Merge pull request #95 from USEPA/main

Merging main branch into state level

.github/workflows/build_fredi.yml

@@ -0,0 +1,80 @@
+### 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: Build FrEDI Package
+
+on: [workflow_dispatch]
+
+jobs:
+  compile_data:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    name: Load Package Code
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup R package dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-version: 1
+          packages: |
+            any::tidyverse
+            any::ggpubr
+            any::openxlsx
+            any::devtools
+
+      - name: Remove existing build
+        run: |
+          rm *.tar.gz
+
+
+      - name: Run create_DoW_results
+        run: |
+          Rscript -e '
+          ### Main repo path, FrEDI project path, scripts path
+          rPath0   <- ".";
+          pPath0   <- rPath0 |> file.path("FrEDI")
+          oPath0   <- pPath0 |> file.path("data", "defaultResults.rda")
+
+          ###### Create Default Results ######
+          pPath0 |> devtools::load_all()
+          defaultResults <- run_fredi()
+          save(defaultResults, file=oPath0))
+
+          ###### Update Documentation ######
+          ###### - Build Manual
+          ###### - Add and build vignettes
+          ###### - Generate Documentation
+          roxygen2::roxygenise(pPath0)
+          devtools::document(pkg = pPath0)
+          # devtools::build_manual(pkg = pPath0)
+          # devtools::build_vignettes(pkg = pPath0)
+
+          ###### Build Package ######
+          ###### - Build Package but don't include vignettes
+          devtools::build(pkg=pPath0, path=rPath0)
+          '
+
+
+      - name: Commit results
+        run: |
+          git config --local core.autocrlf false
+          git config --local user.email "${{ github.actor }}@users.noreply.github.com"
+          git config --local user.name  "${{ github.actor }}"
+          git add *.tar.gz
+          git pull origin ${{ github.head_ref }} --autostash --rebase -X ours
+          git commit -a -m "New package build"
+          git push
+

.github/workflows/test_fredi.yml

@@ -0,0 +1,168 @@
+### 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: Test FrEDI Package
+
+# on: [workflow_dispatch]
+on:
+  workflow_dispatch:
+    inputs:
+      run_tests:
+        type: choice
+        description: Run general tests
+        required: true
+        options:
+        - no
+        - yes
+      make_figures:
+        type: choice
+        description: Create report figures
+        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 }} ${{ inputs.make_figures }}"
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Setup R package dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-version: 1
+          packages: |
+            any::tidyverse
+            any::ggpubr
+            any::openxlsx
+            any::devtools
+
+      - name: Install FrEDI
+        run: |
+          Rscript -e '
+            devtools::install_github(
+              repo    = "https://github.com/USEPA/FrEDI",
+              ref     = "main",
+              subdir  = "FrEDI",
+              dependencies = FALSE,
+              upgrade = "never",
+              force   = TRUE,
+              type    = "source"
+            )'
+
+      - name: Run create_DoW_results
+        run: |
+          Rscript -e '
+          ### Which tests to do
+          do_tests <- "${{ inputs.run_tests    }}" == "true"
+          do_figs  <- "${{ inputs.make_figures }}" == "true"
+
+          ### Main repo path, FrEDI project path, scripts path
+          rPath0   <- ".";
+          pPath0   <- rPath0 |> file.path("FrEDI")
+          sPath0   <- pPath0 |> file.path("scripts")
+          rPath0 |> list.files() |> print()
+          pPath0 |> list.files() |> print()
+          sPath0 |> list.files() |> print()
+
+          ### Load FrEDI
+          pPath0 |> devtools::load_all()
+
+          ### Where to save results
+          oPath0   <- pPath0 |> file.path("data_tests")
+          oPath1   <- oPath0 |> file.path("general")
+          oPath2   <- oPath0 |> file.path("report_figures")
+
+          ### 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(results0, test0, listResults)
+          }
+
+          ### Create report results
+          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",
+              silent   = FALSE,
+              testing  = TRUE,
+              return   = FALSE,
+              fpath    = pPath0
+            )
+
+            ### Figure H results
+            results0 <- run_fredi(aggLevels=c("modelaverage", "national"))
+            results0 <- results0 |> filter(year %in% seq(2010, 2090, by=5))
+            save0    <- write.csv(results0, file=oPath1 |> file.path("FigH_results.csv", row.names=F)) |> try()
+          }
+          '
+
+      - name: Upload Tests
+        if: |
+          inputs.run_tests == 'yes'
+        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 Report Figures
+        if: |
+          inputs.make_figures == 'yes'
+        uses: actions/upload-artifact@v3
+        with:
+          name: Report 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
+

FrEDI/DESCRIPTION

@@ -2,25 +2,28 @@ Package: FrEDI
 Title: The Framework for Evaluating Damages and Impacts (FrEDI)
 Version: 3.4
 Authors@R: c(person("Corinne", "Hartin",
-                    email = "[email protected]",
-                    role = c("aut","cre"),
+                    email   = "[email protected]",
+                    role    = c("aut","cre"),
                     comment = c(ORCID = "0000-0003-1834-6539",
-                    github = "cahartin")),
-              person("Erin","McDuffie",
-                      email = "[email protected]",
-                      role = c("aut","ctb"),
-                      comment = c(ORCID = "0000-0002-6845-6077",
-                                  github = "emcduffie")),
-              person("Karen","Noiva",
-                      role = c("aut","ctb"),
-                      comment = c(github = "knoiva-indecon")),
-              person("Will","Maddock",
-                      role = "ctb",
-                      comment = c(github = "maddockw")),
-              person("Tony","Gardella",
-                      role = "ctb",
-                      comment = c(github = "tonygard-indecon"))
-              )
+                                github = "cahartin")),
+             person("Erin","McDuffie",
+                     email   = "[email protected]",
+                     role    = c("aut","ctb"),
+                     comment = c(ORCID = "0000-0002-6845-6077",
+                                 github = "emcduffie")),
+             person("Karen","Noiva",
+                     role    = c("aut","ctb"),
+                     comment = c(ORCID = "0000-0002-4412-5302", 
+                                 github = "knoiva-indecon")),
+             person("Will","Maddock",
+                     role    = "ctb",
+                     comment = c(ORCID = "0000-0002-6107-0315",
+                                 github = "maddockw")),
+             person("Tony","Gardella",
+                     role    = "ctb",
+                     comment = c(ORCID = "0000-0003-4380-3412",
+                                 github = "tonygard-indecon"))
+             )
 URL: https://usepa.github.io/FrEDI, https://epa.gov/cira/FrEDI/, https://github.com/USEPA/FrEDI/
 Description: This R package models damages and impacts from climate change in the contiguous United States (CONUS) 
     using the Framework for Evaluating Damages and Impacts (FrEDI) developed as part of the Climate Change Impacts and 
@@ -33,13 +36,11 @@ License: file LICENSE
 Encoding: UTF-8
 Depends: R (>= 3.5.0),
     tidyverse,
-    dplyr,
-    ggplot2,
-    tidyr,
+    ggpubr,
     openxlsx
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 LazyData: TRUE
-Suggests: knitr, rmarkdown, prettydoc
+Suggests: knitr, rmarkdown, prettydoc, devtools
 VignetteBuilder: knitr
 Language: en-US