ci.yml

name: CI

on:
  push:
  pull_request:

env:
# on CI, better dump stack trace in case there is an error
  PLUMED_STACK_TRACE: yes
# use two threads for openMP tests
  PLUMED_NUM_THREADS: 2
# these are used to build required packages
  CC: gcc
  CXX: g++

jobs:
  linux:
    runs-on: ubuntu-22.04
    strategy:
      fail-fast: false
      matrix:
        variant:
        - -doc-mpi-
        - -mpi-
        - -coverage-mpi-
        - -debug-
        - -debug-mpi-
# temporarily commented out
# see https://github.com/plumed/plumed2/issues/976
#        - -intel-
    steps:
    - uses: actions/checkout@v4
    - uses: actions/cache@v4
      with:
        path: ~/.ccache
        key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }}
        restore-keys: ccache-reset1-linux${{ matrix.variant }}hash-
    - name: Removed unused stuff
      run: |
        df -h
        sudo rm -rf /usr/share/dotnet
        sudo rm -rf /usr/local/lib/android
        sudo rm -rf /opt/ghc
        df -h
    - name: Set up Python
      uses: actions/setup-python@v5
      with:
        python-version: 3.9
    - name: Set paths
      run: |
        echo "$HOME/opt/bin" >> $GITHUB_PATH
        # path required for pytest:
        echo "$HOME/.local/bin" >> $GITHUB_PATH
        echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
        echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
        echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
        echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
        echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
        # this is to avoid errors on ubuntu 22. this is overridden in intel build
        echo "FC=gfortran -fallow-argument-mismatch" >> $GITHUB_ENV
    - name: Install generic packages
      run: |
        sudo apt-get update -qq
        sudo apt-get install -y libatlas-base-dev
        sudo apt-get install -y libfftw3-dev
        sudo apt-get install -y gsl-bin
        sudo apt-get install -y libgsl0-dev
        sudo apt-get install -y ccache
    - name: Install system boost
      if: ${{ ! contains( matrix.variant, '-debug-' ) }}
      run: |
        sudo apt-get install -y libboost-serialization-dev
    - name: Install boost with debug flags
      if: contains( matrix.variant, '-debug-' )
      run: |
        .ci/install.boost
    - name: Install python packages needed for tests
      run: |
        python -m pip install --upgrade pip
        pip install --user Cython
        pip install --user numpy
        pip install --user pytest
        pip install --user six ;
        pip install --user pandas ;
        pip install --user mdtraj ;
        pip install --user MDAnalysis ;
        python -c "import MDAnalysis" ;
        python -c "import mdtraj" ;
    - name: Install Libtorch
      if: ${{ ! contains( matrix.variant, '-debug-' ) }} # libtorch is not compiled with GLIBCXX_DEBUG
      run: |
        # added by luigibonati
        mkdir -p $HOME/opt/
        cd $HOME/opt/ # GB: install in $HOME/opt/libtorch
        wget --no-check-certificate https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-1.13.1%2Bcpu.zip ;
        unzip libtorch-cxx11-abi-shared-with-deps-1.13.1+cpu.zip ;
        echo "LIBRARY_PATH=$PWD/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
        echo "LD_LIBRARY_PATH=$PWD/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
        echo "CPATH=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
        echo "INCLUDE=$PWD/libtorch/include/torch/csrc/api/include/:$PWD/libtorch/include/:$PWD/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
        echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-libtorch" >> $GITHUB_ENV
    - name: Install Doxygen
      if: contains( matrix.variant, '-doc-' )
      run: |
        sudo apt-get install -y graphviz
        sudo apt-get install -y doxygen-latex
        .ci/install.doxygen Release_1_8_17
        echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-pdfdoc" >> $GITHUB_ENV
        # make sure all tests are run
        echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV
    - name: Install lcov
      if: contains( matrix.variant, '-coverage-' )
      run: |
        .ci/install.lcov v1.16
        echo "PLUMED_CONFIG=$PLUMED_CONFIG --disable-external-lapack --disable-external-blas --enable-gcov CXXFLAGS=-O" >> $GITHUB_ENV
        # make sure all tests are run
        echo "PLUMED_ALL_TESTS=yes" >> $GITHUB_ENV
    - name: Setup debug flags
      if: contains( matrix.variant, '-debug-' )
      run: |
        echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-debug --enable-debug-glibcxx" >> $GITHUB_ENV
    - name: Install INTEL compiler
      # install INTEL at last since it modifies CC and CXX
      if: contains( matrix.variant, '-intel-' )
      run: |
        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
        sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
        rm GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
        echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
        sudo apt-get update
        sudo apt-get install intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mkl intel-oneapi-mkl-devel intel-oneapi-compiler-fortran
        source /opt/intel/oneapi/setvars.sh
        printenv >> $GITHUB_ENV
        echo "CXX=icpc" >> $GITHUB_ENV
        echo "CC=icc" >> $GITHUB_ENV
        echo "FC=ifort" >> $GITHUB_ENV
    - name: Install MPI
      # install MPI at last since it modifies CC and CXX
      if: contains( matrix.variant, '-mpi-' )
      run: |
        sudo apt-get install -y libopenmpi-dev openmpi-bin
        echo "CC=mpicc" >> $GITHUB_ENV
        echo "CXX=mpic++" >> $GITHUB_ENV
        echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV
        echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV
        echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV
        echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV
        echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV
        pip install --user mpi4py
        python -c "import mpi4py"
    - name: Build PLUMED
      run: |
        ccache -s -M 100M
        ./configure CXX="ccache $CXX" --enable-boost_serialization --disable-dependency-tracking --enable-modules=all LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH $PLUMED_CONFIG --prefix="$HOME/opt"
        make -j 4
        make install
        # check for global symbols, see https://github.com/plumed/plumed2/issues/549
        make nmcheck
        ccache -s -M 100M
    - name: Run tests
      if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) }}
      run: |
         (while true; do  # see https://github.com/actions/virtual-environments/issues/1860
              df -h
              sleep 15
              done) &
         make --no-print-directory -C regtest testclean
         # these can fail for numerical reasons
         make -C regtest checkfail
    - name: Run python tests
      run: |
         cd python
         pytest -v
    - name: Build doc
      env:
        GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
      if: contains( matrix.variant, '-doc-' )
      run: |
         make doc >/dev/null
    - name: Coverage
      env:
        GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
      if: contains( matrix.variant, '-coverage-' )
      run: |
         make -C developer-doc coverage
         .ci/push coverage
         # this is hanging for some reason now (2024-04-03) - GB
         #bash <(curl -s https://codecov.io/bash) > /dev/null
    - name: Push doc
      if: contains( matrix.variant, '-doc-' )
      env:
        GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
      run: |
         .ci/push doc

  codecheck:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v4
    - name: Set path
      run: |
         echo "$HOME/opt/bin" >> $GITHUB_PATH
    - name: Install requirements
      run: |
        .ci/install.cppcheck 2.10.3
        # it is important that this is the same version used to generate the actual ./configure
        .ci/install.autoconf 2.69
    - name: Build astyle
      run: |
        make -j 4 -C astyle
    - name: Checking code
      run: |
        # this is required so as to have all the include files in place
        # notice that this is done automatically in build
        # first make sure that dirslinks are generated for all modules
        ./configure --enable-modules=all
        # then generate the links
        make -C src/lib/ dirslinks
        make codecheck

  # We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12)
  fedora37:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v4
    - name: Build and run tests
      run: |
        make -C docker fedora37

  # We test on rockylinux8 as well
  rocky8:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v4
    - name: Build and run tests
      run: |
        make -C docker rocky8

  macports:
    runs-on: macos-13
    strategy:
      fail-fast: false
      matrix:
        variant: [ "" , "+allmodules" ]
        # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions
    env:
      PYVERS: "py39 py310"
    steps:
    - uses: actions/checkout@v4
    - uses: actions/cache@v4
      with:
        path: ~/.macports-ci-ccache
        key: ccache-macports-${{ matrix.variant }}-${{ github.sha }}
        restore-keys: ccache-macports-${{ matrix.variant }}-
    - name: Install MacPorts
      run: |
        wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci
        source ./macports-ci install
        source ./macports-ci ccache
    - name: Build local Portfile
      run: |
        make macports
        source ./macports-ci localports macports
    - name: Build PLUMED
      run: |
        sudo port -N -k install plumed ${{ matrix.variant }}
        plumed config show
        for p in $PYVERS ; do
          sudo port -N install $p-plumed
        done
        source ./macports-ci ccache --save
    - name: Run tests
      run: |
        sudo port -N -d test plumed ${{ matrix.variant }}
    - name: Run python tests
      run: |
        for p in $PYVERS ; do
          sudo port test $p-plumed
        done

  macsimple:
    runs-on: macos-13
    steps:
    - uses: actions/checkout@v4
    - name: Set paths
      run: |
        echo "$HOME/opt/bin" >> $GITHUB_PATH
        echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
        echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
        echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
        echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
    - name: Build PLUMED
      run: |
        # it seems brew update is screwing up something
        # GB on Mar 8, 2024
        #brew update > /dev/null
        brew install gawk
        ./configure --disable-dependency-tracking --prefix="$HOME/opt"
        make -j 4
        make install
    - name: Run tests
      run: |
         make --no-print-directory -C regtest
         # these can fail for numerical reasons
         make -C regtest checkfail

  conda:
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-20.04 , macos-13, macos-14 ]
    runs-on: ${{ matrix.os }}
    steps:
    - uses: actions/checkout@v4
    - name: Install conda
      run: |
        curl -LO https://raw.githubusercontent.com/GiovanniBussi/conda-ci/master/conda-ci
        source ./conda-ci install
        source ./conda-ci install-conda-build
    - name: Build PLUMED
      run: |
        source activate base
        export VERSION=none
        if [[ $GITHUB_REF == "refs/tags/"* ]]; then
          VERSION=${GITHUB_REF#refs/tags/}
          VERSION=${VERSION//-/_}
          VERSION=${VERSION#v}
        fi
        make -C conda
    - name: Deploy
      env:
        CONDA_UPLOAD_TOKEN: ${{ secrets.CONDA_UPLOAD_TOKEN }}
      if: ${{ startsWith( github.ref , 'refs/tags/' ) }}
      run: |
        source activate base
        export CONDA_LABEL=tag
        make -C conda upload