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IximielIximiel
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Setting up a test on multiple python versions
typo typo II artifact:name artifact:name? Chnaging step order installing the actual module may help in testing checking that plumed exists now with dependencies typo III typo IV try to remove the installation some cleanup some cleanup II readded the codecov action restored space
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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: Iximiel/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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