Draft implementation of proposed syntax changes (feedback requested) #266
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| name: PSI/J-SLURM | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| python-version: [3.11.5] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| env: | |
| DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1 | |
| steps: | |
| - name: Disable etelemetry | |
| run: echo "NO_ET=TRUE" >> $GITHUB_ENV | |
| - uses: actions/checkout@v4 | |
| - name: Pull docker image | |
| run: | | |
| docker pull $DOCKER_IMAGE | |
| # Have image running in the background | |
| docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE | |
| - name: Display previous jobs with sacct | |
| run: | | |
| echo "Allowing ports/daemons time to start" && sleep 10 | |
| docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'" | |
| docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null | |
| if [ $? -ne 0 ]; then | |
| echo "Slurm docker image error" | |
| exit 1 | |
| fi | |
| - name: Setup Python | |
| run: | | |
| docker exec slurm bash -c "echo $NO_ET" | |
| docker exec slurm bash -c "ls -la && echo list top level dir" | |
| docker exec slurm bash -c "ls -la /pydra && echo list pydra dir" | |
| if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then | |
| docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5" | |
| fi | |
| docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}" | |
| docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test,psij] && python -c 'import pydra; print(pydra.__version__)'" | |
| - name: Run pytest | |
| run: | | |
| docker exec slurm bash -c "pytest --color=yes -vs -n auto --psij=slurm --cov pydra --cov-config /pydra/.coveragerc --cov-report xml:/pydra/cov.xml --doctest-modules /pydra/pydra/ -k 'not test_audit_prov and not test_audit_prov_messdir_1 and not test_audit_prov_messdir_2 and not test_audit_prov_wf and not test_audit_all'" | |
| - name: Upload to codecov | |
| run: | | |
| docker exec slurm bash -c "pip install urllib3==1.26.6" | |
| docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests" | |
| docker rm -f slurm |