Merge pull request #101 from mlr-org/update_workflows

Update workflows

Author: RaphaelS1

.github/workflows/rcmdcheck.yml

@@ -16,66 +16,87 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: "release" }
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Query dependencies
+      - name: Install pak and 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")
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v1
+      - name: Restore R package cache
+        uses: actions/cache@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-
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
       - name: Install system dependencies
+        if: runner.os == 'Linux'
         run: |
-          set -x
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
+        shell: Rscript {0}
 
       - name: Install dependencies
         run: |
-          install.packages(c("remotes"))
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install CatBoost
+        run: |
+          install.packages("remotes")
+          remotes::install_url('https://github.com/catboost/catboost/releases/download/v0.24.1/catboost-R-Linux-0.24.1.tgz', INSTALL_opts = c("--no-multiarch"))
         shell: Rscript {0}
 
       - name: Install Python
         run: |
-          remotes::install_github('rstudio/reticulate')
+          pak::pkg_install('rstudio/reticulate')
           reticulate::install_miniconda()
-          remotes::install_local()
           install.packages('keras')
           keras::install_keras(tensorflow = '2.0.1', extra_packages = c('IPython', 'requests', 'certifi', 'urllib3', 'tensorflow-hub', 'tabnet==0.1.4.1'))
           reticulate::py_install(c('torch', 'pycox'), pip = TRUE)
         shell: Rscript {0}
 
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

.github/workflows/test_C50.yml

@@ -1,70 +1,96 @@
 on:
-  push:
-    branches: main
-    paths: '**/C50**'
   pull_request:
     branches: main
     paths: '**/C50**'
-  schedule:
-    - cron: "0 4 * * *"
 
 name: C50 (ubuntu-latest, release)
 
 jobs:
-  all:
+  R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.env.TEST }} Test
+    name: ${{ matrix.env.test }} Test
 
     strategy:
+      fail-fast: false
       matrix:
         env:
           - { test: "Learner"}
           - { test: "Param"}
         config:
-          - { os: ubuntu-latest, r: "release" }       
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       PKG: C50
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RGL_USE_NULL: true
-      TEST: ${{ matrix.env.test }}
-      
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2.2.0
+      - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
-          Ncpus: 4
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-tinytex@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = FALSE), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ env.PKG }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ env.PKG }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
-      - name: "[Stage] Prepare"
-        if: runner.os == 'Linux'
+      - name: Install system dependencies
         run: |
-          sudo R CMD javareconf
-          sudo apt install ccache libcurl4-openssl-dev libgit2-dev
-          mkdir -p ~/.R && echo -e 'CXX_STD = CXX14\n\nCC=ccache gcc -std=gnu99\nCXX=ccache g++\nCXX11=ccache g++ -std=gnu99\nCXX14=ccache g++ -std=gnu99\nC11=ccache g++\nC14=ccache g++\nFC=ccache gfortran\nF77=ccache gfortran' > $HOME/.R/Makevars
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("testthat", execute = TRUE)
+        shell: Rscript {0}
 
-      - name: "[Custom block] [Stage] [Linux] Install pkgdown system lib req"
-        if: runner.os == 'Linux'
-        run: sudo apt install libharfbuzz-dev libfribidi-dev
+      - name: Install package dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE, dependencies = FALSE)
+          pak::pkg_install("testthat")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          sessionInfo()
+        shell: Rscript {0}
+
+      - name: Install
+        run: |
+          pak::local_install()
+        shell: Rscript {0}
 
-      - name: "[Stage] Install"
+      - name: Learner test
+        if: ${{ matrix.env.test == 'Learner' }}
         run: |
-          Rscript -e "install.packages('remotes', type = 'source')" -e "remotes::install_github('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+          options(crayon.enabled = TRUE)
+          testthat::test_local(filter = sprintf("%s_", "${{ env.PKG }}"))
+        shell: Rscript {0}
 
-      - name: "[Stage] Script"
+      - name: Parameter test
+        if: ${{ matrix.env.test == 'Param' }}
         run: |
-          R CMD INSTALL .
-          Rscript -e "tic::script()"
+          options(crayon.enabled = TRUE)
+          testthat::test_dir(system.file("paramtest", package = "mlr3extralearners"), filter = sprintf("_%s_", "${{ env.PKG }}"))
+        shell: Rscript {0}
 
-      - name: "[Stage] Upload R CMD check artifacts"
+      - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-r${{ matrix.env.PKG }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-${{ env.PKG }}-results
           path: check

.github/workflows/test_CoxBoost.yml

@@ -1,70 +1,98 @@
 on:
-  push:
-    branches: main
-    paths: '**/CoxBoost**'
   pull_request:
     branches: main
     paths: '**/CoxBoost**'
-  schedule:
-    - cron: "0 4 * * *"
 
 name: CoxBoost (ubuntu-latest, release)
 
 jobs:
-  all:
+  R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.env.TEST }} Test
+    name: ${{ matrix.env.test }} Test
 
     strategy:
+      fail-fast: false
       matrix:
         env:
           - { test: "Learner"}
           - { test: "Param"}
         config:
-          - { os: ubuntu-latest, r: "release" }       
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       PKG: CoxBoost
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RGL_USE_NULL: true
-      TEST: ${{ matrix.env.test }}
-      
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
-      - uses: actions/checkout@v2.2.0
+      - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
-          Ncpus: 4
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
-      - uses: r-lib/actions/setup-tinytex@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = FALSE), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ${{ matrix.config.os }}-${{ env.PKG }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ matrix.config.os }}-${{ env.PKG }}-${{ steps.install-r.outputs.installed-r-version }}-1-
 
-      - name: "[Stage] Prepare"
-        if: runner.os == 'Linux'
+      - name: Install system dependencies
         run: |
-          sudo R CMD javareconf
-          sudo apt install ccache libcurl4-openssl-dev libgit2-dev
-          mkdir -p ~/.R && echo -e 'CXX_STD = CXX14\n\nCC=ccache gcc -std=gnu99\nCXX=ccache g++\nCXX11=ccache g++ -std=gnu99\nCXX14=ccache g++ -std=gnu99\nC11=ccache g++\nC14=ccache g++\nFC=ccache gfortran\nF77=ccache gfortran' > $HOME/.R/Makevars
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("testthat", execute = TRUE)
+          pak::pkg_system_requirements("remotes", execute = TRUE)
+        shell: Rscript {0}
 
-      - name: "[Custom block] [Stage] [Linux] Install pkgdown system lib req"
-        if: runner.os == 'Linux'
-        run: sudo apt install libharfbuzz-dev libfribidi-dev
+      - name: Install package dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE, dependencies = FALSE)
+          pak::pkg_install("testthat")
+          pak::pkg_install("remotes")
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          sessionInfo()
+        shell: Rscript {0}
+
+      - name: Install
+        run: |
+          pak::local_install()
+        shell: Rscript {0}
 
-      - name: "[Stage] Install"
+      - name: Learner test
+        if: ${{ matrix.env.test == 'Learner' }}
         run: |
-          Rscript -e "install.packages('remotes', type = 'source')" -e "remotes::install_github('ropensci/tic')" -e "print(tic::dsl_load())" -e "tic::prepare_all_stages()" -e "tic::before_install()" -e "tic::install()"
+          options(crayon.enabled = TRUE)
+          testthat::test_local(filter = sprintf("%s_", "${{ env.PKG }}"))
+        shell: Rscript {0}
 
-      - name: "[Stage] Script"
+      - name: Parameter test
+        if: ${{ matrix.env.test == 'Param' }}
         run: |
-          R CMD INSTALL .
-          Rscript -e "tic::script()"
+          options(crayon.enabled = TRUE)
+          testthat::test_dir(system.file("paramtest", package = "mlr3extralearners"), filter = sprintf("_%s_", "${{ env.PKG }}"))
+        shell: Rscript {0}
 
-      - name: "[Stage] Upload R CMD check artifacts"
+      - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-r${{ matrix.env.PKG }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-${{ env.PKG }}-results
           path: check