From 946e9746d6b7d28d76f10cfe887b92ae15f6f297 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <kirill@cynkra.com>
Date: Thu, 27 Jun 2024 00:09:12 +0200
Subject: [PATCH] ci: Recent updates

---
 .github/workflows/R-CMD-check-dev.yaml        |   2 +-
 .github/workflows/R-CMD-check.yaml            | 106 ++++++------------
 .github/workflows/commit/action.yml           |   2 +-
 .github/workflows/install/action.yml          |  25 +++++
 .github/workflows/update-status/action.yml    |  34 ++++++
 .../workflows/versions-matrix-read/action.yml |  21 ++++
 .github/workflows/versions-matrix/action.R    |  34 ++++++
 .github/workflows/versions-matrix/action.yml  |   9 ++
 8 files changed, 159 insertions(+), 74 deletions(-)
 create mode 100644 .github/workflows/update-status/action.yml
 create mode 100644 .github/workflows/versions-matrix-read/action.yml
 create mode 100644 .github/workflows/versions-matrix/action.R
 create mode 100644 .github/workflows/versions-matrix/action.yml

diff --git a/.github/workflows/R-CMD-check-dev.yaml b/.github/workflows/R-CMD-check-dev.yaml
index 23c4a6b..9b00903 100644
--- a/.github/workflows/R-CMD-check-dev.yaml
+++ b/.github/workflows/R-CMD-check-dev.yaml
@@ -147,4 +147,4 @@ jobs:
 
       - uses: ./.github/workflows/check
         with:
-          results: ${{ matrix.package }}
+          results: ${{ matrix.package }}
\ No newline at end of file
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 921c120..baf5c56 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -56,6 +56,9 @@ jobs:
       - uses: ./.github/workflows/custom/after-install
         if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''
 
+      - uses: ./.github/workflows/versions-matrix
+        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
+
       - uses: ./.github/workflows/update-snapshots
         if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
 
@@ -117,91 +120,45 @@ jobs:
       - uses: ./.github/workflows/pkgdown-deploy
         if: github.event_name == 'push'
 
-  # Windows checks can be run in parallel and independently
-  # when they alone take as long as the smoke and full tests combined.
-  # To achieve this, remove the "needs:" element below.
-  rcc-windows:
-    # Begin custom: early run
-    needs: rcc-smoke
-    # End custom: early run
-
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.desc }}
-
-    # Begin custom: services
-    # End custom: services
+  versions-matrix:
+    runs-on: ubuntu-22.04
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
 
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
+    name: Collect versions
 
     steps:
       - uses: actions/checkout@v4
         with:
-          ref: ${{ needs.rcc-smoke.outputs.sha }}
-
-      - uses: ./.github/workflows/custom/before-install
-        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''
+          fetch-depth: 0
 
-      - uses: ./.github/workflows/install
+      - uses: ./.github/workflows/rate-limit
         with:
-          r-version: ${{ matrix.config.r }}
-          cache-version: rcc-windows-1
           token: ${{ secrets.GITHUB_TOKEN }}
-          needs: check
-
-      - uses: ./.github/workflows/custom/after-install
-        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''
 
-      - uses: ./.github/workflows/update-snapshots
-        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
-
-      - uses: ./.github/workflows/check
+      - uses: r-lib/actions/setup-r@v2
         with:
-          results: ${{ runner.os }}-r${{ matrix.config.r }}
+          install-r: false
+          use-public-rspm: true
+
+      - id: set-matrix
+        uses: ./.github/workflows/versions-matrix-read
 
   rcc-full:
-    needs: rcc-smoke
+    needs:
+      - rcc-smoke
+      - versions-matrix
 
-    runs-on: ${{ matrix.config.os }}
+    runs-on: ${{ matrix.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.desc }}
+    name: ${{ matrix.os }} (${{ matrix.r }}) ${{ matrix.desc }}
 
     # Begin custom: services
     # End custom: services
 
     strategy:
       fail-fast: false
-      matrix:
-        config:
-          - {os: macos-latest,   r: 'release'}
-
-          - {os: ubuntu-20.04,   r: 'release'}
-
-          # Use older ubuntu to maximise backward compatibility
-          - {os: ubuntu-22.04,   r: 'devel',     http-user-agent: 'release'}
-          - {os: ubuntu-22.04,   r: 'release',   covr: true,                  desc: 'with covr'}
-          - {os: ubuntu-22.04,   r: 'oldrel-1'}
-
-          # Begin custom: R 3.6
-          - {os: ubuntu-22.04,   r: 'oldrel-2'}
-          # End custom: R 3.6
-
-          # Begin custom: R 3.5
-          - {os: ubuntu-22.04,   r: 'oldrel-3'}
-          # End custom: R 3.5
-
-          # Begin custom: R 3.4
-          - {os: ubuntu-22.04,   r: 'oldrel-4'}
-          # End custom: R 3.4
-
-          # Begin custom: matrix elements
-          # End custom: matrix elements
+      matrix: ${{fromJson(needs.versions-matrix.outputs.matrix)}}
 
     steps:
       - uses: actions/checkout@v4
@@ -213,7 +170,7 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          r-version: ${{ matrix.config.r }}
+          r-version: ${{ matrix.r }}
           cache-version: rcc-full-1
           token: ${{ secrets.GITHUB_TOKEN }}
           needs: check
@@ -226,7 +183,12 @@ jobs:
 
       - uses: ./.github/workflows/check
         with:
-          results: ${{ runner.os }}-r${{ matrix.config.r }}
+          results: ${{ runner.os }}-r${{ matrix.r }}
+
+      - uses: ./.github/workflows/update-status
+        if: always()
+        with:
+          sha: ${{ needs.rcc-smoke.outputs.sha }}
 
   suggests-matrix:
     runs-on: ubuntu-22.04
@@ -252,13 +214,13 @@ jobs:
       - id: set-matrix
         uses: ./.github/workflows/dep-matrix-suggests
 
-  check-matrix:
+  check-suggests-matrix:
     runs-on: ubuntu-22.04
     needs: suggests-matrix
 
-    name: Check deps
+    name: Check suggests deps
 
-    if: ${{ needs.matrix.outputs.matrix != '' }}
+    if: ${{ needs.suggests-matrix.outputs.matrix != '' }}
 
     steps:
       - name: Install json2yaml
@@ -267,15 +229,15 @@ jobs:
 
       - name: Check matrix definition
         run: |
-          matrix='${{ needs.matrix.outputs.matrix }}'
+          matrix='${{ needs.suggests-matrix.outputs.matrix }}'
           echo $matrix
           echo $matrix | jq .
           echo $matrix | json2yaml
 
   rcc-suggests:
     needs:
-      - suggests-matrix
       - rcc-smoke
+      - suggests-matrix
 
     runs-on: ubuntu-22.04
 
diff --git a/.github/workflows/commit/action.yml b/.github/workflows/commit/action.yml
index 89be422..bd375d3 100644
--- a/.github/workflows/commit/action.yml
+++ b/.github/workflows/commit/action.yml
@@ -22,7 +22,7 @@ runs:
             git stash pop
           fi
           git add .
-          git commit -m "Auto-update from GitHub Actions"$'\n'$'\n'"Run: ${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
+          git commit -m "chore: Auto-update from GitHub Actions"$'\n'$'\n'"Run: ${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}"
           git push -u origin HEAD
           echo sha=$(git rev-parse HEAD) >> $GITHUB_OUTPUT
         fi
diff --git a/.github/workflows/install/action.yml b/.github/workflows/install/action.yml
index cf83bdb..449cd8c 100644
--- a/.github/workflows/install/action.yml
+++ b/.github/workflows/install/action.yml
@@ -39,12 +39,32 @@ runs:
         echo "_R_CHECK_FUTURE_FILE_TIMESTAMPS_=false" | tee -a $GITHUB_ENV
         # prevent rgl issues because no X11 display is available
         echo "RGL_USE_NULL=true" | tee -a $GITHUB_ENV
+        # from https://github.com/r-devel/r-dev-web/blob/main/CRAN/QA/Kurt/lib/R/Scripts/check_CRAN_incoming.R
+        echo "_R_CHECK_CRAN_INCOMING_CHECK_FILE_URIS_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_PACKAGE_DEPENDS_IGNORE_MISSING_ENHANCES_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_BASHISMS_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CODE_CLASS_IS_STRING_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CODOC_VARIABLES_IN_USAGES_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CONNECTIONS_LEFT_OPEN_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_DATALIST_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_NEWS_IN_PLAIN_TEXT_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_PACKAGES_USED_CRAN_INCOMING_NOTES_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_RD_CONTENTS_KEYWORDS_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_R_DEPENDS_=warn" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_S3_METHODS_SHOW_POSSIBLE_ISSUES_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_THINGS_IN_TEMP_DIR_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_UNDOC_USE_ALL_NAMES_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_URLS_SHOW_301_STATUS_=true" | tee -a $GITHUB_ENV
+        echo "_R_CXX_USE_NO_REMAP_=true" | tee -a $GITHUB_ENV
       shell: bash
 
     - name: Update apt
       if: runner.os == 'Linux'
       run: |
         sudo apt-get update
+        sudo apt-get install -y aspell
+        echo "_R_CHECK_CRAN_INCOMING_USE_ASPELL_=true" | tee -a $GITHUB_ENV
       shell: bash
 
     - uses: r-lib/actions/setup-pandoc@v2
@@ -115,3 +135,8 @@ runs:
         git rm -rf .ccache || true
         rm -rf .ccache
       shell: bash
+
+    - name: Show R CMD config --all
+      run: |
+        R CMD config --all
+      shell: bash
diff --git a/.github/workflows/update-status/action.yml b/.github/workflows/update-status/action.yml
new file mode 100644
index 0000000..1c66320
--- /dev/null
+++ b/.github/workflows/update-status/action.yml
@@ -0,0 +1,34 @@
+name: 'Update status'
+description: 'Update status'
+inputs:
+  sha:
+    description: 'SHA to update'
+    required: true
+  state:
+    description: 'state to update'
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    # It's difficult to get the URL of the current job.
+    # The /jobs API and/or the `github` context are misaligned.
+    # The duckdbneo repository contains several failed attempts.
+    - run: |
+        set -x
+        if [ -n '${{ inputs.sha }}' ]; then
+          export GH_TOKEN=${{ github.token }}
+
+          html_url=$(gh api \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/${{ github.repository }}/actions/runs/${{ github.run_id }} | jq -r .html_url)
+
+          gh api \
+            --method POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            /repos/${{ github.repository }}/statuses/${{ inputs.sha }} \
+            -f "state=${{ job.status }}" -f "target_url=$html_url" -f "description=${{ github.workflow }} / ${{ github.job }}" -f "context=actions-sync"
+        fi
+      shell: bash
diff --git a/.github/workflows/versions-matrix-read/action.yml b/.github/workflows/versions-matrix-read/action.yml
new file mode 100644
index 0000000..3e20f1d
--- /dev/null
+++ b/.github/workflows/versions-matrix-read/action.yml
@@ -0,0 +1,21 @@
+name: "Actions to read a matrix with all R and OS versions, computed with the versions-matrix action"
+outputs:
+  matrix:
+    description: "Generated matrix"
+    value: ${{ steps.set-matrix.outputs.matrix }}
+
+runs:
+  using: "composite"
+  steps:
+    - name: Install json2yaml
+      run: |
+        sudo npm install -g json2yaml
+      shell: bash
+
+    - id: set-matrix
+      run: |
+        matrix=$(cat .github/versions-matrix.json || echo '{"include":[]}')
+        echo $matrix | jq .
+        echo $matrix | json2yaml
+        echo "matrix=$matrix" | tee -a $GITHUB_OUTPUT
+      shell: bash
diff --git a/.github/workflows/versions-matrix/action.R b/.github/workflows/versions-matrix/action.R
new file mode 100644
index 0000000..bbcc71a
--- /dev/null
+++ b/.github/workflows/versions-matrix/action.R
@@ -0,0 +1,34 @@
+# FIXME: Dynamic lookup by parsing https://svn.r-project.org/R/tags/
+r_versions <- c("devel", paste0("4.", 4:0))
+macos <- data.frame(os = "macos-latest", r = r_versions[2:3])
+windows <- data.frame(os = "windows-latest", r = r_versions[1:3])
+linux_devel <- data.frame(os = "ubuntu-22.04", r = r_versions[1], `http-user-agent` = "release", check.names = FALSE)
+linux <- data.frame(os = "ubuntu-22.04", r = r_versions[-1])
+covr <- data.frame(os = "ubuntu-22.04", r = r_versions[2], covr = "true", desc = "with covr")
+
+include_list <- list(macos, windows, linux_devel, linux, covr)
+print(include_list)
+
+filter <- read.dcf("DESCRIPTION")[1,]["Config/gha/filter"]
+if (!is.na(filter)) {
+  filter_expr <- parse(text = filter)[[1]]
+  subset_fun_expr <- bquote(function(x) subset(x, .(filter_expr)))
+  subset_fun <- eval(subset_fun_expr)
+  include_list <- lapply(include_list, subset_fun)
+  print(include_list)
+}
+
+to_json <- function(x) {
+  if (nrow(x) == 0) return(character())
+  parallel <- vector("list", length(x))
+  for (i in seq_along(x)) {
+    parallel[[i]] <- paste0('"', names(x)[[i]], '":"', x[[i]], '"')
+  }
+  paste0("{", do.call(paste, c(parallel, sep = ",")), "}")
+}
+
+configs <- unlist(lapply(include_list, to_json))
+json <- paste0('{"include":[', paste(configs, collapse = ","), ']}')
+
+writeLines(json, ".github/versions-matrix.json")
+writeLines(json)
diff --git a/.github/workflows/versions-matrix/action.yml b/.github/workflows/versions-matrix/action.yml
new file mode 100644
index 0000000..6ac164b
--- /dev/null
+++ b/.github/workflows/versions-matrix/action.yml
@@ -0,0 +1,9 @@
+name: "Actions to compute a matrix with all R and OS versions"
+
+runs:
+  using: "composite"
+  steps:
+    - id: set-matrix
+      run: |
+        Rscript ./.github/workflows/versions-matrix/action.R
+      shell: bash