Update CI to handle stochtree changes expecting OpenMP and autoconf for the R package

Author: andrewherren

.github/workflows/cpp-test.yml

@@ -56,11 +56,17 @@ jobs:
       shell: bash
       run: |
         echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+    
+    - name: Set up dependencies (linux clang)
+      # Set up openMP on ubuntu-latest with clang compiler toolset (doesn't ship with the compiler suite like GCC and MSVC)
+      if: matrix.os == 'ubuntu-latest' && matrix.cpp_compiler == 'clang++'
+      run: | 
+        sudo apt-get update && sudo apt-get install -y libomp-dev
 
     - name: Configure CMake
       # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
       # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: >
+      run: |
         cmake -B ${{ steps.strings.outputs.build-output-dir }}
         -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
         -DCMAKE_C_COMPILER=${{ matrix.c_compiler }}
@@ -69,6 +75,7 @@ jobs:
         -DUSE_SANITIZER=OFF
         -DBUILD_TEST=ON
         -DBUILD_DEBUG_TARGETS=OFF
+        -DUSE_OPENMP=ON
         -S ${{ github.workspace }}
 
     - name: Build

.github/workflows/pypi-wheels.yml

@@ -34,6 +34,12 @@ jobs:
       - uses: actions/checkout@v4
         with:
           submodules: 'recursive'
+    
+      - name: Set up openmp (macos)
+        # Set up openMP on MacOS since it doesn't ship with the apple clang compiler suite
+        if: matrix.os == 'macos-13' || matrix.os == 'macos-14'
+        run: | 
+          brew install libomp
 
       - name: Build wheels
         uses: pypa/[email protected]

.github/workflows/python-test.yml

@@ -30,6 +30,12 @@ jobs:
       with:
         python-version: "3.10"
         cache: "pip"
+    
+    - name: Set up openmp (macos)
+      # Set up openMP on MacOS since it doesn't ship with the apple clang compiler suite
+      if: matrix.os == 'macos-latest'
+      run: | 
+        brew install libomp
 
     - name: Install Package with Relevant Dependencies
       run: |

cran-bootstrap.R

@@ -60,6 +60,8 @@ if (!dir.exists(cran_dir)) {
 src_files <- list.files("src", pattern = ".[^o]$", recursive = TRUE, full.names = TRUE)
 pybind_src_files <- list.files("src", pattern = "^(py_)", recursive = TRUE, full.names = TRUE)
 r_src_files <- src_files[!(src_files %in% pybind_src_files)]
+r_src_files <- r_src_files[!(r_src_files %in% c("src/Makevars"))]
+cat(r_src_files)
 pkg_core_files <- c(
     ".Rbuildignore",
     "cran-comments.md",
@@ -136,9 +138,14 @@ if (all(file.exists(pkg_core_files))) {
 }
 
 # Overwrite PKG_CPPFLAGS in src/Makevars
-cran_makevars <- file.path(cran_dir, "src/Makevars")
+cran_makevars <- file.path(cran_dir, "src/Makevars.in")
 makevars_lines <- readLines(cran_makevars)
-makevars_lines[grep("^(PKG_CPPFLAGS)", makevars_lines)] <- "PKG_CPPFLAGS= -I$(PKGROOT)/src/include $(STOCHTREE_CPPFLAGS)"
+makevars_lines[grep("    -I$(PKGROOT)/include \\", makevars_lines, fixed = T)] <- "    -I$(PKGROOT)/src/include \\"
+makevars_lines <- makevars_lines[-c(
+    grep("    -I$(PKGROOT)/deps/eigen \\", makevars_lines, fixed = T), 
+    grep("    -I$(PKGROOT)/deps/fmt/include \\", makevars_lines, fixed = T), 
+    grep("    -I$(PKGROOT)/deps/fast_double_parser/include \\", makevars_lines, fixed = T)
+)]
 writeLines(makevars_lines, cran_makevars)
 
 # Remove vignette deps from DESCRIPTION if no vignettes