Skip to content

Added code to generate mermaid graphs for plumed inputs #154

Added code to generate mermaid graphs for plumed inputs

Added code to generate mermaid graphs for plumed inputs #154

Workflow file for this run

name: CI
on: [push, pull_request]
jobs:
build:
runs-on: ubuntu-latest
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v2
- uses: actions/cache@v2
with:
path: |
~/opt
~/.ccache
key: ccache-${{ 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
- 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" >> $GITHUB_ENV
- name: Install plumed
run: |
sudo apt update
sudo apt install mpi-default-bin mpi-default-dev
sudo apt install libfftw3-dev gsl-bin libgsl0-dev libboost-serialization-dev
sudo apt install ccache
sudo apt-get update
pip install PyYAML pytz
git clone --bare https://github.com/plumed/plumed2.git
sudo ln -s ccache /usr/local/bin/mpic++
export PATH=/usr/lib/ccache:${PATH}
ccache -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
run: |
mkdir json
cp /home/runner/opt/lib/plumed/json/syntax.json json
- name: Put json file so it can be downloaded
uses: actions/upload-artifact@v2
with:
name: json-syntax
path: json
- name: Install PlumedToHTML
# And install the package
run: python setup.py install
- name: Run tests
run: |
pip install tox
tox
- name: Upload Coverage to Codecov
uses: codecov/codecov-action@v2