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‎.github/workflows/testpsijlocal.yml

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@@ -1,45 +1,45 @@
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name: PSI/J-Local
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on:
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push:
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branches:
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- master
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pull_request:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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jobs:
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test:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ['3.11']
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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repository: ${{ github.repository }}
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- name: Setup Python version ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies for PSI/J
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run: |
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pip install -e ".[test, psij]"
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- name: Run tests for PSI/J
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run: |
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pytest --color=yes -vs --psij=local -n auto pydra/engine --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
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- name: Upload to codecov
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run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW
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name: PSI/J-Local
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on:
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push:
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branches:
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- master
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pull_request:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: read
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jobs:
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test:
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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python-version: ['3.11']
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fail-fast: false
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runs-on: ${{ matrix.os }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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repository: ${{ github.repository }}
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- name: Setup Python version ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies for PSI/J
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run: |
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pip install -e ".[test, psij]"
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- name: Run tests for PSI/J
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run: |
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pytest --color=yes -vs --psij=local -n auto pydra/engine --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
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- name: Upload to codecov
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run: codecov -f cov.xml -F unittests -e GITHUB_WORKFLOW

‎.github/workflows/testpsijslurm.yml

Lines changed: 54 additions & 54 deletions
Original file line numberDiff line numberDiff line change
@@ -1,54 +1,54 @@
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name: PSI/J-SLURM
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on:
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push:
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branches:
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- master
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pull_request:
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jobs:
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build:
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strategy:
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matrix:
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python-version: [3.11.5]
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fail-fast: false
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runs-on: ubuntu-latest
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env:
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DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
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steps:
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- name: Disable etelemetry
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run: echo "NO_ET=TRUE" >> $GITHUB_ENV
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- uses: actions/checkout@v4
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- name: Pull docker image
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run: |
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docker pull $DOCKER_IMAGE
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# Have image running in the background
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docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
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- name: Display previous jobs with sacct
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run: |
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echo "Allowing ports/daemons time to start" && sleep 10
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docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
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docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
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if [ $? -ne 0 ]; then
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echo "Slurm docker image error"
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exit 1
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fi
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- name: Setup Python
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run: |
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docker exec slurm bash -c "echo $NO_ET"
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docker exec slurm bash -c "ls -la && echo list top level dir"
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docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
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if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
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docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
44-
fi
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docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
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docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test,psij] && python -c 'import pydra; print(pydra.__version__)'"
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- name: Run pytest
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run: |
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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'"
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- name: Upload to codecov
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run: |
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docker exec slurm bash -c "pip install urllib3==1.26.6"
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docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
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docker rm -f slurm
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name: PSI/J-SLURM
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on:
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push:
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branches:
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- master
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pull_request:
8+
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jobs:
10+
build:
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strategy:
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matrix:
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python-version: [3.11.5]
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fail-fast: false
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runs-on: ubuntu-latest
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env:
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DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
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steps:
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- name: Disable etelemetry
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run: echo "NO_ET=TRUE" >> $GITHUB_ENV
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- uses: actions/checkout@v4
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- name: Pull docker image
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run: |
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docker pull $DOCKER_IMAGE
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# Have image running in the background
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docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
28+
- name: Display previous jobs with sacct
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run: |
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echo "Allowing ports/daemons time to start" && sleep 10
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docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
32+
docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
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if [ $? -ne 0 ]; then
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echo "Slurm docker image error"
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exit 1
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fi
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- name: Setup Python
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run: |
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docker exec slurm bash -c "echo $NO_ET"
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docker exec slurm bash -c "ls -la && echo list top level dir"
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docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
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if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
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docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
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fi
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docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
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docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test,psij] && python -c 'import pydra; print(pydra.__version__)'"
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- name: Run pytest
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run: |
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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'"
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- name: Upload to codecov
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run: |
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docker exec slurm bash -c "pip install urllib3==1.26.6"
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docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
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docker rm -f slurm

‎.github/workflows/testslurm.yml

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@@ -1,54 +1,54 @@
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name: SLURM
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on:
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push:
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branches:
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- master
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pull_request:
8-
9-
jobs:
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build:
11-
strategy:
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matrix:
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python-version: [3.8.16, 3.9.16, 3.10.9, 3.11.5]
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fail-fast: false
15-
runs-on: ubuntu-latest
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env:
17-
DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
18-
19-
steps:
20-
- name: Disable etelemetry
21-
run: echo "NO_ET=TRUE" >> $GITHUB_ENV
22-
- uses: actions/checkout@v4
23-
- name: Pull docker image
24-
run: |
25-
docker pull $DOCKER_IMAGE
26-
# Have image running in the background
27-
docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
28-
- name: Display previous jobs with sacct
29-
run: |
30-
echo "Allowing ports/daemons time to start" && sleep 10
31-
docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
32-
docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
33-
if [ $? -ne 0 ]; then
34-
echo "Slurm docker image error"
35-
exit 1
36-
fi
37-
- name: Setup Python
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run: |
39-
docker exec slurm bash -c "echo $NO_ET"
40-
docker exec slurm bash -c "ls -la && echo list top level dir"
41-
docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
42-
if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
43-
docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
44-
fi
45-
docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
46-
docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test] && python -c 'import pydra; print(pydra.__version__)'"
47-
- name: Run pytest
48-
run: |
49-
docker exec slurm bash -c "pytest --color=yes -vs --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'"
50-
- name: Upload to codecov
51-
run: |
52-
docker exec slurm bash -c "pip install urllib3==1.26.6"
53-
docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
54-
docker rm -f slurm
1+
name: SLURM
2+
3+
on:
4+
push:
5+
branches:
6+
- master
7+
pull_request:
8+
9+
jobs:
10+
build:
11+
strategy:
12+
matrix:
13+
python-version: [3.8.16, 3.9.16, 3.10.9, 3.11.5]
14+
fail-fast: false
15+
runs-on: ubuntu-latest
16+
env:
17+
DOCKER_IMAGE: adi611/docker-centos7-slurm:23.02.1
18+
19+
steps:
20+
- name: Disable etelemetry
21+
run: echo "NO_ET=TRUE" >> $GITHUB_ENV
22+
- uses: actions/checkout@v4
23+
- name: Pull docker image
24+
run: |
25+
docker pull $DOCKER_IMAGE
26+
# Have image running in the background
27+
docker run `bash <(curl -s https://codecov.io/env)` -itd -h slurmctl --cap-add sys_admin -d --name slurm -v `pwd`:/pydra -e NO_ET=$NO_ET $DOCKER_IMAGE
28+
- name: Display previous jobs with sacct
29+
run: |
30+
echo "Allowing ports/daemons time to start" && sleep 10
31+
docker exec slurm bash -c "sacctmgr -i add account none,test Cluster=linux Description='none' Organization='none'"
32+
docker exec slurm bash -c "sacct && sinfo && squeue" 2&> /dev/null
33+
if [ $? -ne 0 ]; then
34+
echo "Slurm docker image error"
35+
exit 1
36+
fi
37+
- name: Setup Python
38+
run: |
39+
docker exec slurm bash -c "echo $NO_ET"
40+
docker exec slurm bash -c "ls -la && echo list top level dir"
41+
docker exec slurm bash -c "ls -la /pydra && echo list pydra dir"
42+
if [[ "${{ matrix.python-version }}" == "3.11.5" ]]; then
43+
docker exec slurm bash -c "CONFIGURE_OPTS=\"-with-openssl=/opt/openssl\" pyenv install -v 3.11.5"
44+
fi
45+
docker exec slurm bash -c "pyenv global ${{ matrix.python-version }}"
46+
docker exec slurm bash -c "pip install --upgrade pip && pip install -e /pydra[test] && python -c 'import pydra; print(pydra.__version__)'"
47+
- name: Run pytest
48+
run: |
49+
docker exec slurm bash -c "pytest --color=yes -vs --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'"
50+
- name: Upload to codecov
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run: |
52+
docker exec slurm bash -c "pip install urllib3==1.26.6"
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docker exec slurm bash -c "codecov --root /pydra -f /pydra/cov.xml -F unittests"
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docker rm -f slurm

‎.pre-commit-config.yaml

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 23.9.1
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hooks:
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- id: black
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.5
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hooks:
18-
- id: codespell
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additional_dependencies:
20-
- tomli
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- repo: https://github.com/PyCQA/flake8
22-
rev: 6.1.0
23-
hooks:
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- id: flake8
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# See https://pre-commit.com for more information
2+
# See https://pre-commit.com/hooks.html for more hooks
3+
repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
6+
hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- repo: https://github.com/psf/black
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rev: 23.9.1
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hooks:
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- id: black
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.5
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hooks:
18+
- id: codespell
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additional_dependencies:
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- tomli
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- repo: https://github.com/PyCQA/flake8
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rev: 6.1.0
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hooks:
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- id: flake8

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