3. Test FrEDI Package #98
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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: 3. Test FrEDI Package | |
| # on: [workflow_dispatch] | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| run_tests: | |
| type: choice | |
| description: Run general tests? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| figH_results: | |
| type: choice | |
| description: Fig H results? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| make_appx_figs: | |
| type: choice | |
| description: Create appendix figures for report? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| make_tots_figs: | |
| type: choice | |
| description: Make figures for impact type totals? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| jobs: | |
| compile_data: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: Load Package Code | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Send input status | |
| run: | | |
| echo "${{ inputs.run_tests }} ${{ inputs.figH_results }} ${{ inputs.make_appx_figs }} ${{ inputs.make_tots_figs }}" | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup R package dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: true | |
| cache-version: 1 | |
| packages: | | |
| any::tidyverse | |
| any::ggpubr | |
| any::openxlsx | |
| any::devtools | |
| - name: Install FrEDI | |
| run: | | |
| Rscript -e ' | |
| devtools::install_github( | |
| repo = "https://github.com/USEPA/FrEDI", | |
| ref = "${{ github.ref_name }}", | |
| subdir = "FrEDI", | |
| dependencies = FALSE, | |
| upgrade = "never", | |
| force = TRUE, | |
| type = "source" | |
| ) | |
| ' | |
| - name: Run tests & create figures | |
| run: | | |
| Rscript -e ' | |
| ### Main repo path, FrEDI project path, scripts path | |
| rPath0 <- "."; | |
| pPath0 <- rPath0 |> file.path("FrEDI") | |
| sPath0 <- pPath0 |> file.path("scripts") | |
| tPath0 <- pPath0 |> file.path("testing") | |
| ### Load FrEDI | |
| pPath0 |> devtools::load_all() | |
| ### Load test code | |
| tFiles0 <- tPath0 |> list.files(full.names=TRUE) | |
| for(file_i in tFiles0){file_i |> source(); rm(file_i)} | |
| ### Load source | |
| sPath0 |> file.path("create_DoW_results.R") |> source() | |
| ### Which tests to do | |
| do_tests <- "${{ inputs.run_tests }}" == "true" | |
| do_figH <- "${{ inputs.figH_results }}" == "true" | |
| do_appx <- "${{ inputs.make_appx_figs }}" == "true" | |
| do_tots <- "${{ inputs.make_tots_figs }}" == "true" | |
| do_figs <- do_appx | do_tots | |
| ### Where to save results | |
| oPath0 <- pPath0 |> file.path("data_tests") | |
| oPath1 <- oPath0 |> file.path("general") | |
| oPath2 <- oPath0 |> file.path("report_figures") | |
| ### Whether paths exist | |
| exists0 <- oPath0 |> dir.exists() | |
| exists1 <- oPath1 |> dir.exists() | |
| exists2 <- oPath2 |> dir.exists() | |
| ### Check if path exists and, if not, create it | |
| if(!exists0){ oPath0 |> dir.create(recursive = TRUE)} | |
| if(!exists1){ oPath1 |> dir.create(recursive = TRUE)} | |
| if(!exists2){ oPath2 |> dir.create(recursive = TRUE)} | |
| ### Test results | |
| if(do_tests){ | |
| ### Run FrEDI | |
| results0 <- run_fredi() | |
| ### Run tests | |
| tests0 <- results0 |> general_fredi_test( | |
| outPath = oPath1, | |
| save = TRUE, | |
| return = TRUE, | |
| overwrite = TRUE | |
| ) | |
| ### Create plot totals | |
| listResults <- create_default_tablePlot() | |
| save0 <- listResults |> save(file= oPath1 |> file.path("defaultScenarioTotals.rda")) |> try() | |
| ### Remove results | |
| rm(exists0, results0, tests0, listResults, save0) | |
| } ### End if(do_tests) | |
| ### Create Fig H results | |
| if(do_figH){ | |
| ### Figure H results | |
| results0 <- run_fredi(aggLevels=c("modelaverage", "national", "impactYear")) | |
| results0 <- results0 |> filter(year %in% seq(2010, 2090, by=5)) | |
| save0 <- results0 |> write.csv(file=oPath2 |> file.path("FigH_results.csv"), row.names=F) |> try() | |
| ### Remove reslts | |
| rm(results0, save0) | |
| } ### End if(do_figH) | |
| ### Create report figures | |
| if(do_figs){ | |
| ### Load source | |
| sPath0 |> file.path("create_DoW_results.R") |> source() | |
| ### Create report figures | |
| reports0 <- create_DoW_results( | |
| outPath = oPath2, | |
| saveFile = TRUE, | |
| loadCode = "project", | |
| totals = do_tots, | |
| silent = FALSE, | |
| testing = TRUE, | |
| return = FALSE, | |
| fpath = pPath0 | |
| ) | |
| } ### End if(do_figs) | |
| ' | |
| - name: Upload Tests | |
| if: | | |
| inputs.run_tests == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Test Data | |
| path: | | |
| ./FrEDI/data_tests/general/defaultScenarioTotals.rda | |
| ./FrEDI/data_tests/general/testResults_fredi_general.xlsx | |
| - name: Upload FigH Results | |
| if: | | |
| inputs.figH_results == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: FigH results | |
| path: | | |
| ./FrEDI/data_tests/report_figures/ | |
| - name: Upload Report Appendix Figures | |
| if: | | |
| inputs.make_appx_figs == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Report appendix figures & data | |
| path: | | |
| ./FrEDI/data_tests/report_figures/ | |
| - name: Upload Report Fig7 Figures | |
| if: | | |
| inputs.make_tots_figs == 'true' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Fig7 report figures & data | |
| path: | | |
| ./FrEDI/data_tests/report_figures/ | |
| # ./FrEDI/data_tests/general/FigH_results.csv | |
| # # | |
| # - 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 | |