Trying to debug RTD #196
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| name: CI | |
| on: | |
| # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming | |
| # Existing codes likely still have "master" as the primary branch | |
| # Both are tracked here to keep legacy and new codes working | |
| push: | |
| branches: | |
| - "master" | |
| - "main" | |
| pull_request: | |
| branches: | |
| - "master" | |
| - "main" | |
| # schedule: | |
| # # Nightly tests run on master by default: | |
| # # Scheduled workflows run on the latest commit on the default or base branch. | |
| # # (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule) | |
| # - cron: "0 0 * * *" | |
| jobs: | |
| test: | |
| name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] # [macOS-latest, ubuntu-latest, windows-latest] | |
| python-version: [3.8] #, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Additional info about the build | |
| shell: bash | |
| run: | | |
| uname -a | |
| df -h | |
| ulimit -a | |
| # More info on options: https://github.com/conda-incubator/setup-miniconda | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/conda-envs/test_env.yaml | |
| channels: conda-forge,defaults | |
| activate-environment: test | |
| auto-update-conda: false | |
| auto-activate-base: false | |
| show-channel-urls: true | |
| #- name: Build OpenMM | |
| # shell: bash -l {0} | |
| # run: | | |
| # git clone https://github.com/openmm/openmm.git | |
| # mkdir -p /home/runner/work/build/bin | |
| # cd openmm | |
| # mkdir build | |
| # cd build | |
| # cmake -DCMAKE_INSTALL_PREFIX=/home/runner/work/build/bin/openmm .. | |
| # make | |
| # make install | |
| # make PythonInstall | |
| # cd ../.. | |
| - name: Get NAMD | |
| shell: bash -l {0} | |
| env: | |
| # NAMD_ACCESS_TOKEN: ${{ secrets.NAMD_ACCESS_TOKEN }} | |
| NAMD_ACCESS_TOKEN2: ${{ secrets.NAMD_ACCESS_TOKEN2 }} | |
| run: | | |
| git clone https://github.com/UIUC-PPL/charm | |
| cd charm | |
| ./build charm++ multicore-linux-x86_64 --with-production | |
| export CHRMDIR=${PWD} | |
| cd .. | |
| wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl8.5.9-linux-x86_64.tar.gz | |
| tar xzf tcl8.5.9-linux-x86_64.tar.gz | |
| mkdir tcl | |
| mv tcl8.5.9-linux-x86_64 tcl | |
| export TCLINC=${PWD}/tcl/tcl8.5.9-linux-x86_64/lib/ | |
| export TCLLIB=${PWD}/tcl/tcl8.5.9-linux-x86_64/include/ | |
| export LD_LIBRARY_PATH=${PWD}/tcl/tcl8.5.9-linux-x86_64/include/:$LD_LIBRARY_PATH | |
| export TCLDIR=${PWD}/tcl/tcl8.5.9-linux-x86_64 | |
| # This was commented before | |
| #wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz | |
| #tar xzf fftw-linux-x86_64.tar.gz | |
| #mkdir fftw | |
| #mv linux-x86_64 fftw | |
| #export FFTWDIR=${PWD}/fftw/linux-x86_64 | |
| git clone https://oauth2:${NAMD_ACCESS_TOKEN2}@gitlab.com/tcbgUIUC/namd.git | |
| cd namd | |
| ./config Linux-x86_64-g++ --charm-base $CHRMDIR --tcl-prefix $TCLDIR --without-fftw #--fftw-prefix ${FFTWDIR} | |
| cd Linux-x86_64-g++ | |
| make | |
| pwd | |
| ls | |
| export PATH="$PWD:$PATH" | |
| echo "PATH: $PATH" | |
| cd ../.. | |
| - name: Install package | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| python -m pip install . --no-deps | |
| conda list | |
| # Install seekr systems repository | |
| git clone https://github.com/seekrcentral/seekr2_systems.git | |
| # Install seekr openmm plugin | |
| git clone https://github.com/seekrcentral/seekr2_openmm_plugin.git | |
| cd seekr2_openmm_plugin/seekr2plugin | |
| mkdir build | |
| cd build | |
| export OPENMM_INSTALL_DIR=${CONDA_PREFIX} | |
| export OPENMM_LIB_PATH=$OPENMM_INSTALL_DIR/lib | |
| export OPENMM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins | |
| export LD_LIBRARY_PATH=$OPENMM_LIB_PATH:$OPENMM_PLUGIN_DIR:$LD_LIBRARY_PATH | |
| cmake -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} -DSEEKR2_BUILD_OPENCL_LIB=OFF -DOPENMM_DIR=${CONDA_PREFIX} .. | |
| make | |
| make install | |
| make PythonInstall | |
| make test | |
| - name: Install BrownDye | |
| shell: bash -l {0} | |
| run: | | |
| sudo apt-get install libexpat1 apbs | |
| wget https://browndye.ucsd.edu/downloads/browndye2-ubuntu-20.04.tar.gz | |
| tar -xzf browndye2-ubuntu-20.04.tar.gz | |
| cd browndye2/bin | |
| export PATH="$PWD:$PATH" | |
| echo "PATH: $PATH" | |
| ls | |
| cd ../.. | |
| - name: Run tests | |
| # conda setup requires this special shell | |
| shell: bash -l {0} | |
| run: | | |
| export PATH="/home/runner/work/seekr2/seekr2/browndye2/bin:$PATH" | |
| export PATH="/home/runner/work/seekr2/seekr2/namd/Linux-x86_64-g++/:$PATH" | |
| python -m pip install . | |
| python -m openmm.testInstallation | |
| pytest -v --cov=seekr2 --cov-report=xml --color=yes -m "not needs_cuda" seekr2/tests/ seekr2_systems/tests/ | |
| # pytest -v --cov=seekr2 --cov-report=xml --color=yes -m "not needs_cuda" seekr2/tests/ | |
| # pytest -v --cov=seekr2_systems --cov-append --cov-report=xml --color=yes -m "not needs_cuda" seekr2_systems/tests/ | |
| - name: CodeCov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| directory: ./coverage/reports/ | |
| flags: unittests | |
| name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} | |
| fail_ci_if_error: true | |
| path_to_write_report: ./coverage/codecov_report.txt | |
| verbose: true |