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backing out of sge test job
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‎.github/workflows/ci-cd.yml‎

Lines changed: 114 additions & 114 deletions
Original file line numberDiff line numberDiff line change
@@ -222,124 +222,124 @@ jobs:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: ./cov.xml
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test-sge:
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needs: ["build"]
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strategy:
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matrix:
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python-version: [3.11]
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fail-fast: false
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runs-on: ubuntu-latest
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steps:
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- name: Install system packages
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run: |
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export DEBIAN_FRONTEND=noninteractive
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sudo apt update
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sudo apt install -y gridengine-common gridengine-exec gridengine-master gridengine-client
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- name: Configuring SGE
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run: |
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# Get hostname
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HOSTNAME=$(hostname)
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# test-sge:
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# needs: ["build"]
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# strategy:
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# matrix:
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# python-version: [3.11]
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# fail-fast: false
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# runs-on: ubuntu-latest
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# steps:
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# - name: Install system packages
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# run: |
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# export DEBIAN_FRONTEND=noninteractive
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# sudo apt update
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# sudo apt install -y apt-get install gridengine-master gridengine-client gridengine-exec gridengine-qmon cpp
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# - name: Configuring SGE
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# run: |
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# # Get hostname
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# HOSTNAME=$(hostname)
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# Set act_qmaster manually
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echo "$HOSTNAME" | sudo tee /var/lib/gridengine/default/common/act_qmaster
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# # Set act_qmaster manually
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# echo "$HOSTNAME" | sudo tee /var/lib/gridengine/default/common/act_qmaster
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# Add execution host (auto-generate config file)
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EXEC_HOST_FILE=/tmp/exec_host.conf
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cat <<EOF > "$EXEC_HOST_FILE"
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hostname $HOSTNAME
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load_scaling NONE
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complex_values NONE
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user_lists NONE
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xuser_lists NONE
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projects NONE
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department NONE
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use_start_proc FALSE
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queue_sort_method load
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EOF
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# # Add execution host (auto-generate config file)
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# EXEC_HOST_FILE=/tmp/exec_host.conf
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# cat <<EOF > "$EXEC_HOST_FILE"
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# hostname $HOSTNAME
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# load_scaling NONE
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# complex_values NONE
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# user_lists NONE
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# xuser_lists NONE
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# projects NONE
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# department NONE
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# use_start_proc FALSE
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# queue_sort_method load
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# EOF
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sudo qconf -Ae "$EXEC_HOST_FILE"
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# sudo qconf -Ae "$EXEC_HOST_FILE"
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# Add queue (auto-generate config file)
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QUEUE_FILE=/tmp/queue.conf
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cat <<EOF > "$QUEUE_FILE"
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qname test.q
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hostlist $HOSTNAME
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seq_no 0
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load_thresholds np_load_avg=1.75
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suspend_thresholds NONE
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nsuspend 1
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suspend_interval 00:05:00
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priority 0
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min_cpu_interval 00:05:00
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processors UNDEFINED
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qtype BATCH INTERACTIVE
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ckpt_list NONE
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pe_list make
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rerun FALSE
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slots 2
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tmpdir /tmp
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shell /bin/bash
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prolog NONE
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epilog NONE
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shell_start_mode posix_compliant
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starter_method NONE
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suspend_method NONE
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resume_method NONE
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terminate_method NONE
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notify 00:00:60
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owner_list NONE
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user_lists NONE
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xuser_lists NONE
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subordinate_list NONE
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complex_values NONE
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projects NONE
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xprojects NONE
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calendar NONE
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initial_state default
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s_rt INFINITY
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h_rt INFINITY
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s_cpu INFINITY
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h_cpu INFINITY
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s_fsize INFINITY
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h_fsize INFINITY
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s_data INFINITY
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h_data INFINITY
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s_stack INFINITY
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h_stack INFINITY
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s_core INFINITY
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h_core INFINITY
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s_rss INFINITY
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h_rss INFINITY
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EOF
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sudo qconf -Aq "$QUEUE_FILE"
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- name: Restart services
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run: |
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sudo service gridengine-master restart
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sudo service gridengine-exec restart
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- name: Confirm setup
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run: qhost -q
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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: Fetch tags
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run: git fetch --prune --unshallow
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- name: Setup Python version ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install package
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run: |
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pip install -e ".[test]"
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- name: Run tests for Dask
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run: |
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pytest -v pydra/engine/tests/test_submitter.py --only-worker=sge \
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--rootdir pydra --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v2
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with:
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fail_ci_if_error: true
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token: ${{ secrets.CODECOV_TOKEN }}
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# # Add queue (auto-generate config file)
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# QUEUE_FILE=/tmp/queue.conf
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# cat <<EOF > "$QUEUE_FILE"
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# qname test.q
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# hostlist $HOSTNAME
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# seq_no 0
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# load_thresholds np_load_avg=1.75
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# suspend_thresholds NONE
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# nsuspend 1
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# suspend_interval 00:05:00
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# priority 0
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# min_cpu_interval 00:05:00
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# processors UNDEFINED
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# qtype BATCH INTERACTIVE
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# ckpt_list NONE
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# pe_list make
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# rerun FALSE
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# slots 2
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# tmpdir /tmp
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# shell /bin/bash
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# prolog NONE
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# epilog NONE
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# shell_start_mode posix_compliant
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# starter_method NONE
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# suspend_method NONE
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# resume_method NONE
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# terminate_method NONE
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# notify 00:00:60
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# owner_list NONE
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# user_lists NONE
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# xuser_lists NONE
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# subordinate_list NONE
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# complex_values NONE
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# projects NONE
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# xprojects NONE
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# calendar NONE
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# initial_state default
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# s_rt INFINITY
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# h_rt INFINITY
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# s_cpu INFINITY
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# h_cpu INFINITY
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# s_fsize INFINITY
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# h_fsize INFINITY
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# s_data INFINITY
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# h_data INFINITY
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# s_stack INFINITY
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# h_stack INFINITY
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# s_core INFINITY
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# h_core INFINITY
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# s_rss INFINITY
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# h_rss INFINITY
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# EOF
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# sudo qconf -Aq "$QUEUE_FILE"
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# - name: Restart services
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# run: |
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# sudo service gridengine-master restart
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# sudo service gridengine-exec restart
319+
# - name: Confirm setup
320+
# run: qhost -q
321+
# - name: Checkout repository
322+
# uses: actions/checkout@v4
323+
# with:
324+
# repository: ${{ github.repository }}
325+
# - name: Fetch tags
326+
# run: git fetch --prune --unshallow
327+
# - name: Setup Python version ${{ matrix.python-version }}
328+
# uses: actions/setup-python@v5
329+
# with:
330+
# python-version: ${{ matrix.python-version }}
331+
# - name: Install package
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# run: |
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# pip install -e ".[test]"
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# - name: Run tests for Dask
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# run: |
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# pytest -v pydra/engine/tests/test_submitter.py --only-worker=sge \
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# --rootdir pydra --cov pydra --cov-config .coveragerc --cov-report xml:cov.xml
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# - name: Upload coverage to Codecov
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# uses: codecov/codecov-action@v2
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# with:
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# fail_ci_if_error: true
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# token: ${{ secrets.CODECOV_TOKEN }}
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build-docs:
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needs: ['build']

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