CI.yaml

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