Create open-science-for-bioinformaticians blogpost #1994
Workflow file for this run
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| name: CI for push and PR | |
| on: [push, pull_request] | |
| jobs: | |
| check-internal-links: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: ruby/setup-ruby@v1 | |
| with: | |
| ruby-version: "3.0" | |
| - name: Install dependencies | |
| run: | | |
| gem install bundler | |
| bundle install | |
| - name: Build website | |
| run: bundle exec jekyll build --strict_front_matter | |
| - name: Validate HTML and check links | |
| run: | | |
| bundle exec htmlproofer \ | |
| --allow_missing_href=true \ | |
| --ignore-urls "/.*localhost.*/","/.*gitter\.im.*/" \ | |
| --enforce-https=false \ | |
| --disable-external=true \ | |
| --ignore_empty_alt=true \ | |
| --ignore_missing_alt=true \ | |
| --check-internal-hash=false \ | |
| ./_site | |
| lint: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.11'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install tox | |
| run: python -m pip install 'tox>=1.8.0' | |
| - name: Lint | |
| run: tox -e lint | |
| test-other-workflows: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| activate-environment: ols-website | |
| environment-file: environment.yml | |
| - name: Update Open Seeds schedule | |
| shell: bash -el {0} | |
| run: | | |
| bash bin/openseeds/update_schedule.sh | |
| - name: Update Open Seeds library | |
| shell: bash -el {0} | |
| run: | | |
| python bin/prepare_website_data.py buildlibrary -p "openseeds" | |
| - name: Update Nebula schedule | |
| shell: bash -el {0} | |
| run: | | |
| bash bin/nebula/update_schedule.sh | |
| - name: Update people data artifacts | |
| shell: bash -el {0} | |
| run: | | |
| python bin/prepare_website_data.py extractfullpeopledata | |
| - name: Update Open Seeds library artifacts | |
| shell: bash -el {0} | |
| run: | | |
| python bin/prepare_website_data.py extractlibrary -p "openseeds" | |
| - name: Update Open Seeds projects | |
| shell: bash -el {0} | |
| run: | | |
| python bin/prepare_website_data.py createprojecttable -p "openseeds" | |
| - name: Update bibliography | |
| shell: bash -el {0} | |
| env: | |
| ZOTERO_API: ${{ secrets.ZoteroAPI }} | |
| run: | | |
| python bin/prepare_website_data.py updatebibliography -a "$ZOTERO_API" |