flare.yml

# Adapted from: https://github.com/satu0king/Github-Documentation-With-Doxygen
# This is a basic workflow to help you get started with Actions

name: flare

# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the master branch
on: [push, pull_request]


# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
  # This workflow contains a single job called "build"
  build:
    strategy:
      matrix:
        omp: [OFF, ON]
        lapack: [OFF, ON]
        python-version: ["3.7", "3.8"]
    name: "(OpenMP, Lapack, Python) ="

    # The type of runner that the job will run on
    runs-on: ubuntu-latest

    env:
      BUILD_DIR: build_${{ matrix.omp }}_${{ matrix.lapack }}
      CC: gcc-9
      CXX: g++-9

    # Steps represent a sequence of tasks that will be executed as part of the job
    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Build
      run: |
        sudo apt install liblapacke liblapacke-dev libopenmpi-dev
        mkdir ${BUILD_DIR}
        cd ${BUILD_DIR}

        if [ "${{ matrix.omp }}" = "ON" ]; then
          unset NO_OMP
        else
          export NO_OMP=1
        fi

        if [ "${{ matrix.lapack }}" = "ON" ]; then
          unset NO_LAPACK
        else
          export NO_LAPACK=1
        fi

        echo "OpenMP ${{ matrix.omp }}"
        echo "Lapack ${{ matrix.lapack }}"

        cmake ..
        cmake --build . -j4
        cp _C_flare* ../flare/bffs/sgp
        cd ctests
        ./tests

    - name: Install LAMMPS
      run: |
        git clone --depth 1 https://github.com/lammps/lammps.git lammps

        cd lammps/src
        cp pair_hybrid.* pair_lj_cut.* ..
        rm pair_*.cpp pair_*.h
        mv ../pair_hybrid.* ../pair_lj_cut.* .
        cp MANYBODY/pair_tersoff.* .
        rm MANYBODY/pair_*.*
        rm MANYBODY/fix_*.*
        mv pair_tersoff.* MANYBODY/
        cp KOKKOS/pair_kokkos.* .
        rm KOKKOS/pair_*.*
        mv pair_kokkos.* KOKKOS/
        cd ../..

        cd lammps_plugins
        ./install.sh $(pwd)/../lammps
        cd ..
        sudo cp -r ${BUILD_DIR}/External/Eigen3/Eigen /usr/include
        cd lammps
        mkdir build
        cd build
        cmake ../cmake -DPKG_KOKKOS=ON -DKokkos_ENABLE_OPENMP=ON -DPKG_MANYBODY=ON
        make -j4

    - name: Pip install
      run: |
        pip install -U codecov pytest pytest-cov pytest_mock Sphinx sphinx-rtd-theme breathe nbsphinx
        pip install -r requirements.txt

    - name: Patch ASE
      run: |
        ase_file="$(dirname $(python3 -c 'import ase; print(ase.__file__)'))/calculators/lammpsrun.py"
        sed -i 's/line.startswith(_custom_thermo_mark)/line.strip\(\).startswith\("Step"\)/g' $ase_file

    - name: Run tests
      run: |
        export lmp=$(pwd)/lammps/build/lmp
        cd tests
        pytest

    - name: Run LAMMPS tests with Kokkos
      run: |
        export lmp="$(pwd)/lammps/build/lmp -k on t 4 -sf kk -pk kokkos newton on neigh full"
        cd tests
        pytest test_lammps.py

    - name: Install Sphinx and Breathe
      run: |
        sudo apt-get update
        sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx

    - name: Run Doxygen
      uses: mattnotmitt/doxygen-action@v1.1.0
      with:
        # Path to Doxyfile
        doxyfile-path: "./Doxyfile" # default is ./Doxyfile
        # Working directory
        working-directory: "./docs" # default is .

    - name: Run Sphinx
      run: |
        export PYTHONPATH=$PYTHONPATH:$PWD/lammps/python
        cd docs
        pwd
        ls
        make html

    - name: Publish the docs
      uses: peaceiris/actions-gh-pages@v3
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        # Default Doxyfile build documentation to html directory.
        # Change the directory if changes in Doxyfile
        publish_dir: ./docs/build/html
      if: github.event_name == 'pull_request' && matrix.lapack == 'on' && matrix.omp == 'on'

#     - name: Run tutorial
#       run: |
#         cd tests
#         # Download colab notebook
#         export fileid="18_pTcWM19AUiksaRyCgg9BCpVyw744xv"
#         wget -O tutorial.ipynb 'https://docs.google.com/uc?export=download&id='${fileid}
#         # Convert notebook into python script
#         pip install -U jupyter nbconvert
#         jupyter nbconvert --to script tutorial.ipynb
#         # Remove bash commands in the notebook
#         sed '/!/d' tutorial.txt > tutorial.py
#         cat test_tutorial.py tutorial.py > tuttest.py
#         # Download datasets needed for the tutorial
#         wget http://quantum-machine.org/gdml/data/npz/aspirin_dft.npz
#         wget https://www.ctcms.nist.gov/potentials/Download/1999--Mishin-Y-Farkas-D-Mehl-M-J-Papaconstantopoulos-D-A--Al/2/Al99.eam.alloy
#         # Run script
#         pytest -s tuttest.py
#         # Remove output files
#         rm Al* aspirin_dft.npz tutorial.ipynb tuttest.py tutorial.py tutorial.txt