bioconductor.org/.startup.sh"]

‎Gemfile

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raise 'Ruby version must be 2.3 or greater' unless RUBY_VERSION.to_f >= 2.3
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source 'http://rubygems.org'
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gem "nanoc", "~> 4.0"
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gem "nanoc", "~> 4.9.5"
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gem "pry"
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gem "pry-byebug"
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gem "rdiscount"

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