try installing in editable mode #454
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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 | |
| 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 | |
| # # 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 ${BUILD_DIR}/External/Eigen3/Eigen /usr/include | |
| # cd lammps | |
| # mkdir build | |
| # cd build | |
| # cmake ../cmake -DPKG_KOKKOS=ON -DKokkos_ENABLE_OPENMP=ON -DPKG_MANYBODY=ON | |
| # make -j4 | |
| - name: Pip install | |
| run: | | |
| pip install -e . | |
| # pip install -v -C cmake.define.CMAKE_PREFIX_PATH=$CONDA_PREFIX .[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="$(pwd)/lammps/build/lmp -k on t 4 -sf kk -pk kokkos newton on neigh full" | |
| # cd tests | |
| # pytest test_lammps.py | |
| # - name: Run tutorial | |
| # run: | | |
| # pip install -U jupyter nbconvert | |
| # cp tutorials/sparse_gp_tutorial.ipynb tutorial.ipynb | |
| # jupyter nbconvert --to script tutorial.ipynb | |
| # sed -i '/^get_ipython()/s/^/# /' tutorial.py | |
| # sed -i '/^plt/s/^/# /' tutorial.py | |
| # wget http://quantum-machine.org/gdml/data/npz/md17_aspirin.npz | |
| # wget https://www.ctcms.nist.gov/potentials/Download/1999--Mishin-Y-Farkas-D-Mehl-M-J-Papaconstantopoulos-D-A--Al/2/Al99.eam.alloy | |
| # python tutorial.py | |
| # rm Al* aluminum.txt aspirin.txt md17_aspirin.npz tutorial.ipynb tutorial.py | |
| # - name: Install Sphinx and Breathe | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install python3-sphinx python3-sphinx-rtd-theme python3-breathe python3-nbsphinx | |
| # - name: Run Doxygen | |
| # uses: mattnotmitt/[email protected] | |
| # with: | |
| # # Path to Doxyfile | |
| # doxyfile-path: "./Doxyfile" # default is ./Doxyfile | |
| # # Working directory | |
| # working-directory: "./docs" # default is . | |
| # - name: Run Sphinx | |
| # run: | | |
| # export PYTHONPATH=$PYTHONPATH:$PWD/lammps/python | |
| # cd docs | |
| # pwd | |
| # ls | |
| # make html | |
| # - name: Publish the docs | |
| # uses: peaceiris/actions-gh-pages@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' |