Merge branch 'main' into poc

Rapporteket · Jan 23, 2025 · bee3964 · bee3964
2 parents 9e5f05b + 79ae9c4
commit bee3964
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diff --git a/.github/.gitignore b/.github/.gitignore
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -10,6 +10,10 @@ on:
 
 name: R-CMD-check
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,16 +26,16 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-24.04, r: 'release'}
+          - {os: ubuntu-24.04, r: 'devel'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -53,50 +57,29 @@ jobs:
           else
             echo "GITHUB_ACTIONS_RUN_DB_UNIT_TESTS=false" >> $GITHUB_ENV
           fi
+
       - name: Set up MySQL, ubuntu only
         if: runner.os == 'Linux'
         run: |
           sudo /etc/init.d/mysql start
           mysql -e 'CREATE DATABASE IF NOT EXISTS testdb;' -uroot -proot
 
-      - 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
-        if: runner.os != 'Windows'
-        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 system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -9,15 +9,19 @@ on:
   schedule:
     - cron: '0 21 * * 6' # run every Saturday at 21
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   push_to_registries:
     name: Push Docker image to docker hub
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     env:
       IMAGE_NAME: ${{ github.repository }}
     steps:
       - name: Check out the repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: R setup
         uses: r-lib/actions/setup-r@v2
       - name: Build package (tarball)
@@ -28,11 +32,11 @@ jobs:
           dockerfile: "Dockerfile"
       - name: Prepare tags
         id: docker_meta
-        uses: docker/metadata-action@v3.6.2
+        uses: docker/metadata-action@v5
         with:
           images: ${{ env.IMAGE_NAME }}
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
       - name: Login to DockerHub
         if: github.event_name != 'pull_request'
         uses: docker/login-action@v1

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -8,37 +8,27 @@ on:
 
 name: lint
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   lint:
-    runs-on: macOS-latest
+    runs-on: ubuntu-24.04
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - 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)
-          remotes::install_cran("lintr")
-        shell: Rscript {0}
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: false
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -5,9 +5,13 @@ on:
 
 name: pkgdown
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-24.04
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
     steps:
@@ -17,25 +21,10 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@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: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
-        shell: Rscript {0}
+          extra-packages: any::pkgdown, local::.
+          needs: website
 
       - name: Install package
         run: R CMD INSTALL .

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,9 +8,13 @@ on:
 
 name: test-coverage
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   test-coverage:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       GITHUB_ACTIONS_RUN_DB_UNIT_TESTS: true
@@ -29,27 +33,11 @@ jobs:
           sudo /etc/init.d/mysql start
           mysql -e 'CREATE DATABASE IF NOT EXISTS testdb;' -uroot -proot
 
-      - 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)
-          remotes::install_cran("covr")
-        shell: Rscript {0}
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
         shell: Rscript {0}
diff --git a/NAMESPACE b/NAMESPACE
@@ -42,7 +42,6 @@ export(getProms)
 export(getPromsData)
 export(getPros)
 export(getProsData)
-export(getProsPatientData)
 export(getRand12)
 export(getRand12Data)
 export(indik_akuttsuksess)

diff --git a/R/getData.R b/R/getData.R
@@ -771,7 +771,6 @@ getBaseregPros <- function(registryName,
     d_mcepatientdata <- rapbase::loadRegData(registryName, query_mcepatientdata)
 
 
-    # nocov end
   } else {
     d_mce <- rapbase::loadRegData(registryName, query_mce)
     d_patientlist <- rapbase::loadRegData(registryName, query_patientlist)