Merge pull request #35 from TanguyBarthelemy/develop

Add Github action to check the package

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

@@ -0,0 +1,68 @@
+# 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:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    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-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf on Windows
+        if: runner.os == 'Windows'
+        run: choco install protoc
+
+      - name: Set up for RProtoBuf on macos
+        if: runner.os == 'macOS'
+        run: brew install protobuf
+
+      - name: Set up for RProtoBuf on ubuntu
+        if: runner.os == 'Linux'
+        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::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          error-on: '"error"'

.github/workflows/lint.yaml

@@ -0,0 +1,42 @@
+# 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:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -22,11 +22,11 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v4
         with:
           distribution: 'zulu' # See 'Supported distributions' for available options
           java-version: '17'

.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 "[email protected]"
+
+      # 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 "[email protected]"
+
+      # 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 }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,60 @@
+# 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:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: actions/setup-java@v4
+        with:
+          distribution: 'zulu' # See 'Supported distributions' for available options
+          java-version: '17'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Set up for RProtoBuf
+        run: sudo apt-get update -y && sudo apt-get install protobuf-compiler libprotobuf-dev libprotoc-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.lintr

@@ -0,0 +1,27 @@
+linters: linters_with_defaults(
+        indentation_linter = lintr::indentation_linter(indent = 4L),
+        indentation_linter = NULL,
+        trailing_blank_lines_linter = NULL,
+        trailing_whitespace_linter = NULL,
+        assignment_linter = NULL,
+        whitespace_linter = NULL,
+        brace_linter = NULL,
+        infix_spaces_linter = NULL,
+        paren_body_linter = NULL,
+        indentation_linter = NULL,
+        function_left_parentheses_linter = NULL,
+        spaces_left_parentheses_linter = NULL,
+        commas_linter = NULL,
+        quotes_linter = NULL,
+        spaces_inside_linter = NULL,
+        vector_logic_linter = NULL,
+        seq_linter = NULL,
+        object_length_linter = NULL,
+        semicolon_linter = NULL,
+        cyclocomp_linter = NULL,
+        object_usage_linter = NULL,
+        object_name_linter = NULL,
+        line_length_linter = NULL,
+        commented_code_linter = NULL
+    )
+encoding: "UTF-8"

R/calendars.R

@@ -15,12 +15,12 @@ SINGLEDAY='JD3_SINGLEDAY'
     vp<-jd3.ValidityPeriod$new()
     if (is.null(start)) {
         pstart=DATE_MIN
-    }else{
+    } else{
         pstart=parseDate(start)
     }
     if (is.null(end)){
         pend=DATE_MAX
-    }else{
+    } else{
         pend=parseDate(end)
     }
     vp$start<-pstart
@@ -50,7 +50,7 @@ SINGLEDAY='JD3_SINGLEDAY'
 .length_ts <- function(s){
     if(is.mts(s)){
         nrow(s)
-    }else{
+    } else{
         length(s)
     }
 }

R/decomposition.R

@@ -14,14 +14,14 @@ sadecomposition<-function(y, sa, t, s, i, mul){
   if (is.null(s)){
     if (mul){
       s=ts(rep(1,1,n), start = start(y), frequency = frequency(y))
-    }else{
+    } else{
       s=ts(rep(0,1,n), start = start(y), frequency = frequency(y))
     }
   } else if (! is.ts(s))stop("Invalid SA decomposition")
   if (is.null(i)){
     if (mul){
       i=ts(rep(1,1,n), start = start(y), frequency = frequency(y))
-    }else{
+    } else{
       i=ts(rep(0,1,n), start = start(y), frequency = frequency(y))
     }
   } else if (! is.ts(i))stop("Invalid SA decomposition")