Refactor actionlist.pyx #279
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| name: Python Package using Conda | |
| on: | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| # Enable bash login shell to activate conda environment | |
| shell: bash -l {0} | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Cache conda | |
| uses: actions/cache@v4 | |
| env: | |
| CACHE_NUMBER: 1 # Increase this value to reset cache if environment.yml has changed | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }} | |
| - name: Install prerequisite packages | |
| run: | | |
| sudo apt-get install -y gfortran libbz2-dev libblas-dev liblapack-dev libfftw3-dev clang cmake-data cmake | |
| - name: Get latest cpptraj commit hash | |
| id: get-hash | |
| run: | | |
| latest_hash=$(git ls-remote https://github.com/Amber-MD/cpptraj.git refs/heads/master | awk '{print $1}') | |
| echo "::set-output name=hash::$latest_hash" | |
| - name: Cache cpptraj | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/cpptraj | |
| key: ${{ runner.os }}-cpptraj-${{ steps.get-hash.outputs.hash }} | |
| restore-keys: | | |
| ${{ runner.os }}-cpptraj- | |
| - name: Install CPPTRAJ dependencies | |
| run: | | |
| curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz | |
| tar -zxf v4.9.2.tar.gz | |
| cd netcdf-c-4.9.2 | |
| ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME | |
| make -j2 | |
| make install | |
| cd .. | |
| export PATH=$HOME/bin:$PATH | |
| - name: Install cpptraj | |
| run: | | |
| if [ ! -d "$HOME/cpptraj" ]; then | |
| echo $HOME | |
| pwd | |
| git clone https://github.com/Amber-MD/cpptraj | |
| cd cpptraj | |
| export CPPTRAJHOME=`pwd` | |
| yes | ./configure -shared -openmp gnu | |
| make libcpptraj | |
| cd ../ | |
| fi | |
| - name: Set up Miniconda # Do this after installing cpptraj to avoid "yes: standard output: Broken pipe" error | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| auto-update-conda: true | |
| auto-activate-base: false | |
| activate-environment: pytraj-gha | |
| environment-file: environment.yml | |
| mamba-version: "*" | |
| channels: conda-forge | |
| channel-priority: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Check conda environment | |
| run: | | |
| conda --version | |
| which conda | |
| which python | |
| which python3 | |
| - name: Install pytraj | |
| run: | | |
| which python3 | |
| python3 setup.py install | |
| - name: Test with pytest | |
| run: | | |
| export CPPTRAJHOME=`pwd`/cpptraj && cd tests && pytest -vs --ignore=test_parallel_pmap --ignore=test_run_mpi.py --ignore=test_energy/test_pmap_sander.py --ignore=test_parallel_mpi --ignore=test_actionlist.py |