Change package installation #135
Workflow file for this run
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| --- | |
| name: Publish Catalog 📰 | |
| on: | |
| workflow_call: | |
| workflow_dispatch: | |
| push: | |
| tags: | |
| - "v*" | |
| branches: | |
| - main | |
| - stable-tlg-catalog | |
| schedule: | |
| - cron: "17 17 * * 3,6" | |
| jobs: | |
| publish-latest: | |
| name: Build & Deploy TLGC (latest) 📖 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Cache artifacts 📀 | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/package/.staged.dependencies | |
| book/_freeze | |
| key: ${{ runner.os }}-tlg-catalog-latest | |
| - name: Run Staged dependencies 🎦 | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| env: | |
| GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| with: | |
| path: "./package" | |
| enable-check: false | |
| direction: upstream | |
| - name: Render catalog 🖨 | |
| run: | | |
| cd book | |
| quarto render | |
| shell: bash | |
| - name: Create artifact 📂 | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| run: | | |
| pushd book/_site | |
| zip -r9 $OLDPWD/site.zip * | |
| popd | |
| shell: bash | |
| - name: Upload docs ⬆ | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: site.zip | |
| path: site.zip | |
| # - name: Publish docs | |
| # uses: peaceiris/actions-gh-pages@v3 | |
| # with: | |
| # github_token: ${{ secrets.GITHUB_TOKEN }} | |
| # publish_dir: ./book/_site | |
| publish-stable: | |
| name: Build & Deploy TLGC (stable) 📖 | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Cache artifacts 📀 | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/package/.staged.dependencies | |
| book/_freeze | |
| key: ${{ runner.os }}-tlg-catalog-stable | |
| - name: Install packages 🎦 | |
| # env: | |
| # GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| run: | | |
| r = 'https://insightsengineering.r-universe.dev/' | |
| install.packages(c( | |
| 'shinycssloaders', 'binom', 'broom', 'DescTools', 'dplyr', 'forcats', | |
| 'ggplot2', 'ggpubr', 'ggrepel', 'grid', 'lubridate', 'renv', 'scales', | |
| 'stats', 'stringr', 'tibble', 'tidyr', 'knitr', 'quarto', 'testthat', | |
| 'vdiffr', 'withr' | |
| )) | |
| install.packages('formatters', repos=r) | |
| install.packages('nestcolor', repos=r) | |
| install.packages('rlistings', repos=r) | |
| install.packages('rtables', repos=r) | |
| install.packages('scda', repos=r) | |
| install.packages('scda.2022', repos=r) | |
| install.packages('goshawk', repos=r) | |
| install.packages('osprey', repos=r) | |
| install.packages('teal', repos=r) | |
| install.packages('teal.logger', repos=r) | |
| install.packages('teal.widgets', repos=r) | |
| install.packages('teal.code', repos=r) | |
| install.packages('teal.data', repos=r) | |
| install.packages('teal.transform', repos=r) | |
| install.packages('teal.slice', repos=r) | |
| install.packages('teal.modules.clinical', repos=r) | |
| install.packages('teal.modules.general', repos=r) | |
| install.packages('teal.goshawk', repos=r) | |
| install.packages('teal.osprey', repos=r) | |
| install.packages('tern', repos=r) | |
| install.packages('tern.mmrm', repos=r) | |
| install.packages('tern.rbmi', repos=r) | |
| install.packages('binom', repos=r) | |
| install.packages('broom', repos=r) | |
| install.packages('DescTools', repos=r) | |
| install.packages('dplyr', repos=r) | |
| install.packages('forcats', repos=r) | |
| install.packages('ggplot2', repos=r) | |
| install.packages('ggpubr', repos=r) | |
| install.packages('ggrepel', repos=r) | |
| install.packages('grid', repos=r) | |
| install.packages('lubridate', repos=r) | |
| install.packages('renv', repos=r) | |
| install.packages('scales', repos=r) | |
| install.packages('stats', repos=r) | |
| install.packages('stringr', repos=r) | |
| install.packages('tibble', repos=r) | |
| install.packages('tidyr', repos=r) | |
| install.packages('knitr', repos=r) | |
| install.packages('quarto', repos=r) | |
| install.packages('testthat', repos=r) | |
| install.packages('vdiffr', repos=r) | |
| install.packages('withr', repos=r) | |
| shell: Rscript {0} | |
| - name: Render catalog 🖨 | |
| run: | | |
| cd book | |
| quarto render --verbose | |
| shell: bash | |
| - name: Create artifact 📂 | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| run: | | |
| pushd book/_site | |
| zip -r9 $OLDPWD/site.zip * | |
| popd | |
| shell: bash | |
| - name: Upload docs ⬆ | |
| if: startsWith(github.ref, 'refs/tags/v') | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: site-stable.zip | |
| path: site.zip | |
| upload-release-assets: | |
| name: Upload assets 🔼 | |
| needs: [publish-latest, publish-stable] | |
| runs-on: ubuntu-latest | |
| if: > | |
| startsWith(github.ref, 'refs/tags/v') | |
| && !contains(github.event.commits[0].message, '[skip docs]') | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Download artifact ⏬ | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: site.zip | |
| - name: Upload binaries to release ⤴ | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: site.zip | |
| asset_name: catalog.zip | |
| tag: ${{ github.ref }} | |
| overwrite: true |