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Merged
gtribello merged 2 commits into from
Feb 3, 2025
Merged

Setting up a test on multiple python versions #6

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Setting up a test on multiple python versions
Iximiel Dec 16, 2024
71d2723
changed the install-plumed action author
Iximiel Jan 17, 2025
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151 changes: 98 additions & 53 deletions .github/workflows/main.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,76 +3,121 @@ name: CI
on: [push, pull_request]

jobs:
build:
#this is setting up a new "test workflow" following the one we use for the plumed-testcenter
setup-plumed:
runs-on: ubuntu-latest

steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2

- uses: actions/cache@v2
- name: calculate cache key for the compilation
id: get-key
env:
GH_TOKEN: ${{ github.token }}
run: |
mastersha=$(gh api repos/plumed/plumed2/branches --paginate --jq '.[] | select( .name | match("^master$")) | .commit.sha')
echo "key=$mastersha" >> $GITHUB_OUTPUT
- uses: actions/cache@v4
with:
path: |
~/opt
~/.ccache
key: ccache-${{ runner.os }}-${{ github.sha }}
restore-keys: ccache-${{ runner.os }}-

- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: 3.8

~/opt
key: ccache-${{ runner.os }}-master-${{ steps.get-key.outputs.key }}
restore-keys: ccache-${{ runner.os }}-master
- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
# needed to avoid MPI warning
echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV

- name: Install plumed
echo "$HOME/opt/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
# needed to avoid MPI warning
echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV
#we need to checkout to access .ci/install.libtorch
# - uses: actions/checkout@v4
# with:
# persist-credentials: false

- name: Install dependencies
run: |
sudo apt update
sudo apt install mpi-default-bin mpi-default-dev
sudo apt install libfftw3-dev gsl-bin libgsl0-dev libboost-serialization-dev
sudo apt install ccache
sudo apt-get update
pip install PyYAML pytz
git clone --bare https://github.com/plumed/plumed2.git
sudo ln -s ccache /usr/local/bin/mpic++
export PATH=/usr/lib/ccache:${PATH}
ccache -p
ccache -s
# .ci/install.libtorch
# version=master or version=f123f12f3 to select a specific version
# pick newest release branch (alphabetic, will fail at v2.10)
# CXX="mpic++" .ci/install.plumed version="$(cd plumed2.git ; git branch | sed "s/^ *//" | grep '^v2\.[0-9]$' | tail -n 1)" repo=$PWD/plumed2.git
# GB: in addition, we install master version as plumed_master
CXX="mpic++" .ci/install.plumed version=master repo=$PWD/plumed2.git
ccache -s

- name: Copy json syntax to directory to upload
mkdir -p ~/.ccache/ccache
- name: Install plumed
uses: plumed/install-plumed@v1
with:
CC: "ccache mpicc"
CXX: "ccache mpic++"
version: master
extra_options: --enable-modules=all --enable-boost_serialization --enable-fftw --enable-libtorch LDFLAGS=-Wl,-rpath,$LD_LIBRARY_PATH --disable-basic-warnings
- name: prepare plumed tar
run: |
mkdir json
cp /home/runner/opt/lib/plumed/json/syntax.json json
- name: Put json file so it can be downloaded
cd $HOME
tar cf plumed-master.tar opt/

- name: Upload artifact
uses: actions/upload-artifact@v4
with:
name: json-syntax
path: json

- name: Install PlumedToHTML
# And install the package
run: python setup.py install

name: plumed-master
path: ~/plumed-master.tar
retention-days: 1

build-and-test:
needs: setup-plumed
strategy:
fail-fast: false
matrix:
# as now the various plumed support sites use 3.9 and 3.8 (and with 3.10 starts to fail...)
python-version: ["3.8", "3.9"] #, "3.10", "3.11", "3.12"]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
persist-credentials: false
- name: Install plumed dependencies
run: |
sudo apt update
sudo apt install mpi-default-bin mpi-default-dev
sudo apt install libfftw3-dev gsl-bin libgsl0-dev libboost-serialization-dev

- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$HOME/opt/libtorch/include/torch/csrc/api/include/:$HOME/opt/libtorch/include/:$HOME/opt/libtorch/include/torch:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$HOME/opt/libtorch/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
# needed to avoid MPI warning
echo "OMPI_MCA_btl=^openib" >> $GITHUB_ENV
- name: Download artifacts with plumed
uses: actions/download-artifact@v4
with:
name: plumed-master
path: ~
- name: Unpacking the artifacts
run: |
cd $HOME
tar xf ${GITHUB_WORKSPACE}/plumed-master.tar
- name: Confirming that plumed can execute
run: |
plumed info --root
cat $(plumed info --root)/json/syntax.json | jq '.["ENDPLUMED"]'
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
cache: 'pip'
cache-dependency-path: setup.py
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install tox
- name: Run tests
run: |
pip install tox
tox
python -m tox

- name: Upload Coverage to Codecov
uses: codecov/codecov-action@v2
uses: codecov/codecov-action@v2
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