rewrite get_regional_data so it uses Google when there is no country-specific class #406

.Rbuildignore

@@ -28,3 +28,5 @@ SMG.md
 ^inst/paper$
 ^inst/examples$
 ^\.devcontainer$
+^CRAN-SUBMISSION$
+^\.covrignore$

.covrignore

@@ -0,0 +1,25 @@
+R/Brazil.R
+R/Belgium.R
+R/Canada.R
+R/Colombia.R
+R/Covid19DataHub.R
+R/Cuba.R
+R/ECDC.R
+R/Estonia.R
+R/France.R
+R/Germany.R
+R/Google.R
+R/India.R
+R/Italy.R
+R/JHU.R
+R/JRC.R
+R/Lithuania.R
+R/Mexico.R
+R/Netherlands.R
+R/SouthAfrica.R
+R/Switzerland.R
+R/UK.R
+R/USA.R
+R/WHO.R
+R/test-DataClass.R
+R/get_linelist.R

.devcontainer/devcontainer.json

@@ -2,12 +2,7 @@
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r
 {
 	"name": "covidregionaldata",
-	"build": {
-		"dockerfile": "Dockerfile",
-		// Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0
-		"args": { "VARIANT": "latest" },
-		"context": ".."
-	},
+	"image": "ghcr.io/epiforecasts/covidregionaldata:master",
 
 	// Set *default* container specific settings.json values on container create.
 	"settings": {
@@ -26,7 +21,8 @@
 		"shan.code-settings-sync",
 		"searking.preview-vscode",
 		"tht13.html-preview-vscode",
-		"formulahendry.code-runner"
+		"formulahendry.code-runner",
+		"github.vscode-pull-request-github"
 	],
 
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.

.github/workflows/Belgium.yaml

@@ -7,34 +7,17 @@ name: Belgium
 
 jobs:
   Belgium:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Brazil.yaml

@@ -7,34 +7,17 @@ name: Brazil
 
 jobs:
   Brazil:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Canada.yaml

@@ -7,34 +7,18 @@ name: Canada
 
 jobs:
   Canada:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: actions/checkout@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Colombia.yaml

@@ -7,34 +7,17 @@ name: Colombia
 
 jobs:
   Colombia:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Covid19DataHub.yaml

@@ -7,34 +7,17 @@ name: Covid19DataHub
 
 jobs:
   Covid19DataHub:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Cuba.yaml

@@ -7,34 +7,17 @@ name: Cuba
 
 jobs:
   Cuba:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/ECDC.yaml

@@ -7,34 +7,17 @@ name: ECDC
 
 jobs:
   ECDC:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .

.github/workflows/Estonia.yaml

@@ -7,34 +7,17 @@ name: Estonia
 
 jobs:
   Estonia:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("devtools")
-        shell: Rscript {0}
+          extra-packages: devtools
 
       - name: Install package
         run: R CMD INSTALL .