Merge branch 'main' into replace-devtools-with-pak

walkowif · walkowif · commit 21e7a4741502 · 2024-06-26T16:03:00.000+02:00
diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
@@ -694,9 +694,12 @@ jobs:
         if: inputs.skip-r-cmd-check != true
         run: |
           find ${{ env.PKGNAME }}.Rcheck -type f -regextype posix-egrep \
-            -regex '.*00install.out|.*00check.log|.*00build.out' -print0 | while IFS= read -r -d $'\0' file; do
-            printf "==================================\n$file\n==================================\n"
-            cat $file
+            -regex '.*00install.out|.*00check.log|.*00build.out|.*-Ex.Rout|.*tests/testthat\.Rout.*' \
+            -print0 | while IFS= read -r -d $'\0' file; do
+              # Grouping allows to collapse/expand logs when needed.
+              echo "::group::$file"
+              cat $file
+              echo "::endgroup::"
           done
         shell: bash
 
@@ -782,6 +785,18 @@ jobs:
           path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/${{ env.PKGBUILD }}
           name: ${{ env.PKGBUILD }}
 
+      - name: Upload logs artifact 🗞️
+        uses: actions/upload-artifact@v4
+        with:
+          path: |
+            ${{ env.PKGNAME }}.Rcheck/*00install.out
+            ${{ env.PKGNAME }}.Rcheck/*00check.log
+            ${{ env.PKGNAME }}.Rcheck/*00build.out
+            ${{ env.PKGNAME }}.Rcheck/*-Ex.Rout
+            ${{ env.PKGNAME }}.Rcheck/tests/testthat.Rout
+            ${{ env.PKGNAME }}.Rcheck/tests/testthat.Rout.fail
+          name: check-logs-${{ env.PKGNAME }}-${{ inputs.concurrency-group }}
+
   publish-junit-html-report:
     name: Publish JUnit HTML report 📰
     runs-on: ubuntu-latest
@@ -813,7 +828,7 @@ jobs:
 
       - name: Upload JUnit HTML report to GitHub pages 🗞️
         if: needs.build-install-check.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
@@ -823,7 +838,7 @@ jobs:
         if: >
           needs.build-install-check.outputs.is-latest-tag == 'true'
             && needs.build-install-check.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
@@ -833,15 +848,15 @@ jobs:
         if: >
           needs.build-install-check.outputs.is-rc-tag == 'true'
             && needs.build-install-check.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
           destination_dir: ${{ inputs.release-candidate-alt-name }}/unit-test-report
 
       - name: Upload JUnit HTML report to GitHub pages (non-multiversion) 🗞️
         if: needs.build-install-check.outputs.multiversion-docs == 'false'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
diff --git a/.github/workflows/links.yaml b/.github/workflows/links.yaml
@@ -16,11 +16,29 @@ on:
   workflow_dispatch:
   workflow_call:
     inputs:
-      additional_args:
+      lychee-additional-args:
         description: Additional arguments to pass to lychee
         required: false
         type: string
+        default: "--exclude-private"
+      lychee-fail:
+        description: Fail workflow run on error (i.e. when lychee exit code is not 0)
+        required: false
+        type: boolean
+        default: false
+      package-subdirectory:
+        description: Subdirectory in the repository, where the R package is located.
+        required: false
+        type: string
         default: ""
+      link-checking-method:
+        description: |
+          Which link checking method should be used? Supported methods are:
+          lychee
+          urlchecker
+        required: false
+        type: string
+        default: "urlchecker"
 
 concurrency:
   group: links-${{ github.event.pull_request.number || github.ref }}
@@ -33,6 +51,7 @@ jobs:
     if: >
       !contains(github.event.commits[0].message, '[skip links]')
         && github.event.pull_request.draft == false
+        && inputs.link-checking-method == 'lychee'
     steps:
       - name: Get branch names 🌿
         id: branch-name
@@ -65,18 +84,69 @@ jobs:
           SKIP_INSTRUCTION: "[skip links]"
 
       - name: Check URLs in docs 🔬
-        uses: lycheeverse/lychee-action@v1.8.0
+        uses: lycheeverse/lychee-action@v1.10.0
         with:
           args: >-
-            --exclude-private
             --exclude "https://github.com.*.git|https://insightsengineering.github.io.*|lewagon.*|knightdave.*|.*users.noreply.github.com|lycheeverse.*"
             --verbose
             --no-progress
-            ${{ inputs.additional_args }}
+            ${{ inputs.lychee-additional-args }}
             **/*.md
             **/*.html
             **/*.Rmd
             **/*.yaml
             **/*.yml
+            *.md
+          fail: ${{ inputs.lychee-fail }}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  urlchecker:
+    name: URL Checker 🔎
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/tidyverse:latest
+    if: >
+      !contains(github.event.commits[0].message, '[skip links]')
+        && github.event.pull_request.draft == false
+        && inputs.link-checking-method == 'urlchecker'
+    steps:
+      - name: Get branch names 🌿
+        id: branch-name
+        uses: tj-actions/branch-names@v7
+
+      - name: Checkout repo (PR) 🛎
+        uses: actions/checkout@v4.1.1
+        if: github.event_name == 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v4.1.1
+        if: github.event_name != 'pull_request'
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+
+      - name: Check commit message 💬
+        run: |
+          git config --global --add safe.directory $(pwd)
+          export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')"
+          echo "head_commit_message = $head_commit_message"
+          if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then
+            echo "Skip instruction detected - cancelling the workflow."
+            exit 1
+          fi
+        shell: bash
+        env:
+          SKIP_INSTRUCTION: "[skip links]"
+
+      - name: Check URLs with urlchecker 🔬
+        run: |
+          # For unexplained reasons, parallel = FALSE is required to prevent some false positives.
+          bad_urls <- nrow(print(urlchecker::url_check(".", parallel = FALSE)))
+          if (bad_urls > 0) {
+            stop("Looks like a total of ", bad_urls, " URL(s) were found! Please correct them.")
+          }
+        shell: Rscript {0}
+        working-directory: ${{ inputs.package-subdirectory }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -419,7 +419,7 @@ jobs:
 
       - name: Upload coverage report to GitHub pages 🗞️
         if: needs.coverage.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./coverage-report
@@ -429,7 +429,7 @@ jobs:
         if: >
           needs.coverage.outputs.is-latest-tag == 'true'
             && needs.coverage.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./coverage-report
@@ -439,15 +439,15 @@ jobs:
         if: >
           needs.coverage.outputs.is-rc-tag == 'true'
             && needs.coverage.outputs.multiversion-docs == 'true'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./coverage-report
           destination_dir: ${{ inputs.release-candidate-alt-name }}/coverage-report
 
       - name: Upload coverage report to GitHub pages (non-multiversion) 🗞️
         if: needs.coverage.outputs.multiversion-docs == 'false'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./coverage-report
diff --git a/.github/workflows/verdepcheck.yaml b/.github/workflows/verdepcheck.yaml
@@ -28,6 +28,14 @@ on:
           Strategy to test package dependencies. One of: min_isolate, min_cohort, release, max.
         required: true
         type: string
+      extra-deps:
+        description: |
+          Extra dependencies specified similarly as in the `DESCRIPTION` file,
+          i.e. `"<package name> (<operator> <version>)"` where both `<operator>`
+          and `<version>` are optional. Multiple entries are possible separated by `";"`.
+        required: false
+        default: ""
+        type: string
       additional-env-vars:
         description: |
           Extra environment variables, as a 'key=value' pair, with each pair on a new line.
@@ -104,10 +112,11 @@ jobs:
         uses: insightsengineering/r-verdepcheck-action@main
         with:
           github-token: ${{ steps.github-token.outputs.token }}
-          check-args: ${{ inputs.check-args }}
+          extra-deps: ${{ inputs.extra-deps }}
           build-args: ${{ inputs.build-args }}
-          additional-env-vars:  ${{ inputs.additional-env-vars }}
+          check-args: ${{ inputs.check-args }}
           strategy: ${{ env.strategy }}
+          additional-env-vars: ${{ inputs.additional-env-vars }}
 
       - name: GChat notification 🔔
         if: (failure() || cancelled()) && steps.verdepcheck.outcome != 'success' && env.gchat_webhook != ''
diff --git a/.github/workflows/wasm.yaml b/.github/workflows/wasm.yaml
@@ -0,0 +1,76 @@
+---
+name: WASM 🧭
+
+on:
+  workflow_call:
+    inputs:
+      package-subdirectory:
+        description: Subdirectory in the repository, where the R package is located.
+        required: false
+        type: string
+        default: ""
+
+jobs:
+  wasm:
+    name: WASM 🧭
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Get branch names 🌿
+        id: branch-name
+        uses: tj-actions/branch-names@v7
+
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v4.1.1
+        with:
+          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
+          path: ${{ github.event.repository.name }}
+
+      - name: Get package name 📦
+        run: |
+          echo "PKGNAME=$(echo $(awk -F: '/Package:/{gsub(/[ ]+/,"") ; print $2}' DESCRIPTION))" >> $GITHUB_ENV
+        shell: bash
+        working-directory: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
+
+      - name: Build WASM packages 🧭
+        uses: r-wasm/actions/build-rwasm@v1
+        with:
+          packages: |
+            ${{ github.repository_owner }}/${{ env.PKGNAME }}@${{ steps.branch-name.outputs.tag }}
+
+      - name: Upload WASM packages ⬆
+        uses: actions/upload-artifact@v4
+        with:
+          name: wasm-${{ env.PKGNAME }}
+          path: |
+            _site/bin/emscripten/contrib/*/${{ env.PKGNAME }}*.tgz
+            _site/src/contrib/${{ env.PKGNAME }}*.tar.gz
+
+      - name: Check if release exists ⚙️
+        id: check-if-release-exists
+        uses: insightsengineering/release-existence-action@v1
+
+      - name: Download artifact ⏬
+        if: >-
+          steps.check-if-release-exists.outputs.release-exists == 'true'
+        uses: actions/download-artifact@v4
+        with:
+          name: wasm-${{ env.PKGNAME }}
+          path: wasm-${{ env.PKGNAME }}
+
+      - name: Prepare WASM release artifact 🗜️
+        if: >-
+          steps.check-if-release-exists.outputs.release-exists == 'true'
+        run: |
+          zip -r9 wasm-${{ env.PKGNAME }}.zip wasm-${{ env.PKGNAME }}
+
+      - name: Upload WASM build to release 🔼
+        if: >-
+          steps.check-if-release-exists.outputs.release-exists == 'true'
+        uses: svenstaro/upload-release-action@v2
+        with:
+          file: ./wasm-${{ env.PKGNAME }}.zip
+          asset_name: wasm-${{ env.PKGNAME }}.zip
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref }}
+          overwrite: true
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -77,6 +77,6 @@ repos:
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
         # `exclude: <regex>` to allow committing specific files.
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.40.0
+    rev: v0.41.0
     hooks:
       - id: markdownlint
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: r.pkg.template
 Title: R Package Template
-Version: 0.1.0.9159
-Date: 2024-05-14
+Version: 0.1.0.9169
+Date: 2024-06-25
 Authors@R:
     person("insightsengineering", , , "insightsengineering@example.com", role = c("aut", "cre"))
 Description: R package template with GitHub Actions workflows included.
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# r.pkg.template 0.1.0.9159
+# r.pkg.template 0.1.0.9169
 
 ### New features
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# r.pkg.template 0.1.0.9159`
	`1`	`+# r.pkg.template 0.1.0.9169`
`2`	`2`
`3`	`3`	`### New features`
`4`	`4`