usegalaxy-eu/website (opens in new tab)

# This Action will run in the following scenarios:
# - on Pull Requests containing images (not including forks)
# - on pushing of images to `master` (for forks)
# - on demand (https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/)
# - at 11 PM every Sunday if anything gets missed with any of the above scenarios
# For Pull Requests, the images are added to the PR.
# For other scenarios, a new PR will be opened if any images are compressed.
name: Compress images
on:
  pull_request:
    paths:
      - '**.jpg'
      - '**.jpeg'
      - '**.png'
      - '**.webp'
      - '**.avif'
  push:
    branches:
      - master
    paths:
      - '**.jpg'
      - '**.jpeg'
      - '**.png'
      - '**.webp'
      - '**.avif'
  workflow_dispatch:
  schedule:
    - cron: '00 23 * * 0'

permissions:
  contents: write
  pull-requests: write

jobs:
  build:
    name: calibreapp/image-actions
    runs-on: ubuntu-latest
    # Only run on main repo on and PRs that match the main repo.
    if: |
      github.repository == 'usegalaxy-eu/website' &&
      (github.event_name != 'pull_request' ||
       github.event.pull_request.head.repo.full_name == github.repository)
    steps:
      - name: Checkout Branch
        uses: actions/checkout@v6

      - name: Compress Images
        id: calibre
        uses: calibreapp/image-actions@main
        with:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Create Pull Request
        # If it's not a Pull Request then commit any changes as a new PR.
        if: |
          github.event_name != 'pull_request' &&
          steps.calibre.outputs.markdown != ''
        uses: peter-evans/create-pull-request@v8
        with:
          title: Auto Compress Images
          branch-suffix: timestamp
          commit-message: Compress Images
          body: ${{ steps.calibre.outputs.markdown }}

name: Update Citations
on:
  workflow_dispatch:
  schedule:
    - cron: '00 23 * * 0'

permissions:
  contents: write
  pull-requests: write

jobs:
  update-citations:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Branch
        uses: actions/checkout@v6

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: '3.12'

      - name: Install dependencies
        ## 1.5.27 does not seem to work
        run: pip install bibtexparser Pyzotero==1.5.25

      - name: Run update script
        run: python update_citations-eu.py

      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v8
        with:
            commit-message: Update citations
            title: Update Citations
            body: |
              This is an auto-generated PR with the updated `citations` of [Galaxy EU](https://usegalaxy.eu)
            branch: update-citations
            delete-branch: true

name: Update Genome count
on:
  workflow_dispatch:
  schedule:
    - cron: '00 23 * * 0'

permissions:
  contents: write
  pull-requests: write

jobs:
  update-citations:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Branch
        uses: actions/checkout@v6

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: '3.12'

      - name: Install dependencies
        run:  pip install pandas

      - name: Run update script
        run: python annotate_genome_count.py

      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v8
        with:
            commit-message: Update VGP/ERGA Genome count
            title: Update VGP/ERGA Genome count
            body: |
              This is an auto-generated PR with the updated `genome count` of the [Galaxy Assembly](https://assembly.usegalaxy.eu) site.
            branch: update-genome-count
            delete-branch: true

name: Update Tools Report
on:
  workflow_dispatch:
  schedule:
    - cron: '00 23 * * 0'

permissions:
  contents: write
  pull-requests: write

jobs:
  update-tools:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout Branch
        uses: actions/checkout@v6

      - name: Setup Python
        uses: actions/setup-python@v6
        with:
          python-version: '3.12'

      - name: Install dependencies
        run: pip install requests

      - name: Run update script
        run: python update_tools.py

      - name: Create Pull Request
        uses: peter-evans/create-pull-request@v8
        with:
            commit-message: Update tools
            title: Update Tools Report
            body: |
              This is an auto-generated PR with the updated inventory of tools available at [Galaxy EU](https://usegalaxy.eu)
            branch: update-tools-report
            delete-branch: true