NF: Add Environment class, with initial Native/Docker implementations #1108
Workflow file for this run
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| name: SLURM | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| DOCKER_IMAGE: giovtorres/docker-centos7-slurm:latest | |
| 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 cluster name=linux \ | |
| && supervisorctl restart slurmdbd \ | |
| && supervisorctl restart slurmctld \ | |
| && 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" | |
| docker exec slurm bash -c "pip3.9 install --upgrade pip && pip3.9 install -e /pydra[test] && python3.9 -c 'import pydra; print(pydra.__version__)'" | |
| - name: Run pytest | |
| run: | | |
| docker exec slurm bash -c "pytest --color=yes -vs -n auto --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 "pip3.9 install urllib3==1.26.6" | |
| docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests" | |
| docker rm -f slurm |