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ci: Run htcondor in docker container #4

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merged 2 commits into from
Mar 23, 2024
Merged

ci: Run htcondor in docker container #4

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d724d10
Run htcondor in docker container
jannisspeer Mar 21, 2024
72c0a1e
Adapted steps for submitting to HTCondor
jannisspeer Mar 23, 2024
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46 changes: 32 additions & 14 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -66,29 +66,47 @@ jobs:

testing:
runs-on: ubuntu-latest
container:
image: htcondor/mini
env:
PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/submituser/.local/bin
steps:
- uses: actions/checkout@v3

- uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
- name: Install Python and more yum
run: |
yum install -y python${{ env.PYTHON_VERSION }}
yum install -y python${{ env.PYTHON_VERSION }}-pip
yum install -y python${{ env.PYTHON_VERSION }}-devel
yum install -y gcc

- name: HTCondor master
run: condor_master

- name: Test submit to HTCondor
run: su -c "condor_submit tests/sleep.sub" submituser

- name: Install poetry
run: pip install poetry
run: su -c "pip${{ env.PYTHON_VERSION }} install poetry" submituser

- name: Determine dependencies
run: poetry lock

- uses: actions/setup-python@v4
with:
python-version: ${{ env.PYTHON_VERSION }}
cache: poetry
run: su -c "poetry lock" submituser

- name: Install dependencies
run: poetry install
run: su -c "poetry install" submituser

- name: Run pytest
run: poetry run coverage run -m pytest tests/tests.py

run: su -c "poetry run coverage run -m pytest tests/tests.py -vvv" submituser

- name: Check HTCondor logs
run: |
ls /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor
for file in /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor/*.log; do cat "$file"; done

- name: Check HTCondor errors
run: |
ls /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor
for file in /tmp/pytest-of-submituser/pytest-0/test_simple_workflow0/simple/.snakemake/htcondor/*.err; do cat "$file"; done

- name: Run Coverage
run: poetry run coverage report -m
run: su -c "poetry run coverage report -m --omit=Snakefile" submituser
5 changes: 5 additions & 0 deletions tests/sleep.sub
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@@ -0,0 +1,5 @@
# sleep.sub -- simple sleep job

executable = /bin/sleep
arguments = 5s
queue
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