1.4.2 release - Bug fixes, new features #395
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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="$(pwd)/lammps/build/lmp -k on t 4 -sf kk -pk kokkos newton on neigh full" | |
| cd tests | |
| pytest test_lammps.py | |
| - name: Install Sphinx and Breathe | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx | |
| - name: Run Doxygen | |
| uses: mattnotmitt/[email protected] | |
| with: | |
| # Path to Doxyfile | |
| doxyfile-path: "./Doxyfile" # default is ./Doxyfile | |
| # Working directory | |
| working-directory: "./docs" # default is . | |
| - name: Run Sphinx | |
| run: | | |
| export PYTHONPATH=$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 |