better gh actions

pachadotdev · Feb 14, 2024 · 5baad79 · 5baad79
1 parent cd75b35
commit 5baad79
Show file tree

Hide file tree

Showing 34 changed files with 1,143 additions and 1,003 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,5 +1,9 @@
 # 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -12,20 +16,33 @@ jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.custom }}
 
     strategy:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+
+          # Use older ubuntu to maximise backward compatibility
+          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04,   r: 'release'}
+          - {os: ubuntu-20.04,   r: 'release', custom: 'gcc 4.8'}
+          - {os: ubuntu-20.04,   r: 'oldrel-1'}
+          - {os: ubuntu-20.04,   r: 'oldrel-2'}
+          - {os: ubuntu-20.04,   r: 'oldrel-3'}
+          - {os: ubuntu-20.04,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -35,6 +52,28 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      - name : Install compiler version
+        # We check on this old compiler specifically to support CentOS 7,
+        # which uses this gcc version. RStudio products support CentOS 7 through
+        # June 2024.
+        # https://github.com/r-lib/cpp11/pull/78
+        # https://www.rstudio.com/about/platform-support/
+        # Ubuntu 20.04 technically dropped support for gcc 4.8, so we have to
+        # add old archives back in manually to install it
+        # https://github.com/r-lib/cpp11/pull/279
+        if: matrix.config.custom == 'gcc 4.8'
+        run: |
+          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial main" | sudo tee -a /etc/apt/sources.list
+          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial universe" | sudo tee -a /etc/apt/sources.list
+          sudo apt update
+          sudo apt-get install -y g++-4.8 libgfortran-*
+          mkdir ~/.R/
+          echo $'CXX1X=g++-4.8\nCXX11=g++-4.8\nCC=gcc-4.8 -std=c99\nCXX=g++-4.8 -std=gnu++11' >> ~/.R/Makevars
+
+      - name: Install macOS system dependencies
+        if: runner.os == 'macOS'
+        run: brew install --cask xquartz
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

diff --git a/.github/workflows/format.yaml b/.github/workflows/format.yaml
@@ -0,0 +1,23 @@
+on:
+  push:
+    branches: main
+  pull_request:
+    branches:
+      - main
+
+name: format_check
+
+jobs:
+  format_check:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install ClangFormat
+        run: sudo apt-get install -y clang-format-14
+
+      - name: Run ClangFormat
+        run: make format clang_format=clang-format-14
+
+      - name: Check for a non-empty diff
+        run: git diff-files -U --exit-code
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -0,0 +1,79 @@
+# 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@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - 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@v2
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,39 @@
+# 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, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-22.04
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Install cpp11armadillotest
+        run: |
+          options(warn = 2)
+          pak::pkg_install("pachadotdev/cpp11armadillo", dependencies = TRUE)
+          pak::local_install_dev_deps("cpp11armadillotest", dependencies = TRUE)
+          install.packages("cpp11armadillotest", repos = NULL, INSTALL_opts = "--install-tests", type = "source")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
diff --git a/Makefile b/Makefile
@@ -0,0 +1,19 @@
+test:
+	@Rscript -e 'devtools::clean_dll(); devtools::test(".")'
+
+clean:
+	@Rscript -e 'devtools::clean_dll()'
+
+document:
+  @Rscript -e 'devtools::document()'
+
+site:
+	@Rscript -e 'pkgdown::build_site()'
+
+install:
+	@Rscript -e 'devtools::install()'
+
+clang_format=`which clang-format-14`
+
+format: $(shell find . -name '*.h') $(shell find . -name '*.hpp') $(shell find . -name '*.cpp')
+	@${clang_format} -i $?
diff --git a/dev/04_pairwise_correlation.cpp b/dev/04_pairwise_correlation.cpp
@@ -13,7 +13,7 @@
 
 // Bubble sort distance between the input array and the sorted array
 
-uint64_t insert_sort_(double* arr, size_t len) {
+uint64_t insert_sort_(double *arr, size_t len) {
   size_t max_j, i;
   uint64_t swap_count = 0;
 
@@ -37,11 +37,11 @@ uint64_t insert_sort_(double* arr, size_t len) {
   return swap_count;
 }
 
-static uint64_t merge_(double* from, double* to, size_t middle, size_t len) {
+static uint64_t merge_(double *from, double *to, size_t middle, size_t len) {
   size_t buf_index, left_len, right_len;
   uint64_t swaps;
-  double* left;
-  double* right;
+  double *left;
+  double *right;
 
   buf_index = 0;
   swaps = 0;
@@ -74,7 +74,7 @@ static uint64_t merge_(double* from, double* to, size_t middle, size_t len) {
   return swaps;
 }
 
-uint64_t merge_sort_(double* x, double* buf, size_t len) {
+uint64_t merge_sort_(double *x, double *buf, size_t len) {
   uint64_t swaps;
   size_t half;
 
@@ -99,7 +99,7 @@ uint64_t merge_sort_(double* x, double* buf, size_t len) {
 
 // Count ties
 
-static uint64_t count_ties_(double* data,
+static uint64_t count_ties_(double *data,
                             size_t len) { /* Assumes data is sorted.*/
   uint64_t sum_counts = 0, tie_count = 0;
   size_t i;
@@ -130,7 +130,7 @@ static uint64_t count_ties_(double* data,
 // arr1 <- arr1[perm]
 // arr2 <- arr2[perm]
 
-double kendall_n_log_n_(const double* arr1, const double* arr2, size_t len) {
+double kendall_n_log_n_(const double *arr1, const double *arr2, size_t len) {
   uint64_t m1 = 0, m2 = 0, tie_count, swap_count, n_pair;
   int64_t s;
   size_t i;
@@ -143,7 +143,7 @@ double kendall_n_log_n_(const double* arr1, const double* arr2, size_t len) {
     if (arr1[i - 1] == arr1[i]) {
       tie_count++;
     } else if (tie_count > 0) {
-      double* arr2_copy = new double[tie_count + 1];
+      double *arr2_copy = new double[tie_count + 1];
       copy(arr2 + i - tie_count - 1, arr2 + i, arr2_copy);
       insert_sort_(arr2_copy, tie_count + 1);
       m1 += tie_count * (tie_count + 1) / 2;
@@ -154,7 +154,7 @@ double kendall_n_log_n_(const double* arr1, const double* arr2, size_t len) {
     }
   }
   if (tie_count > 0) {
-    double* arr2_copy = new double[tie_count + 1];
+    double *arr2_copy = new double[tie_count + 1];
     copy(arr2 + i - tie_count - 1, arr2 + i, arr2_copy);
     insert_sort_(arr2_copy, tie_count + 1);
     m1 += tie_count * (tie_count + 1) / 2;
@@ -163,9 +163,9 @@ double kendall_n_log_n_(const double* arr1, const double* arr2, size_t len) {
     tie_count++;
   }
 
-  double* arr2_sorted = new double[len];
+  double *arr2_sorted = new double[len];
   copy(arr2, arr2 + len, arr2_sorted);
-  swap_count = merge_sort_(arr2_sorted, const_cast<double*>(arr1), len);
+  swap_count = merge_sort_(arr2_sorted, const_cast<double *>(arr1), len);
 
   m2 = count_ties_(arr2_sorted, len);
   s -= (m1 + m2) + 2 * swap_count;
@@ -181,17 +181,17 @@ double kendall_n_log_n_(const double* arr1, const double* arr2, size_t len) {
 
 // Wrapper to R
 
-[[cpp11::register]] double pairwise_cor_(const doubles& y,
-                                         const doubles& yhat) {
+[[cpp11::register]] double pairwise_cor_(const doubles &y,
+                                         const doubles &yhat) {
   size_t len_y = y.size();
   size_t len_yhat = yhat.size();
 
   if (len_y != len_yhat) {
     stop("y and yhat must be the same length");
   }
 
-  const double* y_data = REAL(y);
-  const double* yhat_data = REAL(yhat);
+  const double *y_data = REAL(y);
+  const double *yhat_data = REAL(yhat);
 
   double cor = kendall_n_log_n_(y_data, yhat_data, len_y);