Refactor all_actions.py (mostly beautify it) #87
Workflow file for this run
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| name: Python Package using Conda | |
| on: | |
| push: | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - name: Install prerequisite packages | |
| run: | | |
| sudo apt-get install gfortran | |
| sudo apt-get install libbz2-dev | |
| sudo apt-get install libblas-dev liblapack-dev | |
| sudo apt-get install libfftw3-dev | |
| sudo apt-get install clang | |
| sudo apt-get install cmake-data cmake | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.8 | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| curl -OL https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz | |
| tar -zxf v4.9.2.tar.gz | |
| cd netcdf-c-4.9.2 | |
| ./configure --disable-byterange --disable-libxml2 --disable-netcdf-4 --disable-dap --disable-doxygen --prefix=$HOME | |
| make -j2 | |
| make install | |
| cd .. | |
| export PATH=$HOME/bin:$PATH | |
| - name: Install conda packages | |
| run: | | |
| conda update conda | |
| conda env update --file environment.yml --name base | |
| - 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 |