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Merge pull request #6 from Iximiel/feature/testmultipleversion
Setting up a test on multiple python versions
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‎.github/workflows/main.yml‎

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@@ -3,76 +3,121 @@ name: CI
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on: [push, pull_request]
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jobs:
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build:
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#this is setting up a new "test workflow" following the one we use for the plumed-testcenter
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setup-plumed:
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runs-on: ubuntu-latest
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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- uses: actions/cache@v2
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- name: calculate cache key for the compilation
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id: get-key
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env:
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GH_TOKEN: ${{ github.token }}
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run: |
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mastersha=$(gh api repos/plumed/plumed2/branches --paginate --jq '.[] | select( .name | match("^master$")) | .commit.sha')
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echo "key=$mastersha" >> $GITHUB_OUTPUT
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- uses: actions/cache@v4
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with:
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path: |
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~/opt
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~/.ccache
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key: ccache-${{ runner.os }}-${{ github.sha }}
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restore-keys: ccache-${{ runner.os }}-
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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~/opt
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key: ccache-${{ runner.os }}-master-${{ steps.get-key.outputs.key }}
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restore-keys: ccache-${{ runner.os }}-master
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- name: Set paths
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run: |
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echo "$HOME/opt/bin" >> $GITHUB_PATH
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echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
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echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
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echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
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echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
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echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
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# needed to avoid MPI warning
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echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV
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- name: Install plumed
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echo "$HOME/opt/bin" >> $GITHUB_PATH
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echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
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echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
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echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
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echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
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echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
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# needed to avoid MPI warning
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echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV
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#we need to checkout to access .ci/install.libtorch
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# - uses: actions/checkout@v4
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# with:
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# persist-credentials: false
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- name: Install dependencies
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run: |
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sudo apt update
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sudo apt install mpi-default-bin mpi-default-dev
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sudo apt install libfftw3-dev gsl-bin libgsl0-dev libboost-serialization-dev
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sudo apt install ccache
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sudo apt-get update
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pip install PyYAML pytz
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git clone --bare https://github.com/plumed/plumed2.git
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sudo ln -s ccache /usr/local/bin/mpic++
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export PATH=/usr/lib/ccache:${PATH}
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ccache -p
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ccache -s
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# .ci/install.libtorch
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# version=master or version=f123f12f3 to select a specific version
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# pick newest release branch (alphabetic, will fail at v2.10)
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# CXX="mpic++" .ci/install.plumed version="$(cd plumed2.git ; git branch | sed "s/^ *//" | grep '^v2\.[0-9]$' | tail -n 1)" repo=$PWD/plumed2.git
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# GB: in addition, we install master version as plumed_master
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CXX="mpic++" .ci/install.plumed version=master repo=$PWD/plumed2.git
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ccache -s
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- name: Copy json syntax to directory to upload
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mkdir -p ~/.ccache/ccache
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- name: Install plumed
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uses: plumed/install-plumed@v1
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with:
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CC: "ccache mpicc"
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CXX: "ccache mpic++"
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version: master
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extra_options: --enable-modules=all --enable-boost_serialization --enable-fftw --enable-libtorch LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH --disable-basic-warnings
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- name: prepare plumed tar
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run: |
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mkdir json
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cp /home/runner/opt/lib/plumed/json/syntax.json json
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- name: Put json file so it can be downloaded
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cd $HOME
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tar cf plumed-master.tar opt/
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- name: Upload artifact
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uses: actions/upload-artifact@v4
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with:
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name: json-syntax
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path: json
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- name: Install PlumedToHTML
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# And install the package
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run: python setup.py install
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name: plumed-master
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path: ~/plumed-master.tar
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retention-days: 1
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build-and-test:
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needs: setup-plumed
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strategy:
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fail-fast: false
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matrix:
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# as now the various plumed support sites use 3.9 and 3.8 (and with 3.10 starts to fail...)
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python-version: ["3.8", "3.9"] #, "3.10", "3.11", "3.12"]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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persist-credentials: false
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- name: Install plumed dependencies
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run: |
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sudo apt update
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sudo apt install mpi-default-bin mpi-default-dev
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sudo apt install libfftw3-dev gsl-bin libgsl0-dev libboost-serialization-dev
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- name: Set paths
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run: |
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echo "$HOME/opt/bin" >> $GITHUB_PATH
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echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
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echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
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echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
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echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
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echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
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# needed to avoid MPI warning
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echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV
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- name: Download artifacts with plumed
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uses: actions/download-artifact@v4
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with:
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name: plumed-master
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path: ~
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- name: Unpacking the artifacts
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run: |
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cd $HOME
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tar xf ${GITHUB_WORKSPACE}/plumed-master.tar
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- name: Confirming that plumed can execute
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run: |
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plumed info --root
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cat $(plumed info --root)/json/syntax.json | jq '.["ENDPLUMED"]'
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: setup.py
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install tox
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- name: Run tests
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run: |
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pip install tox
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tox
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python -m tox
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- name: Upload Coverage to Codecov
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uses: codecov/codecov-action@v2
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uses: codecov/codecov-action@v2

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