mamba first #159
Workflow file for this run
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| name: Testing pytraj | ||
| on: [push, pull_request, workflow_dispatch] | ||
| jobs: | ||
| build-linux: | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| max-parallel: 5 | ||
| matrix: | ||
| python-version: [3.9, 3.10, 3.11, 3.12] | ||
| steps: | ||
| - name: Install prerequisite packages | ||
| run: | | ||
| sudo apt-get install -y gfortran libbz2-dev libblas-dev liblapack-dev libfftw3-dev clang cmake-data cmake | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: Install mamba | ||
| run: | | ||
| conda install mamba -n base -c conda-forge | ||
| - name: Add conda to system path | ||
| run: echo $CONDA/bin >> $GITHUB_PATH | ||
| - name: Install conda packages with mamba | ||
| run: | | ||
| mamaba env create --file environment.yml --name env python=${{ matrix.python-version }} | ||
| mamaba activate env | ||
| - name: Install 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: | | ||
| git clone https://github.com/Amber-MD/cpptraj | ||
| cd cpptraj | ||
| export CPPTRAJHOME=`pwd` | ||
| yes | ./configure -shared -openmp gnu | ||
| make libcpptraj | ||
| cd ../ | ||
| - name: Install pytraj | ||
| run: python 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 | ||