1. Compile Main FrEDI Data #67
Workflow file for this run
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| ### https://github.com/actions/upload-artifact | |
| ### https://github.blog/changelog/2021-11-10-github-actions-input-types-for-manual-workflows/ | |
| ### https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows | |
| ### https://github.com/r-lib/actions/tree/v2/setup-r-dependencies | |
| ### https://docs.github.com/en/actions/using-jobs/using-conditions-to-control-job-execution | |
| ### For uploading artifacts: | |
| ### "path:" is the output path where Pandoc will write the compiled PDF. | |
| ### Note, this should be the same directory as the input paper.md | |
| name: Compile FrEDI Data | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| branch_name: | |
| type: string | |
| description: Which FrEDI Package branch do you want to use? | |
| jobs: | |
| compile_data: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: Process Data | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup R package dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: true | |
| cache-version: 1 | |
| packages: | | |
| any::tidyverse | |
| any::ggpubr | |
| any::openxlsx | |
| any::devtools | |
| - name: Install FrEDI | |
| run: | | |
| Rscript -e ' | |
| devtools::install_github( | |
| repo = "https://github.com/USEPA/FrEDI", | |
| ref = "${{ github.event.inputs.branch_name }}", | |
| subdir = "FrEDI", | |
| dependencies = FALSE, | |
| upgrade = "never", | |
| force = TRUE, | |
| type = "source" | |
| )' | |
| - name: Run createsystemData | |
| run: | | |
| Rscript -e ' | |
| projectDir <- "." | |
| scriptDir <- projectDir |> file.path("scripts") | |
| scriptDir |> file.path("configureFrediData.R") |> source() | |
| test0 <- projectDir |> configureFrediData(save=T) | |
| "./data_tests/" |> list.files() |> print() | |
| "./data/" |> list.files() |> print() | |
| ' | |
| - name: Upload Tests | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Data | |
| path: | | |
| ./data_tests/* | |
| ./data/tmp_sysdata.rda | |
| - name: Commit results | |
| run: | | |
| git config --local core.autocrlf false | |
| git config --local user.email "${{ github.actor }}@users.noreply.github.com" | |
| git config --local user.name "${{ github.actor }}" | |
| git add data/tmp_sysdata.rda | |
| git add data_tests/**.xlsx | |
| git pull origin ${{ github.head_ref }} --autostash --rebase -X ours | |
| git commit -a -m "Updated temporary system data and tests" | |
| git push | |