Added logic to testing script to detect slurm environment for quick_run #100
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| name: Build SPARC using conda-build toolchains and perform quick test (no upload) | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| workflow_dispatch: | |
| jobs: | |
| build-linux: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| strategy: | |
| max-parallel: 5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: "3.10" | |
| activate-environment: sparc-test | |
| conda-build-version: "24.3.0" | |
| #mamba-version: "*" | |
| miniforge-variant: "Mambaforge" # Fix according to https://github.com/nextstrain/cli/commit/4a764976519ca5c540c745463548a9d883eae079 | |
| channels: conda-forge,defaults | |
| channel-priority: true | |
| - name: Install boa dependencies | |
| run: | | |
| mamba install -c conda-forge pip "conda-build=24.3.0" "colorama=0.4" "ruamel=1.0" "ruamel.yaml=0.17" "rich=13.6" "mamba=1.5" "jsonschema=4.19" | |
| pip install git+https://github.com/mamba-org/boa.git@00a11ffce59f47c0fc576f93d39baf1f8fc92f32 | |
| - name: Build with mambabuild | |
| run: | | |
| echo $CONDA_PREFIX | |
| conda info | |
| CPU_COUNT=2 conda mambabuild .conda/ | |
| - name: Install local build | |
| run: | | |
| mamba install --use-local sparc | |
| - name: Test simple sparc run | |
| run: | | |
| cd tests/Cu_FCC/standard/ | |
| mpirun -n 2 sparc -name Cu_FCC | |
| - name: Perform comprehensive tests using `quick_run` | |
| run: | | |
| cp $(which sparc) lib/ | |
| cd tests | |
| export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib:${LD_LIBRARY_PATH} | |
| python SPARC_testing_script.py quick_run | tee output | |
| n_failed=$(grep -o 'Tests failed: [0-9]\+' output | grep -o '[0-9]\+$') | |
| # Force fail, see what happens | |
| unset LD_LIBRARY_PATH | |
| python -c "import os, re; match = re.findall(r'Tests failed: (\d+)', open('output').read()); [print('All pass'), os._exit(0)] if int(match[0]) == 0 else [print('Failed'), os._exit(1)]" | |
| rm -rf output |