Merge pull request #36 from TanguyBarthelemy/master

CRAN
InseeFrLab · May 15, 2024 · 26cd701 · 26cd701
2 parents 7646225 + 35646e0
commit 26cd701
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,17 +1,30 @@
-^Meta$
-^docs$
-^_pkgdown\.yml$
+
 ^.*\.Rproj$
 ^\.Rproj\.user$
+
+^\.git$
+^\.github$
+
 ^README\.Rmd$
 ^README-.*\.png$
-.travis.yml
-^pkgdown$
+
+^Meta$
+^docs$
 ^doc$
+^pkgdown$
+^_pkgdown\.yml$
+
+^\.lintr$
+
+^appveyor\.yml$
+.travis.yml
+
 cran-comments.md
-^\.github$
-^LICENCE$
-^LICENCE_en$
 
-TO_DO
-.lintr
+^\.DS_Store$
+
+^revdep$
+^reconf\.sh$
+
+^LICENCE$
+^LICENSE$
diff --git a/.github/workflows/R-CMD-check2.yaml b/.github/workflows/R-CMD-check2.yaml
@@ -0,0 +1,166 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_dispatch
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.os }}
+
+    name: ${{ matrix.os }} (${{ matrix.r }}) java ${{ matrix.java }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        # os: [ 'ubuntu-latest', 'windows-latest', 'macOS-latest' ]
+        # r: [ 'devel', 'release', 'oldrel-1', '4.2.1', '4.1.1', '4.1.3', '4.0.5', '3.6.1' ]
+        # java: [ '11', '13', '17', '19', '21' ]
+        os: [ 'windows-latest' ]
+        r: [ 'devel', 'release' ]
+        # Pb with Java 8
+        java: [ '11' ]
+        include:
+          - http-user-agent: 'release'
+            r: 'devel'
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      # Set-up java
+
+      - name: Setup java (x64)
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{ matrix.java }}
+          java-package: jdk
+          distribution: 'zulu'
+          architecture: x64
+
+      - name: Setup java (x86)
+        uses: actions/setup-java@v4
+        with:
+          java-version: ${{ matrix.java }}
+          java-package: jdk
+          distribution: 'zulu'
+          architecture: x86
+
+
+#
+#       - name: Setup java (x64)
+#         uses: actions/setup-java@v4
+#         if: matrix.java != '19'
+#         with:
+#           java-version: ${{ matrix.java }}
+#           java-package: jdk
+#           distribution: 'zulu'
+#           architecture: x64
+#
+#       - name: Setup java 19 (x64)
+#         uses: actions/setup-java@v4
+#         if: matrix.java == '19'
+#         with:
+#           java-version: ${{ matrix.java }}
+#           java-package: jdk
+#           distribution: 'temurin'
+#           architecture: x64
+#
+#       - name: Setup java (x86)
+#         uses: actions/setup-java@v4
+#         if: runner.os == 'Windows' && matrix.java != '19'
+#         with:
+#           java-version: ${{ matrix.java }}
+#           java-package: jdk
+#           distribution: 'zulu'
+#           architecture: x86
+#
+#       - name: Setup java 19 (x86)
+#         uses: actions/setup-java@v4
+#         if: runner.os == 'Windows' && matrix.java == '19'
+#         with:
+#           java-version: ${{ matrix.java }}
+#           java-package: jdk
+#           distribution: 'temurin'
+#           architecture: x86
+
+      # Some additionnal set up for ubuntu
+      # - name: Installation de libcurl4-openssl-dev
+      #   if: runner.os == 'Linux'
+      #   run: |
+      #     sudo apt-get update
+      #     sudo apt-get install -y libcurl4-openssl-dev
+      #     sudo apt-get install -y default-jre
+      #     sudo find / -name libjvm.so
+      #
+      # - name: Définir LD_LIBRARY_PATH
+      #   if: runner.os == 'Linux'
+      #   run: |
+      #     sudo bash -c 'export LD_LIBRARY_PATH=/usr/lib/jvm/temurin-11-jdk-amd64/lib/server:$LD_LIBRARY_PATH'
+      #     sudo bash -c "echo 'export LD_LIBRARY_PATH=/usr/lib/jvm/temurin-11-jdk-amd64/lib/server:$LD_LIBRARY_PATH' >> $HOME/.profile"
+      #
+      # - name: Afficher le chemin de bibliothèque Java
+      #   if: runner.os == 'Linux'
+      #   run: echo $LD_LIBRARY_PATH
+      #
+      # - name: Vérifier la version de Java
+      #   if: runner.os == 'Linux'
+      #   run: java -version
+      #
+      # - name: Vérifier la valeur de JAVA_HOME
+      #   if: runner.os == 'Linux'
+      #   run: echo $JAVA_HOME
+
+      # Set up R
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.r }}
+          http-user-agent: ${{ matrix.http-user-agent }}
+          use-public-rspm: true
+
+      # Pour MacOS et ubuntu, qqs installation supplémentaires
+      - name: "[Stage] [macOS] Install libgit2"
+        if: runner.os == 'macOS'
+        run: brew install libgit2
+
+      - name: "[Stage] [macOS] Install system libs for pkgdown"
+        if: runner.os == 'macOS'
+        run: brew install harfbuzz fribidi
+
+      - name: "Configure java pour ubuntu et macos"
+        if: runner.os != 'Windows'
+        run: sudo R CMD javareconf
+
+      - name: "[macOS] Install textshaping"
+        run: install.packages('textshaping')
+        shell: Rscript {0}
+        if: ${{ runner.os == 'macOS' && matrix.r == 'devel' }}
+
+      - name: "[macOS] Install systemfonts"
+        run: install.packages('systemfonts')
+        shell: Rscript {0}
+        if: ${{ runner.os == 'macOS' && matrix.r == '3.6.1' }}
+
+      # Dépendances
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        if: ${{ matrix.r != '3.6.1' }}
+        with:
+          packages: knitr, kableExtra, rmarkdown
+          extra-packages: any::rcmdcheck
+
+      # Pour R 3.6.1 qqs installations supplémentaires
+      - name: "[R 3.6.1] Install dependency"
+        run: install.packages(c("rJava", "XML", "RJDemetra", "rcmdcheck"))
+        shell: Rscript {0}
+        if: ${{ matrix.r == '3.6.1' || matrix.java == '11' }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,139 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Config git
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+
+      # Check if there are any changes
+      - name: Check for changes
+        id: check-changes
+        run: |
+          if git diff --quiet -- NAMESPACE man/; then
+            echo "has-changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has-changed=true" >> "$GITHUB_OUTPUT"
+          fi
+          
+      - name: Commit the changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'true' }}
+        run: |
+          git add man/\* NAMESPACE
+          git commit -m '[GHA] Document package'
+
+      # Commit changes or a placeholder commit if no changes
+      - name: Commit no changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'false' }}
+        run: |
+          git commit --allow-empty -m '[GHA] Package already documented'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
+        shell: Rscript {0}
+
+      - name: Config git
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+
+      # Check if there are any changes
+      - name: Check for changes
+        id: check-changes
+        run: |
+          if git diff --quiet -- '*.R'; then
+            echo "has-changed=false" >> "$GITHUB_OUTPUT"
+          else
+            echo "has-changed=true" >> "$GITHUB_OUTPUT"
+          fi
+          
+      - name: Commit the changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'true' }}
+        run: |
+          git add \*.R
+          git commit -m '[GHA] Style package'
+
+      # Commit changes or a placeholder commit if no changes
+      - name: Commit no changes
+        if: ${{ steps.check-changes.outputs.has-changed == 'false' }}
+        run: |
+          git commit --allow-empty -m '[GHA] Package already styled'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}