ci: fix gha

kapsner · May 17, 2024 · f57d08d · f57d08d
1 parent 58d1f66
commit f57d08d
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Showing 8 changed files with 63 additions and 114 deletions.
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.community/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'
@@ -104,7 +95,6 @@ jobs:
           install.packages(c("remotes"))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
-          remotes::install_cran(c("ParBayesianOptimization", "mlr3measures"))
         shell: Rscript {0}
 
       - name: Test coverage

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:
@@ -64,36 +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.community/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/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.community/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/.github/workflows/update-tic.yml b/.github/workflows/update-tic.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mllrnrs
 Title: R6-Based ML Learners for 'mlexperiments'
-Version: 0.0.3.9007
+Version: 0.0.3.9008
 Authors@R: 
     person("Lorenz A.", "Kapsner", , "[email protected]", role = c("cre", "aut", "cph"),
            comment = c(ORCID = "0000-0003-1866-860X"))
@@ -40,7 +40,7 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Config/testthat/parallel: false
-Date/Publication: 2024-04-15 16:09:40.514639 UTC
+Date/Publication: 2024-05-17 12:29:20.149287 UTC
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
+
 # mllrnrs NEWS
 
-## Unreleased (2024-04-12)
+## Unreleased (2024-04-15)
 
 #### New features
 
@@ -26,7 +27,7 @@
     ([323f9cb](https://github.com/kapsner/mllrnrs/tree/323f9cb0dc0e38213154669dccff7a700f5071c2))
 
 Full set of changes:
-[`v0.0.3...1674811`](https://github.com/kapsner/mllrnrs/compare/v0.0.3...1674811)
+[`v0.0.3...58d1f66`](https://github.com/kapsner/mllrnrs/compare/v0.0.3...58d1f66)
 
 ## v0.0.3 (2024-03-07)
 
@@ -51,7 +52,7 @@ Full set of changes:
     ([09cde9d](https://github.com/kapsner/mllrnrs/tree/09cde9d8eb6e38310d405ce4f669eb6fb64a1b37))
 -   temporary fix for compatibility with lightgbm
     ([7a9ef30](https://github.com/kapsner/mllrnrs/tree/7a9ef307926c07ca6f2b33c2d93f4431d2a0a8c8))
--   adaptions to cat\_vars
+-   adaptions to cat_vars
     ([e9f0eff](https://github.com/kapsner/mllrnrs/tree/e9f0effbc2b1274f8f32a86c12b4a68ece9163de))
 
 #### Tests
@@ -61,7 +62,7 @@ Full set of changes:
 
 #### CI
 
--   moving to code\_step
+-   moving to code_step
     ([2e4d11a](https://github.com/kapsner/mllrnrs/tree/2e4d11a96f5f91f62e05772f77237ac384f7e130))
 -   update coverage installing packages
     ([a2aec56](https://github.com/kapsner/mllrnrs/tree/a2aec569a52d66c2ba9feb2c6ae825c1afb3be92))
@@ -157,7 +158,7 @@ Full set of changes:
 
 -   changed order of list to be updated
     ([066eb5a](https://github.com/kapsner/mllrnrs/tree/066eb5a05408e92025c570b58def13c29ed25bab))
--   to metric\_types\_helper from mlexperiments
+-   to metric_types_helper from mlexperiments
     ([1099f1a](https://github.com/kapsner/mllrnrs/tree/1099f1aac600c2cac41a789ca5bdfcc91f2f802b))
 -   code adaptions to upstream changes
     ([c5363fc](https://github.com/kapsner/mllrnrs/tree/c5363fc2be191343ef5ebfd3363a535e0ea5e458))

diff --git a/data-raw/devstuffs.R b/data-raw/devstuffs.R
@@ -19,7 +19,7 @@ my_desc$set_authors(c(
 # Remove some author fields
 my_desc$del("Maintainer")
 # Set the version
-my_desc$set_version("0.0.3.9007")
+my_desc$set_version("0.0.3.9008")
 # The title of your package
 my_desc$set(Title = "R6-Based ML Learners for 'mlexperiments'")
 # The description of your package

diff --git a/vignettes/mllrnrs_ranger_multiclass.Rmd b/vignettes/mllrnrs_ranger_multiclass.Rmd
@@ -502,7 +502,7 @@ perf_ranger
 
 ## Appendix I: Grid-Search with Target Weigths
 
-Here, `ranger`'s [`case.weights`-argument](hthttps://rdrr.io/cran/ranger/man/ranger.html) is used to rescale the case-weights during the training.
+Here, `ranger`'s [`case.weights`-argument](https://rdrr.io/cran/ranger/man/ranger.html) is used to rescale the case-weights during the training.
 
 ```{r}
 # define the target weights