Setting up the tests

.github/workflows/ci.yml

@@ -2,7 +2,13 @@ name: CI
 
 on:
   push:
+  #I am removing this as soon I make  my branch work! 
+    branches:
+    - 'master'
   pull_request:
+  #I am removing this as soon I make  my branch work! 
+    branches:
+    - 'master'
 
 env:
 # on CI, better dump stack trace in case there is an error
@@ -14,317 +20,23 @@ env:
   CXX: g++
 
 jobs:
+
   linux:
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        variant:
-        - -doc-mpi-
-        - -mpi-
-        - -coverage-mpi-
-        - -debug-
-        - -debug-mpi-
-        - -intel-
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/cache@v3
-      with:
-        path: ~/.ccache
-        key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }}
-        restore-keys: ccache-reset1-linux${{ matrix.variant }}hash-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: 3.7
-    - name: Set paths
-      run: |
-        echo "$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
-    - 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 "MPIEXEC=mpirun --oversubscribe" >> $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
-         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
+    uses: ./.github/workflows/linuxWF.yml
+    secrets: inherit
 
   codecheck:
-    runs-on: ubuntu-20.04
-    steps:
-    - uses: actions/checkout@v3
-    - name: Set path
-      run: |
-         echo "$HOME/opt/bin" >> $GITHUB_PATH
-    - name: Install requirements
-      run: |
-        .ci/install.cppcheck 2.10.2
-        # it is important that this is the same version used to generate the actual ./configure
-        .ci/install.autoconf 2.69
-    - name: Build astyle
-      run: |
-        make -j 4 -C astyle
-    - name: Checking code
-      run: |
-        # this is required so as to have all the include files in place
-        # notice that this is done automatically in build
-        # first make sure that dirslinks are generated for all modules
-        ./configure --enable-modules=all
-        # then generate the links
-        make -C src/lib/ dirslinks
-        make codecheck
-
-  # We test on centos7 to make sure we have compatibility with older compilers (gcc 4.8)
-  centos7:
-    runs-on: ubuntu-20.04
-    steps:
-    - uses: actions/checkout@v3
-    - name: Build and run tests
-      run: |
-        make -C docker centos7
-
-  # We test on fedora37 to make sure we have compatibility with newer compilers (gcc 12)
-  fedora37:
-    runs-on: ubuntu-20.04
-    steps:
-    - uses: actions/checkout@v3
-    - name: Build and run tests
-      run: |
-        make -C docker fedora37
-
-  # We test on rockylinux8 as well
-  rocky8:
-    runs-on: ubuntu-20.04
-    steps:
-    - uses: actions/checkout@v3
-    - name: Build and run tests
-      run: |
-        make -C docker rocky8
-
-  macports:
-    runs-on: macos-11
-    strategy:
-      fail-fast: false
-      matrix:
-        variant: [ "" , "+allmodules" ]
-        # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions
-    env:
-      PYVERS: "py37 py38 py39 py310"
-    steps:
-    - uses: actions/checkout@v3
-    - uses: actions/cache@v3
-      with:
-        path: ~/.macports-ci-ccache
-        key: ccache-macports-${{ 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
+    uses: ./.github/workflows/codecheckWF.yml
+    secrets: inherit
 
-  macsimple:
-    runs-on: macos-11
-    steps:
-    - uses: actions/checkout@v3
-    - 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" >> $GITHUB_ENV
-    - name: Build PLUMED
-      run: |
-        brew update > /dev/null
-        brew install gawk
-        ./configure --disable-dependency-tracking --prefix="$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
+  mac:
+    uses: ./.github/workflows/macWF.yml
+    secrets: inherit
+
+  docker:
+    uses: ./.github/workflows/dockerWF.yml
+    secrets: inherit
 
   conda:
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-20.04 , macos-11]
-    runs-on: ${{ matrix.os }}
-    steps:
-    - uses: actions/checkout@v3
-    - 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
+    uses: ./.github/workflows/condaWF.yml
+    secrets: inherit