targets #651
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| # MIT License | |
| # Copyright (c) 2021 Eli Lilly and Company | |
| # Author: William Michael Landau (will.landau at gmail) | |
| # Written with help from public domain (CC0 1.0 Universal) workflow files by Jim Hester: | |
| # * https://github.com/r-lib/actions/blob/master/examples/check-full.yaml | |
| # * https://github.com/r-lib/actions/blob/master/examples/blogdown.yaml | |
| # | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy | |
| # of this software and associated documentation files (the "Software"), to deal | |
| # in the Software without restriction, including without limitation the rights | |
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| # copies of the Software, and to permit persons to whom the Software is | |
| # furnished to do so, subject to the following conditions: | |
| # | |
| # The above copyright notice and this permission notice shall be included in all | |
| # copies or substantial portions of the Software. | |
| # | |
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | |
| # SOFTWARE. | |
| on: | |
| push: | |
| branches: | |
| - main | |
| # run at noon every day | |
| schedule: | |
| - cron: '0 12 * * *' | |
| name: targets | |
| jobs: | |
| targets: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| permissions: | |
| contents: write #gives the action permission to push to targets-runs branch | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "renv" | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - run: | | |
| quarto --version | |
| - name: Install Mac system dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install zeromq | |
| - name: Install Linux system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo apt-get install libssl-dev | |
| sudo apt-get install libzmq3-dev | |
| - name: Cache packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| restore-keys: ${{ runner.os }}-renv- | |
| - name: Restore packages | |
| shell: Rscript {0} | |
| run: | | |
| if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv") | |
| renv::restore() | |
| - name: Check if previous runs exists | |
| id: runs-exist | |
| run: git ls-remote --exit-code --heads origin targets-runs | |
| continue-on-error: true | |
| - name: Checkout previous run | |
| if: steps.runs-exist.outcome == 'success' | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: targets-runs | |
| fetch-depth: 1 | |
| path: .targets-runs | |
| - name: Restore output files from the previous run | |
| if: steps.runs-exist.outcome == 'success' | |
| run: | | |
| for (dest in scan(".targets-runs/.targets-files", what = character())) { | |
| source <- file.path(".targets-runs", dest) | |
| if (!file.exists(dirname(dest))) dir.create(dirname(dest), recursive = TRUE) | |
| if (file.exists(source)) file.rename(source, dest) | |
| } | |
| shell: Rscript {0} | |
| - name: Run targets pipeline | |
| run: targets::tar_make() | |
| shell: Rscript {0} | |
| env: | |
| CONNECT_SERVER: ${{ secrets.CONNECT_URL }} | |
| CONNECT_API_KEY: ${{ secrets.CONNECT_API_KEY }} | |
| - name: Identify files that the targets pipeline produced | |
| run: git ls-files -mo --exclude=renv > .targets-files | |
| - name: Create the runs branch if it does not already exist | |
| if: steps.runs-exist.outcome != 'success' | |
| run: git checkout --orphan targets-runs | |
| - name: Put the worktree in the runs branch if the latter already exists | |
| if: steps.runs-exist.outcome == 'success' | |
| run: | | |
| rm -r .git | |
| mv .targets-runs/.git . | |
| rm -r .targets-runs | |
| - name: Upload latest run | |
| run: | | |
| git config --local user.name "GitHub Actions" | |
| git config --local user.email "[email protected]" | |
| rm -r .gitignore .github/workflows | |
| git add --all -- ':!renv' | |
| for file in $(git ls-files -mo --exclude=renv) | |
| do | |
| git add --force $file | |
| done | |
| git commit -am "Run pipeline" | |
| git push origin targets-runs | |
| - name: Prepare failure artifact | |
| if: failure() | |
| run: rm -rf .git .github .targets-files .targets-runs | |
| - name: Post failure artifact | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: . |