Update peer to compile and work on modern platforms.

.github/workflows/build-python-only.yml

@@ -0,0 +1,37 @@
+name: Package Python
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Miniconda   
+      uses: conda-incubator/[email protected]
+      with:
+        mamba-version: "*"
+        channel-priority: true
+        activate-environment: peer
+        environment-file: peer-environment.yml
+
+    - name: Assemble Python source package
+      run: |
+        pushd conda_forge_python
+        bash create_python_package.sh
+        popd
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package
+        path: conda_forge_python/peer/dist/peer-*.tar.gz

.github/workflows/build-r-only.yml

@@ -0,0 +1,65 @@
+name: Package R
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Miniconda   
+      uses: conda-incubator/[email protected]
+      with:
+        mamba-version: "*"
+        channel-priority: true
+        activate-environment: peer
+        environment-file: peer-environment.yml
+
+    - name: Assemble R source package
+      run: |
+        pushd cran
+        bash package_r_only.sh
+        popd
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: r-package
+        path: cran/peer_*.tar.gz
+
+  r-cran-install:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+    needs: build
+    steps:
+    - name: Download package
+      uses: actions/download-artifact@v4
+      with:
+        name: r-package
+
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: '4.3.3' # The R version to download (if necessary) and use.
+        # Use "renv" to retrieve R version recorded in renv.lock file.
+
+    - name: Install R dependencies
+      run: Rscript -e 'install.packages(c("BH", "RcppEigen"))'
+
+    - name: Install R package
+      run: R CMD INSTALL peer_2.0.tar.gz

.github/workflows/build.yml

@@ -0,0 +1,100 @@
+# This starter workflow is for a CMake project running on a single platform. There is a different starter workflow if you need cross-platform coverage.
+# See: https://github.com/actions/starter-workflows/blob/main/ci/cmake-multi-platform.yml
+name: Package and compile Peer across OSes and archs
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  build:
+    # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac.
+    # You can convert this to a matrix build if you need cross-platform coverage.
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Miniconda   
+      uses: conda-incubator/[email protected]
+      with:
+        mamba-version: "*"
+        channel-priority: true
+        activate-environment: peer
+        environment-file: peer-environment.yml
+
+    - 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: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Assemble R source package
+      run: |
+        pushd cran
+        bash create_source_new.sh
+        popd
+
+    - name: Assemble Python source package
+      run: |
+        pushd standalone_python
+        bash create_python_package.sh
+        popd
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: peertool
+        path: build/src/peertool
+
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: r-python-packages
+        path: |
+          cran/peer_*.tar.gz
+          standalone_python/peer/dist/peer-*.tar.gz
+
+  cibuildwheel:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+    needs: build
+    steps:
+    - uses: actions/download-artifact@v4
+      with:
+        name: r-python-packages
+
+    - name: cibuildwheel for python
+      uses: pypa/[email protected]
+      with:
+        package-dir: standalone_python/peer/dist/peer-2.0.0.tar.gz
+      env:
+        CIBW_ARCHS_MACOS: x86_64 arm64
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+        path: ./wheelhouse/*.whl
+
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+    - run: Rscript -e 'install.packages("BH", "RccpEigen")'
+
+    - name: Test R on this platform
+      run: R CMD check --as-cran cran/peer_2.0.tar.gz

.gitignore

@@ -1,11 +1,22 @@
 build/*
 CMakeFiles/*
-cran/peer/DESCRIPTION
-cran/peer/NAMESPACE
-cran/peer/R
-cran/peer/man
-cran/peer/src/*.cpp
-cran/peer/src/*.so
-cran/peer/src/*.h
-cran/peer_source.tgz
-cran/peer/src/alglib
+cran/peer/
+cran/*.tar.gz
+
+*.Rcheck
+
+# Editor
+.vscode/
+
+# Built python package
+standalone_python/peer
+conda_forge_python/peer
+python/peer.py
+python/peerPYTHON_wrap.cxx
+
+# Generated by swig. Should these go into the bin dir?
+R/peer.R
+R/peerR_wrap.cxx
+
+# Mac hidden dirs
+.DS_Store

CMakeLists.txt

@@ -1,12 +1,13 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 3.20)
 project(PEER)
+set(CMAKE_CXX_STANDARD 14)
 
 #build options
 #bindings
 #PYTHON on by default
 option(BUILD_PYTHON_PACKAGE "Enable Python bindings" ON)
 #R optional
-option(BUILD_R_PACKAGE "Enable R bindings" OFF)
+option(BUILD_R_PACKAGE "Enable R bindings" ON)
 
 #build stuff
 option(BUILD_UNIVERSAL "Build both 32 and 64 bit versions" OFF)
@@ -74,6 +75,12 @@ endif (BUILD_UNIVERSAL)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+find_package(Eigen3 REQUIRED NO_MODULE)
+link_libraries(Eigen3::Eigen)
+
+find_package(Boost REQUIRED)
+include_directories(${Boost_INCLUDE_DIRS})
+
 include_directories(${CMAKE_CURRENT_SOURCE_DIR})
 set(CMAKE_SWIG_FLAGS "")
 
@@ -85,12 +92,10 @@ add_definitions(-g -Wextra -D_BSD_SOURCE)
 #fPic while compiling on
 #this seems to be needed on some linux systems
 #set(CMAKE_CXX_FLAGS "-fPIC -O3 -march=core2")
-set(CMAKE_CXX_FLAGS "-fPIC")
+set(CMAKE_CXX_FLAGS "-fPIC -O3")
 
-include_directories(./External/alglib/src)
 
 #add Cmake modules
-add_subdirectory(./External/alglib/src)
 add_subdirectory(./External/csv_parser)
 add_subdirectory(./src)