really use language: r

Author: lorenzwalthert

.Rbuildignore

@@ -1,19 +1,19 @@
-^README\.Rmd$
 ^.*\.Rproj$
-^\.Rproj\.user$
-^LICENSE\.md$
+^\.github$
+^\.pre-commit-config\.yaml$
 ^\.pre-commit-hooks\.yaml$
-^\.travis\.yml$
+^\.Rproj\.user$
+^API$
 ^CONTRIBUTING\.md$
-^appveyor\.yml$
-^tic\.R$
-^_pkgdown\.yml$
+^cran-comments\.md$
 ^docs$
-^pkgdown$
-^\.pre-commit-config\.yaml$
-^API$
-^inst/consistent-release-tag$
+^inst/hooks/local$
+^inst/renv-update\.R$
 ^inst/WORDLIST$
-^inst/hooks-config-to-inst$
-^cran-comments\.md$
-^\.github$
+^LICENSE\.md$
+^pkgdown$
+^_pkgdown\.yml$
+^README\.Rmd$
+^renv$
+^renv\.lock$
+^scratch$

.github/workflows/R-CMD-check.yaml

@@ -7,10 +7,11 @@
 on:
   push:
     branches:
-      - master
+      - '*'
   pull_request:
     branches:
       - master
+      - main
 
 name: R-CMD-check
 
@@ -34,11 +35,6 @@ jobs:
           # Linux
           - {os: ubuntu-18.04,   r: 'release', installation_method: 'pip', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
           - {os: ubuntu-18.04,   r: 'release', installation_method: 'conda', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-#          - {os: ubuntu-16.04,   r: 'devel', installation_method: 'conda', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-#          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-#          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-#          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-#          - {os: ubuntu-16.04,   r: '3.3',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -49,12 +45,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         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
         run: |
@@ -63,20 +59,20 @@ jobs:
           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@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-
+
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'
         run: |
           while read -r cmd
           do
             eval sudo $cmd
-          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
 
       - name: Install system dependencies (brew)
         if: matrix.config.installation_method == 'brew'
@@ -111,6 +107,7 @@ jobs:
         env:
           _R_CHECK_CRAN_INCOMING_: false
         run: |
+          options(crayon.enabled = TRUE)
           if (Sys.getenv("PRECOMMIT_INSTALLATION_METHOD") != 'conda') {
             Sys.setenv("_R_CHECK_FORCE_SUGGESTS_" = "False")
           }
@@ -129,3 +126,8 @@ jobs:
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
+
+      - name: Don't use tar from old Rtools to store the cache
+        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
+        shell: bash
+        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH

.github/workflows/end-to-end.yml

@@ -1,7 +1,7 @@
 on:
   push:
     branches:
-      - master
+      - '*'
   pull_request:
     branches:
       - master

.github/workflows/hook-dependencies-upate.yml

@@ -0,0 +1,81 @@
+on:
+  schedule:
+    - cron:  '50 08 18 * *'
+  push:
+    branches:
+      - '*' 
+
+name: Hook dependency updates
+
+jobs:
+  hook-dependencies-update:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RENV_PATHS_ROOT: ~/.local/share/renv
+      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+      
+      - name: Cache packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: renv-${{ hashFiles('**/renv.lock') }}
+          restore-keys: |
+            renv-
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "install.packages('remotes'); remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+      - name: update existing packages
+        run: |
+          install.packages('renv')
+          install.packages('jsonlite')
+          renv_deps <- names(jsonlite::read_json('renv.lock')$Packages)
+          renv::load()
+          renv::restore()
+          can_be_updated <- renv::update(renv_deps)
+          renv::snapshot(packages = renv_deps)
+        shell: Rscript {0}
+      - name: update dependency graph among packages
+        run: |
+          # also see corresponding files to update
+          hook_deps <- function(root) {
+            out <- renv::dependencies("inst/hooks/exported/")$Package
+            desc <- desc::desc()
+            deps <- desc$get_deps()
+            dont <- c(
+              "yaml", "usethis", "withr", "rstudioapi", "precommit",
+              "httr" # lintr -> httr  -> curl -> libcurl, but seems to give no erorr on
+              # loading lintr, plus https://github.com/jimhester/lintr/issues/861
+            )
+            out <- c(out, "roxygen2", "spelling", "styler", "pkgload", "lintr", "knitr", "git2r", "digest", "desc")
+            out <- setdiff(c(unique(c(out, deps[deps$type == "Imports", ]$package))), dont)
+            out <- names(renv:::renv_package_dependencies(out))
+            return(out)
+          }
+          
+          options(renv.snapshot.filter = hook_deps)
+          
+          renv::snapshot(type = "custom", prompt = FALSE)
+          # or renv::snapshot(packages = hook_deps(), prompt = FALSE)
+        shell: Rscript {0}
+      - name: Create Pull Request
+        uses: peter-evans/[email protected]
+        with:
+          commit-message: Update renv dependencies
+          branch: hook-dependencies-update
+          delete-branch: true
+          assignees: lorenzwalthert
+          title: 'Hook dependencies update'
+          body: |
+            This PR updates the hook dependencies in `renv.lock`, auto-generated by [create-pull-request][1]. Close and re-open this to trigger `on: pull_request` events to circumvent [limitation of GitHub actions](https://github.com/peter-evans/create-pull-request/blob/master/docs/concepts-guidelines.md#push-pull-request-branches-to-a-fork).
+
+            [1]: https://github.com/peter-evans/create-pull-request

.github/workflows/hook-tests-legacy.yml

@@ -0,0 +1,111 @@
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - master
+
+name: Legacy hook tests
+jobs:
+  hook-test:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+    env:
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+      - name: checkout old hook scripts
+        run: |
+          git fetch origin refs/tags/v0.1.3:refs/tags/v0.1.3
+          git checkout v0.1.3 -- inst/bin
+          git checkout v0.1.3 -- tests/testthat/test-all.R  
+          git checkout v0.1.3 -- R/testing.R
+      - name: Query dependencies
+        run: |
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+      - name: Cache R packages (macOs)
+        if: startsWith(runner.os, 'macOS')
+        uses: actions/cache@v2
+        with:
+          path: ~/Library/Application Support/renv
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('renv.lock') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      - name: Cache R packages (Linux)
+        if: startsWith(runner.os, 'Linux')
+        uses: actions/cache@v2
+        with:
+          path: ~/.local/share/renv
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('renv.lock') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+      - name: Cache R packages (Windows)
+        if: startsWith(runner.os, 'Windows')
+        uses: actions/cache@v2
+        with:
+          path: ~\AppData\Local\renv
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('renv.lock') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies (Linux)
+        if: runner.os == 'Linux'
+        run: |
+          Rscript -e "install.packages('remotes', repos = Sys.getenv('RSPM'))"
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "18.04"), sep = "\n")')
+      - name: Perpare testing environment
+        run: |
+          # testing dependencies (incl. {precommit}) live in global R library, 
+          # hook dependencies in renv, which is only activated when child R
+          # process is invoked, e.g. as in run_test()
+          if (!requireNamespace("renv", quietly = TRUE)) {
+            install.packages("renv", repos = c(CRAN = "https://cloud.r-project.org"))
+          }
+          renv::install(c('testthat', 'devtools', 'desc', 'git2r'))
+          renv::install(desc::desc_get_deps()$package) # install all deps
+          renv::install(getwd()) 
+        shell: Rscript {0}
+      - name: Session info (testing environment)
+        run: |
+          renv::install('sessioninfo', repos = 'cloud.r-project.org')
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+      - name: Test
+        run: |
+          devtools::load_all()
+          testthat::test_file(
+            "tests/testthat/test-all.R",
+            reporter = testthat::MultiReporter$new(list(
+              testthat::CheckReporter$new(), testthat::FailReporter$new()
+            ))
+          )
+        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
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check