do a clean run through of the tutorial notebook #408
Workflow file for this run
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| # 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 |