Draft implementation of proposed syntax changes (feedback requested) #230
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |