2a. Run General Tests #1
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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 | |
| ### Single line conditional can use ${{}} formulation. Multi-line conditional does not. | |
| ### 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: 2a. Run General Tests | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| agg_types: | |
| type: choice | |
| description: Aggregate across impact types? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| doCompare: | |
| type: choice | |
| description: Do you want to compare FrEDI results with those from another branch? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| ref_branch: | |
| type: string | |
| description: To which branch of FrEDI do you want to compare results)? | |
| default: main | |
| jobs: | |
| run_general_tests: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: Load Package Code | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Send input status | |
| run: | | |
| echo "agg_types = ${{ inputs.agg_types }}" | |
| echo "doCompare = ${{ inputs.agg_types }}" | |
| echo "ref_name = ${{ github.ref_name }}" | |
| echo "ref_branch = ${{ inputs.ref_branch }}" | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup R package dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: true | |
| cache-version: 1 | |
| packages: | | |
| any::tidyverse | |
| any::devtools | |
| any::openxlsx | |
| any::ggpubr | |
| ### Install FrEDI from new branch and get results | |
| ### Install FrEDI from ref branch and get results | |
| - name: Test results | |
| # if: | | |
| # inputs.doCompare == 'true' | |
| run: | | |
| Rscript -e ' | |
| ###### Libraries ###### | |
| require(tidyverse) | |
| require(devtools) | |
| require(openxlsx) | |
| require(ggpubr) | |
| ###### Workflow Inputs ###### | |
| aggTypes <- "${{ inputs.agg_types }}" | |
| doCompare <- "${{ inputs.doCompare }}" | |
| newBranch <- "${{ github.ref_name }}" | |
| refBranch <- "${{ inputs.ref_branch }}" | |
| ###### Format Inputs ###### | |
| ### Conditionals | |
| doTests <- doCompare %in% c("true", "yes") | |
| aggAll <- aggTypes %in% c("true", "yes") | |
| ### If aggAll, aggregate, national, model averages, impact years | |
| if (aggTypes) aggLevels <- c("all") | |
| else aggLevels <- c("national", "modelaverage", "impactyear") | |
| ###### Paths ###### | |
| ### Main repo path, FrEDI project path, scripts path | |
| rPath0 <- "."; | |
| # pPath0 <- rPath0 |> file.path("FrEDI") | |
| pPath0 <- rPath0 | |
| ### Load scripts and testing functions | |
| sPath0 <- pPath0 |> file.path("scripts") | |
| tPath0 <- pPath0 |> file.path("testing") | |
| sFiles0 <- sPath0 |> list.files(full.names=TRUE) | |
| tFiles0 <- tPath0 |> list.files(full.names=TRUE) | |
| for(file_i in sFiles0){file_i |> source(); rm(file_i)} | |
| for(file_i in tFiles0){file_i |> source(); rm(file_i)} | |
| ### Where to save results | |
| oPath0 <- pPath0 |> file.path("data_tests") | |
| oFileNew <- oPath0 |> file.path("newResults.rda") | |
| oFileRef <- oPath0 |> file.path("refResults.rda") | |
| ### Check if path exists and, if not, create it | |
| exists0 <- oPath0 |> dir.exists() | |
| if(!exists0) oPath0 |> dir.create(recursive=TRUE) | |
| ### Repo Info | |
| urlRepo <- "https://github.com/USEPA/FrEDI" | |
| c(newBranch, refBranch) |> print() | |
| ###### Compare Results ###### | |
| ### Compare results between branches | |
| ###### ** Install FrEDI from Reference Branch ###### | |
| ### Install FrEDI from ref branch | |
| if(doTests) { | |
| devtools::install_github( | |
| repo=urlRepo, ref=refBranch, | |
| # subdir="FrEDI", | |
| dependencies=F, upgrade="never", force=T, type="source" | |
| ) ### End install_github | |
| } ### End if(installRef) | |
| ###### ** Run FrEDI from Reference Branch ###### | |
| ### Load library, run FrEDI | |
| if(doTests) { | |
| library(FrEDI) | |
| dfRef <- run_fredi(aggLevels=aggLevels) | |
| dfRef |> save(file=oFileRef) | |
| "Finished running FrEDI on " |> paste0(refBranch, " branch.") |> print() | |
| oPath0 |> list.files() |> print() | |
| ### Detach FrEDI package | |
| package:FrEDI |> detach(unload=TRUE) | |
| } ### End if(doTests) | |
| ###### ** Install FrEDI from New Branch ###### | |
| ### Install FrEDI from new branch | |
| devtools::install_github( | |
| repo=urlRepo, ref=newBranch, | |
| dependencies=F, upgrade="never", force=T, type="source" | |
| ) ### End install_github | |
| ###### ** Run FrEDI from New Branch ###### | |
| ### Load library, run FrEDI | |
| library(FrEDI) | |
| dfNew <- run_fredi(aggLevels=aggLevels) | |
| dfNew |> save(file=oFileNew) | |
| "Finished running FrEDI on " |> paste0(newBranch, " branch.") |> print() | |
| oPath0 |> list.files() |> print() | |
| ###### ** Run General Tests ###### | |
| ### Get test results | |
| if(doTests) { | |
| dfTests <- general_fredi_test( | |
| newOutputs = dfNew, | |
| refOutputs = dfRef, | |
| outPath = oPath0 | |
| ) ### End general_fredi_test | |
| "Finished running general tests." |> print() | |
| oPath0 |> list.files() |> print() | |
| rm(dfTests) | |
| } ### End if(doTests) | |
| ###### Return ###### | |
| "Finished running R script." |> print() | |
| ' | |
| - name: Upload General Tests | |
| if: | | |
| inputs.doCompare == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: general_tests | |
| path: | | |
| ./data_tests/* | |