Merge branch 'development' into mm/uq_app

Author: Michael McLeod

.github/workflows/ci.yml

@@ -0,0 +1,287 @@
+name: CI
+
+on:
+  push:
+    branches: [ development ]
+  pull_request:
+    # CI runs when new commits are pushed or when draft PR is marked ready for review
+    types: [opened, synchronize, reopened, ready_for_review]
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        required: false
+        default: false
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+  OMP_NUM_THREADS: 2
+
+jobs:
+  build:
+    # Skip CI if PR is a draft
+    if: github.event.pull_request.draft == false
+    name: build (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}})
+    # 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: ${{matrix.os}}
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+    strategy:
+      fail-fast: false
+      matrix:
+          os:
+            - ubuntu-22.04
+            - macos-14
+          cc:
+            - gcc-12
+            - clang
+          cxx:
+            - g++-12
+            - clang++
+          mpi:
+            - "ON"
+            - "OFF"
+          omp:
+            - "ON"
+            - "OFF"
+          exclude:
+            - os: ubuntu-22.04
+              cc: clang
+            - os: ubuntu-22.04
+              cxx: clang++
+            - os: macos-14
+              cc: gcc-12
+            - os: macos-14
+              cxx: g++-12
+            - os: macos-14
+              mpi: "ON"
+    steps:
+    - uses: actions/checkout@v4
+
+   # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
+
+    - name: Prepare ccache timestamp
+      id: ccache_cache_timestamp
+      run: echo "{date_and_time}={$(date +'%Y-%m-%d-%H;%M;%S')}" >> $GITHUB_OUTPUT
+    - name: Set ccache cache directory
+      shell: bash
+      run: echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}"
+    - name: Cache ccache files
+      uses: actions/cache@v4
+      with:
+        path: ${{runner.workspace}}/.ccache
+        key: ${{matrix.os}}-${{matrix.cxx}}-${{matrix.mpi}}-${{matrix.omp}}-${{ steps.ccache_cache_timestamp.outputs.date_and_time }}
+        restore-keys: |
+          ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
+          ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}
+          ${{ matrix.os }}-${{ matrix.cxx }}
+          ${{ matrix.os }}
+
+#    - name: Clear ccache
+#      run: ccache --clear
+
+    - name: Install Dependencies on Ubunutu
+      if: ${{ contains(matrix.os, 'ubuntu') }}
+      run: |
+        sudo apt update
+        sudo apt install openmpi-bin libopenmpi-dev libyaml-cpp-dev libeigen3-dev libtiff-dev ccache
+
+    - name: Install Dependencies on MacOS
+      if: ${{ contains(matrix.os, 'macos') }}
+      run: |
+        brew install open-mpi libomp yaml-cpp eigen cfitsio ccache
+        echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
+        echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
+
+    - name: Checkout Catch2
+      uses: actions/checkout@v4
+      with:
+        repository: catchorg/Catch2.git
+        path: Catch2
+        ref: v3.4.0
+
+    - name: Build Catch2
+      run: |
+        mkdir Catch2/build
+        cd Catch2/build
+        cmake .. -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local
+        make -j$(nproc --ignore 1) install
+
+    - name: Install FFTW
+      run: |
+        wget --no-check-certificate --no-verbose http://www.fftw.org/fftw-3.3.10.tar.gz -O- | tar --no-same-owner -xz;
+        cd fftw-3.3.10
+        ./configure --prefix=${{github.workspace}}/local --enable-shared
+        make -j$(nproc --ignore 1) install CFLAGS=-fPIC
+        # Fix bug in FFT3 (cf. https://github.com/FFTW/fftw3/issues/332)
+        sed -i -e 's/^.*FFTW3LibraryDepends.cmake.*$//1' ${{github.workspace}}/local/lib*/cmake/*/FFTW3Config.cmake
+
+    - name: Checkout SOPT
+      uses: actions/checkout@v4
+      with:
+        repository: astro-informatics/sopt.git
+        path: sopt
+        ref: development
+
+    - name: Build sopt
+      run: |
+        export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
+        mkdir -p ${{github.workspace}}/sopt/build
+        cd ${{github.workspace}}/sopt/build
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=OFF -Dexamples=OFF
+        make -j$(nproc --ignore 1) install
+
+    - name: Pack dependencies
+      run: |
+        cd ${{github.workspace}}
+        tar cfv dependencies.tar local
+        
+    - uses: actions/upload-artifact@v4
+      with:
+        name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
+        path: ${{github.workspace}}/dependencies.tar
+        retention-days: 5
+
+  test:
+    needs:
+      build
+    name: test (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}})
+    runs-on: ${{matrix.os}}
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+    strategy:
+      fail-fast: false
+      matrix:
+          os:
+            - ubuntu-22.04
+            - macos-14
+          cc:
+            - gcc-12
+            - clang
+          cxx:
+            - g++-12
+            - clang++
+          mpi:
+            - "ON"
+            - "OFF"
+          omp:
+            - "ON"
+            - "OFF"
+          exclude:
+            - os: ubuntu-22.04
+              cc: clang
+            - os: ubuntu-22.04
+              cxx: clang++
+            - os: macos-14
+              cc: gcc-12
+            - os: macos-14
+              cxx: g++-12
+            - os: macos-14
+              mpi: "ON"
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/download-artifact@v4
+      with:
+        name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
+
+    - name: Unpack dependencies
+      run: tar xfv dependencies.tar
+
+    - name: Install Dependencies on Ubunutu
+      if: ${{ contains(matrix.os, 'ubuntu') }}
+      run: |
+        sudo apt update
+        sudo apt install openmpi-bin libopenmpi-dev ccache graphviz libeigen3-dev libtiff-dev libcfitsio-dev libboost-all-dev libyaml-cpp-dev
+
+    - name: Install Dependencies on MacOS
+      if: ${{ contains(matrix.os, 'macos') }}
+      run: |
+        brew install open-mpi libomp eigen ccache cfitsio boost yaml-cpp
+        echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
+        echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
+
+    - name: Build tests
+      # Build your program with the given configuration
+      run: |
+        export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
+        mkdir -p ${{github.workspace}}/build
+        cd ${{github.workspace}}/build
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddocasa=OFF -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}} -Dtests=ON
+        make -j$(nproc --ignore 1) install
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      # Execute tests defined by the CMake configuration.
+      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
+      run: |
+        export LD_LIBRARY_PATH=${{github.workspace}}/local/lib:${{github.workspace}}/local/external/lib:${LD_LIBRARY_PATH}
+        ctest -C ${{env.BUILD_TYPE}} --output-on-failure
+
+  doc:
+    needs:
+      build
+    name: doc (${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}})
+    runs-on: ${{matrix.os}}
+    env:
+      CC: ${{ matrix.cc }}
+      CXX: ${{ matrix.cxx }}
+    strategy:
+      fail-fast: false
+      matrix:
+          os:
+            - ubuntu-22.04
+          cc:
+            - gcc-12
+          cxx:
+            - g++-12
+          mpi:
+            - "OFF"
+          omp:
+            - "OFF"
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/download-artifact@v4
+      with:
+        name: dependencies-${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
+
+    - name: Unpack dependencies
+      run: tar xfv dependencies.tar
+
+    - name: Install Dependencies on Ubunutu
+      if: ${{ contains(matrix.os, 'ubuntu') }}
+      run: |
+        sudo apt update
+        sudo apt install ccache doxygen graphviz libeigen3-dev libtiff-dev libcfitsio-dev libboost-all-dev libyaml-cpp-dev
+
+    - name: Install Dependencies on MacOS
+      if: ${{ contains(matrix.os, 'macos') }}
+      run: |
+        brew install gcc libtiff eigen libyaml ccache cfitsio boost yaml-cpp
+        echo "CMAKE_PREFIX_PATH=/opt/homebrew/opt/libomp" >> $GITHUB_ENV
+        echo "/opt/homebrew/opt/ccache/libexec" >> $GITHUB_PATH
+
+    - name: Build docs
+      run: |
+        export CMAKE_PREFIX_PATH=${{github.workspace}}/local:$CMAKE_PREFIX_PATH
+        mkdir -p ${{github.workspace}}/build
+        cd ${{github.workspace}}/build
+        cmake .. --fresh -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/local -Ddompi=OFF -Dopenmp=OFF -Ddocs=ON
+        make -j$(nproc --ignore 1) install
+
+    - name: Deploy to GH pages
+      if: ${{github.event_name == 'push'}}
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages # The branch the action should deploy to.
+        folder: build/cpp/docs/html # The folder the action should deploy.