test-library.yml

name: "Library"

on:
  push:


jobs:

  basicchecks:

    name: Basic checks
    runs-on: ubuntu-latest
    outputs:
      hassecrets: ${{ steps.checksecrets.outputs.hassecrets }}
    env:
      CCACHE: ccache
      CCACHE_DIR: ${{ github.workspace }}/ccache

    steps:
      - name: Checkout Colvars
        uses: actions/checkout@v4

      - name: Load compiler cache
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/ccache
          key: ${{ runner.os }}-build-basic-${{ github.sha }}
          restore-keys: ${{ runner.os }}-build-basic-

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Install build dependencies for library
        run: |
          sudo apt -y install ccache tcl8.6-dev clang

      - name: Test build recipes
        run: bash devel-tools/check_build_recipes

      - name: Convert BibTeX references to code
        shell: bash
        working-directory: doc
        run: |
          make update-code-refs
          if [ -n "$(git status --porcelain ../src/colvarmodule_refs.h)" ] ; then
              echo "Code citations out of date; please run make update-code-refs in the doc folder" >& 2
              exit 1
          fi

      - name: Build and test library (Clang)
        env:
          CMAKE_BUILD_DIR: build
          CXX: clang++
          CC: clang
        run: cmake -P devel-tools/build_test_library.cmake

      - name: Check documentation of command-line scripting interface
        shell: bash
        working-directory: doc
        run: |
          make update-cvscript-cmdline-doc
          if [ -n "$(git status --porcelain cvscript-tcl.tex)" ] ; then
              echo "Command-line scripting doc out of date; please run make update-cvscript-cmdline-doc and commit changes" >& 2
              exit 1
          fi

      - name: Build and test library (GCC)
        env:
          CMAKE_BUILD_DIR: build-gcc
          CXX: g++
          CC: gcc
        run: cmake -P devel-tools/build_test_library.cmake

      - name: Build library with debug code enabled (GCC)
        run: cmake -D COLVARS_DEBUG=ON -P devel-tools/build_test_library.cmake

      - name: Check whether secrets are available
        id: checksecrets
        env:
          PULL_ORACLE_DEVELOPER_STUDIO: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }}
        run: |
          echo "hassecrets=${{ env.PULL_ORACLE_DEVELOPER_STUDIO != '' }}" >> $GITHUB_OUTPUT

      - name: Print ccache stats
        run: ccache -s -v

      - name: Keep only one cache besides the one from this job
        shell: bash
        env:
          GH_TOKEN: ${{ github.token }}
        run: |
          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-basic-


  build-doc:
    name: Build documentation
    runs-on: ubuntu-latest
    needs: basicchecks

    steps:
      - uses: actions/checkout@v4

      - name: Install Apptainer
        shell: bash
        run: |
          sudo add-apt-repository -y ppa:apptainer/ppa
          sudo apt update
          sudo apt install -y apptainer-suid

      - name: Get container image
        shell: bash
        working-directory: devel-tools
        run: |
          apptainer pull texlive.sif oras://ghcr.io/colvars/devel-containers:texlive

      - name: Checkout website repository
        uses: actions/checkout@v4
        with:
          ssh-key: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }}
          repository: 'Colvars/colvars.github.io'
          path: 'website'

      - name: Build doc for current branch
        working-directory: doc
        run: |
          make clean-all
          apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make

      - name: Install SSH key for access to website repository
        if: contains(github.event.head_commit.message, '[update-doc]')
        env:
          WEBSITE_SSH_KEY: ${{ secrets.PULL_PUSH_COLVARS_GITHUB_IO }}
        run: |
          mkdir -p -m 700 ~/.ssh
          echo "${WEBSITE_SSH_KEY}" > ~/.ssh/website
          chmod 600 ~/.ssh/website

      - name: Push updated doc to website repository
        working-directory: doc
        if: contains(github.event.head_commit.message, '[update-doc]')
        env:
          COLVARS_WEBSITE_TREE: ${{ github.workspace }}/website
        run: |
          apptainer exec ${{ github.workspace }}/devel-tools/texlive.sif make install
          export GIT_SSH="ssh -i ~/.ssh/website"
          git config --global user.email "noreply@github.com"
          git config --global user.name "CI runner"
          bash update_website.sh ${{ github.workspace }}/website


  codeql:
    name: CodeQL analysis
    runs-on: ubuntu-latest
    needs: basicchecks
    if: ${{ ! github.event.repository.private }}

    steps:
      - uses: actions/checkout@v4

      - name: Install build dependencies for library
        run: |
          sudo apt-get -y install tcl8.6-dev

      - name: Checkout OpenMM (for Lepton library)
        uses: actions/checkout@v4
        with:
          repository: 'openmm/openmm'
          ref: 'master'
          path: 'openmm-source'

      - name: Initialize CodeQL
        uses: github/codeql-action/init@v2
        with:
          languages: cpp

      - name: Build Colvars library with CMake
        run: cmake -P devel-tools/build_test_library.cmake

      - name: Perform CodeQL Analysis
        uses: github/codeql-action/analyze@v2


  static-analyser:
    name: Clang 14 Static Analyser
    runs-on: ubuntu-latest
    needs: basicchecks

    steps:
      - uses: actions/checkout@v4

      - name: Install build dependencies for library
        run: |
          sudo apt -y install tcl8.6-dev clang-14 clang-tools-14

      - name: Checkout OpenMM (for Lepton library)
        uses: actions/checkout@v4
        with:
          repository: 'openmm/openmm'
          ref: 'master'
          path: 'openmm-source'

      - name: Perform Clang Static Analyser
        env:
          CXX: clang++-14
          CC: clang-14
        run: |
          scan-build-14 --use-cc=clang-14 --use-c++=clang++-14 cmake -P devel-tools/build_test_library.cmake 2>&1 | tee build_analyser.log
          grep "CMake Error" build_analyser.log > build_errors.log || true
          if [ -s build_errors.log ] ; then
            echo "Found compiler errors during build"
            cat build_analyser.log
            exit 1
          fi

      - name: Analyze logs
        run: | # Retrieve warnings generated but not the ones of OpenMM
          awk '/colvars\/colvars\/[^openmm].*warning:/,/warning.*generated|^$/' build_analyser.log | tee warnings_analyser.log || true
          if [ -s warnings_analyser.log ] ; then
            echo "Found compiler warning during build"
            exit 1
          fi

      - name: Archive warnings artifacts
        uses: actions/upload-artifact@v4
        if: failure()
        with:
          name: warnings_clang_static_analyser
          path: warnings_analyser.log


  address-sanitizer:
    name: Clang 16 address sanitizer
    runs-on: ubuntu-latest
    needs: basicchecks
    env:
      CCACHE: ccache
      CCACHE_DIR: ${{ github.workspace }}/ccache

    steps:
      - uses: actions/checkout@v4

      - name: Load compiler ccache
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/ccache
          key: ${{ runner.os }}-build-asan-${{ github.sha }}
          restore-keys: ${{ runner.os }}-build-asan-

      - name: Checkout OpenMM (for Lepton library)
        uses: actions/checkout@v4
        with:
          repository: 'openmm/openmm'
          ref: 'master'
          path: 'openmm-source'

      - name: Install Apptainer
        shell: bash
        run: |
          sudo add-apt-repository -y ppa:apptainer/ppa
          sudo apt update
          sudo apt install -y apptainer-suid

      - name: Get container images for build dependencies
        shell: bash
        working-directory: devel-tools
        run: |
          apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel

      - name: Build with Clang 16 and address sanitizer
        env:
          CXX: clang++
          CC: clang
          CMAKE_ADDRESS_SANITIZER: ON
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          cmake -P devel-tools/build_test_library.cmake

      - name: Archive warnings artifacts
        uses: actions/upload-artifact@v4
        if: failure()
        with:
          name: Clang_address_sanitizer_output
          path: ${{github.workspace}}/build/Testing/Temporary/LastTest.log

      - name: Keep only one cache besides the one from this job
        shell: bash
        env:
          GH_TOKEN: ${{ github.token }}
        run: |
          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh ${{ runner.os }}-build-asan-


  build-linux-x86_64-many:
    name: Linux x86_64 (GCC, Clang)
    runs-on: ubuntu-latest
    needs: basicchecks
    env:
      CCACHE: ccache
      CMAKE_GENERATOR: Ninja
      CCACHE_DIR: ${{ github.workspace }}/ccache

    steps:
      - uses: actions/checkout@v4

      - name: Load compiler ccache
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/ccache
          key: ${{ runner.os }}-build-multiple-${{ github.sha }}
          restore-keys: ${{ runner.os }}-build-multiple-

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Install Apptainer
        shell: bash
        run: |
          sudo add-apt-repository -y ppa:apptainer/ppa
          sudo apt update
          sudo apt install -y apptainer-suid

      - name: Get container images for build dependencies
        shell: bash
        working-directory: devel-tools
        run: |
          apptainer pull CentOS7-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS7-devel
          apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel

      - name: GCC 4.8, C++11 (CentOS 7)
        env:
          CXX_STANDARD: 11
          CXX: g++
          CXX_VERSION: 4.8
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: Clang 3.4, C++11 (CentOS 7)
        env:
          CXX_STANDARD: 11
          CXX: clang++
          CXX_VERSION: 11
          CC: clang
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: Clang 7, C++17 (CentOS 7)
        env:
          CXX_STANDARD: 17
          CXX: clang++
          CXX_VERSION: 7
          CC: clang
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          scl enable llvm-toolset-${CXX_VERSION} -- \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 8, C++17 (CentOS 7)
        env:
          CXX_STANDARD: 17
          CXX: g++
          CXX_VERSION: 8
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          scl enable devtoolset-${CXX_VERSION} -- \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 9, C++14 (CentOS 7)
        env:
          CXX_STANDARD: 14
          CXX: g++
          CXX_VERSION: 9
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          scl enable devtoolset-${CXX_VERSION} -- \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 10, C++17 (CentOS 7)
        env:
          CXX_STANDARD: 17
          CXX: g++
          CXX_VERSION: 10
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          scl enable devtoolset-${CXX_VERSION} -- \
          cmake3 -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake


      - name: GCC 11, C++11 (CentOS 9)
        env:
          CXX_STANDARD: 11
          CXX: g++
          CXX_VERSION: 11
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 11, C++20 (CentOS 9)
        env:
          CXX_STANDARD: 20
          CXX: g++
          CXX_VERSION: 11
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 12, C++20 (CentOS 9)
        env:
          CXX_STANDARD: 20
          CXX: g++
          CXX_VERSION: 12
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          scl enable gcc-toolset-12 -- \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: GCC 13, C++20 (CentOS 9)
        env:
          CXX_STANDARD: 20
          CXX: g++
          CXX_VERSION: 13
          CC: gcc
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          scl enable gcc-toolset-13 -- \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: Clang 16, C++11 (CentOS 9)
        env:
          CXX_STANDARD: 11
          CXX: clang++
          CXX_VERSION: 16
          CC: clang
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: Clang 16, C++20 (CentOS 9)
        env:
          CXX_STANDARD: 20
          CXX: clang++
          CXX_VERSION: 16
          CC: clang
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel.sif \
          cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake

      - name: Keep only one cache besides the one from this job
        shell: bash
        env:
          GH_TOKEN: ${{ github.token }}
        run: |
          bash ${{ github.workspace }}/devel-tools/cleanup-gh-cache.sh Linux-build-multiple-


  build-linux-x86_64-sun:
    name: Linux x86_64 (Sun compiler)
    runs-on: ubuntu-latest
    needs: basicchecks
    if: needs.basicchecks.outputs.hassecrets == 'true'
    steps:
      - uses: actions/checkout@v4

      - name: Checkout Sun compiler (Oracle Developer Studio)
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/oracle'
          ssh-key: ${{ secrets.PULL_ORACLE_DEVELOPER_STUDIO }}
          ref: 'master'
          path: ${{github.workspace}}/oracle

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Install Apptainer
        shell: bash
        run: |
          sudo add-apt-repository -y ppa:apptainer/ppa
          sudo apt update
          sudo apt install -y apptainer-suid

      - name: Get container images for build dependencies
        shell: bash
        working-directory: devel-tools
        run: |
          apptainer pull CentOS7-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS7-devel

      - name: Build library with Sun compiler (Oracle Developer Studio)
        shell: bash
        env:
          CC: ${{github.workspace}}/oracle/developerstudio12.6/bin/cc
          CXX: ${{github.workspace}}/oracle/developerstudio12.6/bin/CC
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS7-devel.sif \
          cmake3 -D CMAKE_CXX_STANDARD=11 -P devel-tools/build_test_library.cmake


  build-linux-x86_64-intel:
    name: Linux x86_64 (Intel oneAPI)
    runs-on: ubuntu-latest
    needs: basicchecks
    env:
      CCACHE: ccache
      CMAKE_GENERATOR: Ninja
      CCACHE_DIR: ${{ github.workspace }}/ccache
    steps:
      - uses: actions/checkout@v4

      - name: Load compiler ccache
        uses: actions/cache@v4
        with:
          path: ${{ github.workspace }}/ccache
          key: ${{ runner.os }}-build-oneapi-${{ github.sha }}
          restore-keys: ${{ runner.os }}-build-oneapi-

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Install Apptainer
        shell: bash
        run: |
          sudo add-apt-repository -y ppa:apptainer/ppa
          sudo apt update
          sudo apt install -y apptainer-suid

      - name: Get container images for build dependencies
        shell: bash
        working-directory: devel-tools
        run: |
          apptainer pull CentOS9-devel-oneAPI.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel-oneAPI

      - name: Intel oneAPI 2024.2, C++11
        shell: bash
        env:
          CC: icx
          CXX: icpx
          CXX_STANDARD: 11
          BASH_ENV: "/etc/profile.d/oneapi.sh"
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"

      - name: Intel oneAPI 2024.2, C++14
        shell: bash
        env:
          CC: icx
          CXX: icpx
          CXX_STANDARD: 14
          BASH_ENV: "/etc/profile.d/oneapi.sh"
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"

      - name: Intel oneAPI 2024.2, C++17
        shell: bash
        env:
          CC: icx
          CXX: icpx
          CXX_STANDARD: 17
          BASH_ENV: "/etc/profile.d/oneapi.sh"
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"

      - name: Intel oneAPI 2024.2, C++20
        shell: bash
        env:
          CC: icx
          CXX: icpx
          CXX_STANDARD: 20
          BASH_ENV: "/etc/profile.d/oneapi.sh"
        run: |
          apptainer exec ${{github.workspace}}/devel-tools/CentOS9-devel-oneAPI.sif \
          bash -c "cmake -D CMAKE_CXX_STANDARD=${CXX_STANDARD} -P devel-tools/build_test_library.cmake"


  build-windows-x86_64-msvc:
    name: Windows x86_64 (MSVC)
    runs-on: windows-latest
    needs: basicchecks

    steps:

      - uses: actions/checkout@v4

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Build and test library with CMake
        # We need to set CMAKE_SYSTEM_NAME manually in script mode
        run: cmake -D CMAKE_SYSTEM_NAME=Windows -P devel-tools/build_test_library.cmake


  build-macos-ARM64-clang:
    name: macOS ARM64 (AppleClang)
    runs-on: macos-latest
    needs: basicchecks

    steps:

      - uses: actions/checkout@v4

      - name: Get small downloadable packages
        uses: actions/checkout@v4
        with:
          repository: 'Colvars/build-tools-packages'
          ref: 'master'
          path: 'devel-tools/packages'

      - name: Build and test library with CMake
        # We need to set CMAKE_SYSTEM_NAME manually in script mode
        run: cmake -D CMAKE_SYSTEM_NAME=Darwin -P devel-tools/build_test_library.cmake