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

on: [push, pull_request]

jobs:
  # This workflow contains a single job called "build"
  build:
    strategy:
      matrix:
        omp: [OFF, ON]
        lapack: [OFF, ON]
        python-version: ["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@v4
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      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
        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 -e .[docs,tests]
          pip show mir-flare

    - 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: Run tutorial
      run: |
        pip install -U jupyter nbconvert
        cp tutorials/sparse_gp_tutorial.ipynb tutorial.ipynb
        jupyter nbconvert --to script tutorial.ipynb
        sed -i '/^get_ipython()/s/^/# /' tutorial.py
        sed -i '/^plt/s/^/# /' tutorial.py
        wget http://quantum-machine.org/gdml/data/npz/md17_aspirin.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
        python tutorial.py
        rm Al* aluminum.txt aspirin.txt md17_aspirin.npz tutorial.ipynb tutorial.py

    - name: Run Doxygen
      uses: mattnotmitt/doxygen-action@v1.9.8
      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@v4
      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'