generate-artifact-pr.yml

name: On push to protocol branches build the protocol and save the result to an artifact

on:
  push:
    branches: 's[fpioa]p**'

jobs:
  build-and-save:
    runs-on: ubuntu-20.04

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

    steps:
      - name: Checkout repo
        uses: actions/checkout@v2
        with:
          ref: ${{ github.event.pull_request.head.sha }} # checkout PR head commit
          fetch-depth: 0    # Fetch all history for .GitInfo and .Lastmod

      - name: Setup R
        uses: r-lib/actions/setup-r@v2

      - name: Setup pandoc and pandoc-citeproc
        uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-tinytex@v2
      - run: tlmgr --version

      - name: Query dependencies
        run: |
          install.packages('remotes', type = "source")
          saveRDS(remotes::dev_package_deps(dependencies = NA), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}

      - name: Restore R package cache
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          sudo apt-get install libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev libgit2-dev

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = NA, type = "source") #fails to install protocolhelper
          remotes::install_github("inbo/protocolhelper", type = "source")
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - name: Set branch name
        run: |
          echo "branch_name=$(echo ${GITHUB_REF#refs/heads/})" >> $GITHUB_ENV

      - name: Print branch name
        run: |
          echo 'The branch name is' '${{ env.branch_name }}'

      - name: Render protocol (only the one that is the focus of the PR) 
        run: |
          Rscript -e 'protocolhelper::render_protocol("${{ env.branch_name }}", "artifact")'

      - name: Archive protocol to an artifact
        if: ${{ success() }}
        uses: actions/upload-artifact@v2
        with:
          name: pr-${{ env.PR_NUMBER }}-inbo-protocol
          path: ./**/artifact/
        env:
          PR_NUMBER: ${{ github.event.number }}