ci: fixing ci

miracum · May 16, 2024 · 8210403 · 8210403
1 parent 6a6793a
commit 8210403
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Showing 8 changed files with 106 additions and 99 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,3 +18,4 @@
 ^dqagui\.Rproj$
 ^man/figures$
 ^Rplots\.pdf$
+^\.Rproj\.user$
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -44,7 +44,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -64,36 +64,27 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.latex == 'true'
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v4
         if: matrix.config.java == 'true'
         with:
-          java-version: '8'
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Install sys deps for Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt update && sudo apt install -y libgit2-dev libcurl4-openssl-dev
 
-      # set date/week for use in cache creation
-      # https://github.saobby.my.eu.orgmunity/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
-      # - cache R packages daily
       - name: "[Cache] Prepare daily timestamp for cache"
         if: runner.os != 'Windows'
         id: date
-        run: echo "::set-output name=date::$(date '+%d-%m')"
+        run: echo "date=$(date '+%d-%m')" >> $GITHUB_OUTPUT
 
-      - name: "[Cache] Cache R packages"
+      - name: "[Cache] Restore R package cache"
         if: runner.os != 'Windows'
-        uses: pat-s/always-upload-cache@main
+        uses: actions/cache/restore@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
-
-      # for some strange Windows reason this step and the next one need to be decoupled
-      - name: "[Stage] Prepare"
-        run: |
-          Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
-          Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')"
-
-      - name: "[Stage] [Linux] Install curl"
-        if: runner.os == 'Linux'
-        run: sudo apt install libcurl4-openssl-dev
 
       - name: "[Stage] Configure R Java"
         if: runner.os != 'Windows' && matrix.config.java == 'true'

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -44,7 +44,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -64,41 +64,31 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.latex == 'true'
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v4
         if: matrix.config.java == 'true'
         with:
-          java-version: '8'
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Install sys deps for Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt update && sudo apt install -y libgit2-dev libcurl4-openssl-dev
 
-      # set date/week for use in cache creation
-      # https://github.saobby.my.eu.orgmunity/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
-      # - cache R packages daily
       - name: "[Cache] Prepare daily timestamp for cache"
         if: runner.os != 'Windows'
         id: date
-        run: echo "::set-output name=date::$(date '+%d-%m')"
+        run: echo "date=$(date '+%d-%m')" >> $GITHUB_OUTPUT
 
-      - name: "[Cache] Cache R packages"
+      - name: "[Cache] Restore R package cache"
         if: runner.os != 'Windows'
-        uses: pat-s/always-upload-cache@main
+        uses: actions/cache/restore@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
-
-      # for some strange Windows reason this step and the next one need to be decoupled
-      - name: "[Stage] Prepare"
-        run: |
-          Rscript -e "if (!requireNamespace('remotes')) install.packages('remotes', type = 'source')"
-          Rscript -e "if (getRversion() < '3.2' && !requireNamespace('curl')) install.packages('curl', type = 'source')"
-
-      - name: "[Stage] [Linux] Install curl"
-        if: runner.os == 'Linux'
-        run: sudo apt install libcurl4-openssl-dev
 
       - name: "[Stage] Configure R Java"
         if: runner.os != 'Windows' && matrix.config.java == 'true'
-        run: sudo R CMD javareconf
-
+        run: "echo export PATH=$PATH > reconf.sh; echo export JAVA_HOME=$JAVA_HOME >> reconf.sh; echo R CMD javareconf >> reconf.sh; sudo bash reconf.sh"
 
       - name: Install dependencies
         run: |

diff --git a/.github/workflows/tic.yml b/.github/workflows/tic.yml
@@ -38,7 +38,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -47,39 +47,58 @@ jobs:
 
       - uses: r-lib/actions/setup-tinytex@v2
         if: matrix.config.latex == 'true'
-        env:
-          # install full prebuilt version
-          TINYTEX_INSTALLER: TinyTeX
+      - run: tlmgr --version
+
+      - name: Install additional LaTeX packages
+        run: |
+          tlmgr update --self
+          tlmgr install babel-german
+          tlmgr list --only-installed
 
       - uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.latex == 'true'
 
-      - uses: actions/setup-java@v1
+      - uses: actions/setup-java@v4
         if: matrix.config.java == 'true'
         with:
-          java-version: 8
+          distribution: 'temurin'
+          java-version: '11'
+
+      - name: Install sys deps for Ubuntu
+        if: runner.os == 'Linux'
+        run: sudo apt update && sudo apt install -y libgit2-dev libcurl4-openssl-dev
 
       # set date/week for use in cache creation
       # https://github.saobby.my.eu.orgmunity/t5/GitHub-Actions/How-to-set-and-access-a-Workflow-variable/m-p/42970
       # - cache R packages daily
       - name: "[Cache] Prepare daily timestamp for cache"
         if: runner.os != 'Windows'
         id: date
-        run: echo "::set-output name=date::$(date '+%d-%m')"
+        run: echo "date=$(date '+%d-%m')" >> $GITHUB_OUTPUT
 
-      - name: "[Cache] Cache R packages"
+      - name: "[Cache] Restore R package cache"
         if: runner.os != 'Windows'
-        uses: pat-s/always-upload-cache@v3
+        uses: actions/cache/restore@v3
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
+
+      - name: "[Stage] Configure R Java"
+        if: runner.os != 'Windows' && matrix.config.java == 'true'
+        run: "echo export PATH=$PATH > reconf.sh; echo export JAVA_HOME=$JAVA_HOME >> reconf.sh; echo R CMD javareconf >> reconf.sh; sudo bash reconf.sh"
 
       - name: "[Stage] Install pak"
         run: Rscript -e "install.packages('pak', repos = 'https://r-lib.github.io/p/pak/stable')"
 
       - name: "[Stage] Install"
-        run: Rscript -e "if (grepl('Ubuntu', Sys.info()[['version']]) && !grepl('Under development', R.version[['status']])) {options(repos = c(CRAN = sprintf('https://packagemanager.rstudio.com/all/__linux__/%s/latest', system('lsb_release -cs', intern = TRUE))))}else{options(repos = c(CRAN = 'cloud.r-project.org'))}; pak::pkg_install('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+        run: Rscript -e "install.packages('tic', repos = c('https://ropensci.r-universe.dev', if (grepl('Ubuntu', Sys.info()[['version']])) {sprintf('https://packagemanager.rstudio.com/all/__linux__/%s/latest', system('lsb_release -cs', intern = TRUE))} else {'https://cloud.r-project.org'}))" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+
+      - name: "[Cache] Save R package cache"
+        if: runner.os != 'Windows' && always()
+        uses: actions/cache/save@v3
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{steps.date.outputs.date}}
 
       - name: "[Stage] Script"
         run: Rscript -e 'tic::script()'
@@ -89,7 +108,7 @@ jobs:
 
       - name: "[Stage] Upload R CMD check artifacts"
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

diff --git a/.gitignore b/.gitignore
@@ -35,3 +35,4 @@
 !/docker/app.R
 !/docker/shiny-server.conf
 !/docker/show-log.sh
+.Rproj.user
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DQAgui
 Title: Graphical User Interface for Data Quality Assessment
-Version: 0.2.3.9001
+Version: 0.2.3.9002
 Authors@R: c(
     person("Lorenz A.", "Kapsner", , "lorenz.kapsner@gmail.com", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0003-1866-860X")),
@@ -14,7 +14,7 @@ License: GPL-3
 URL: https://github.com/miracum/dqa-dqagui
 BugReports: https://github.com/miracum/dqa-dqagui/issues
 Encoding: UTF-8
-Date: 2023-08-30
+Date: 2024-05-16
 Imports: 
     data.table,
     daterangepicker,
@@ -37,3 +37,4 @@ Imports:
 Suggests: 
     lintr,
     testthat (>= 3.0.0)
+RoxygenNote: 7.3.1