[WIP] Fix CI by upgrading to new GROMACS #362
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| name: ci | |
| on: | |
| push: | |
| branches: | |
| - "master" | |
| pull_request: | |
| branches: | |
| - "master" | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| #- macOS-latest | |
| - macOS-12 | |
| - ubuntu-20.04 | |
| python-version: | |
| - "3.8" | |
| - "3.9" | |
| env: | |
| CI_OS: ${{ matrix.os }} | |
| PYVER: ${{ matrix.python-version }} | |
| PACKAGE: forcebalance | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up conda environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| create-args: >- # beware the >- instead of |, we don't split on newlines but on spaces | |
| python=${{ matrix.python-version }} | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| - name: Environment Information | |
| run: | | |
| conda info --all | |
| conda list | |
| # Need to replace ndcctools with this block | |
| # - name: Install Work Queue | |
| # run: | | |
| # wget https://raw.githubusercontent.com/leeping/forcebalance/master/tools/install-cctools.sh | |
| # bash install-cctools.sh | |
| # echo "Checking for Work Queue import; if successful, no message will be printed" | |
| # python -c "import work_queue" | |
| # export PATH="$GITHUB_WORKSPACE/opt/cctools/current/bin:$PATH" | |
| - name: Install Tinker | |
| run: | | |
| if [[ "$CI_OS" == 'ubuntu-20.04' ]]; then | |
| wget https://dasher.wustl.edu/tinker/downloads/bin-linux-8.8.3.tar.gz -O tinker.tar.gz | |
| fi | |
| if [[ "$CI_OS" == 'macOS-12' ]]; then | |
| wget https://dasher.wustl.edu/tinker/downloads/bin-macos-8.8.3.tar.gz -O tinker.tar.gz | |
| fi | |
| tar xvzf tinker.tar.gz &> untar.log | |
| mkdir -p $GITHUB_WORKSPACE/opt/tinker/8.8.3 | |
| if [[ "$CI_OS" == 'ubuntu-20.04' ]]; then | |
| mv bin-linux $GITHUB_WORKSPACE/opt/tinker/8.8.3/bin | |
| fi | |
| if [[ "$CI_OS" == 'macOS-12' ]]; then | |
| mv bin-macos $GITHUB_WORKSPACE/opt/tinker/8.8.3/bin | |
| fi | |
| echo "$GITHUB_WORKSPACE/opt/tinker/8.8.3/bin" >> $GITHUB_PATH | |
| #- name: Install Gromacs | |
| # run: | | |
| # wget http://ftp.gromacs.org/pub/gromacs/gromacs-5.1.5.tar.gz | |
| # tar xvzf gromacs-5.1.5.tar.gz | |
| # cd gromacs-5.1.5 | |
| # cp -r cmake cmake_s | |
| # cd cmake | |
| # cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_DOUBLE=ON -DGMX_BUILD_OWN_FFTW=ON -DGMX_USE_RDTSCP=OFF .. | |
| # make -j 8 && make install | |
| # cd ../cmake_s | |
| # cmake -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/opt/gromacs/5.1.5 -DGMX_BUILD_OWN_FFTW=ON -DGMX_USE_RDTSCP=OFF .. | |
| # make -j 8 && make install | |
| # cd .. | |
| # . $GITHUB_WORKSPACE/opt/gromacs/5.1.5/bin/GMXRC.bash | |
| # echo "$GITHUB_WORKSPACE/opt/gromacs/5.1.5/bin" >> $GITHUB_PATH | |
| # which gmx | |
| # which gmx_d | |
| - name: Extract data archives | |
| run: | | |
| cd studies/001_water_tutorial | |
| tar xvjf targets.tar.bz2 | |
| cd ../../ | |
| - name: Install package | |
| run: | | |
| python -m pip install --no-deps . | |
| python -c "import forcebalance; print(forcebalance.__version__)" | |
| - name: Run tests | |
| run: | | |
| pytest -v --cov=forcebalance --cov-config=setup.cfg --durations=0 --cov-report=xml -k "not TestEvaluatorBromineStudy" src/tests/ | |
| - name: Run water study | |
| run: | | |
| cd studies/001_water_tutorial | |
| tar xvjf targets.tar.bz2 | |
| ForceBalance very_simple.in | |
| cd ../../ | |
| - name: Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: false |