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Merged
merged 10 commits into from
Aug 2, 2025
Merged

Add integration tests #432

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ddd6e20
Add integration tests
jan-janssen Aug 2, 2025
25dbc17
Update pipeline.yml
jan-janssen Aug 2, 2025
689784c
add sleep
jan-janssen Aug 2, 2025
7a15124
longer wait
jan-janssen Aug 2, 2025
fdb2e02
print state
jan-janssen Aug 2, 2025
dff6f4f
add cores
jan-janssen Aug 2, 2025
7a9b6a1
more adjustments
jan-janssen Aug 2, 2025
b938477
fix flux test
jan-janssen Aug 2, 2025
aca58bd
fix slurm test
jan-janssen Aug 2, 2025
ad58618
is None
jan-janssen Aug 2, 2025
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33 changes: 33 additions & 0 deletions .github/workflows/pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,39 @@ jobs:
pip install . --no-deps --no-build-isolation
python -m unittest discover tests

unittest_slurm:
needs: [black]
runs-on: ubuntu-latest
services:
mysql:
image: mysql:8.0
env:
MYSQL_ROOT_PASSWORD: root
ports:
- "8888:3306"
options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
steps:
- uses: actions/checkout@v4
- uses: koesterlab/setup-slurm-action@v1
timeout-minutes: 5
- name: Conda config
run: echo -e "channels:\n - conda-forge\n" > .condarc
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: "3.13"
miniforge-version: latest
condarc-file: .condarc
environment-file: .ci_support/environment.yml
- name: Test
shell: bash -l {0}
timeout-minutes: 5
run: |
pip install . --no-deps --no-build-isolation
cd tests
sinfo -o "%n %e %m %a %c %C"
srun --mpi=list
python -m unittest test_slurm_integration.py

autobot:
needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
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@coderabbitai coderabbitai bot Aug 2, 2025

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🛠️ Refactor suggestion

Add new integration jobs to autobot dependencies.

The new integration test jobs should be included in the autobot dependencies to ensure they gate automated merges for bot PRs.

-    needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
+    needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage, unittest_slurm, unittest_flux]
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage]
needs: [unittest_old, unittest_matrix, pip_check, notebooks, minimal, coverage, unittest_slurm, unittest_flux]
🤖 Prompt for AI Agents 
In .github/workflows/pipeline.yml at line 280, the 'needs' array for the autobot
job is missing the new integration test jobs. Add the new integration test job
names to the 'needs' list to ensure these tests are completed before the autobot
job runs, properly gating automated merges for bot PRs.

permissions:
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10 changes: 10 additions & 0 deletions tests/test_flux.py
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Expand Up @@ -116,3 +116,13 @@ def test_flux_integration(self):
self.assertEqual(self.flux.get_status_of_job(process_id=job_id), "running")
self.flux.delete_job(process_id=job_id)
self.assertEqual(self.flux.get_status_of_job(process_id=job_id), "error")

def test_flux_integration_dynamic(self):
flux_dynamic = QueueAdapter(queue_type="flux")
job_id = flux_dynamic.submit_job(
cores=1,
command="sleep 1",
)
self.assertEqual(flux_dynamic.get_status_of_job(process_id=job_id), "running")
flux_dynamic.delete_job(process_id=job_id)
self.assertEqual(flux_dynamic.get_status_of_job(process_id=job_id), "error")
32 changes: 32 additions & 0 deletions tests/test_slurm_integration.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
import unittest
import shutil
from pysqa import QueueAdapter

if shutil.which("srun") is not None:
skip_slurm_test = False
else:
skip_slurm_test = True


submission_template = """\
#!/bin/bash
#SBATCH --output=time.out
#SBATCH --job-name={{job_name}}
#SBATCH --chdir={{working_directory}}
#SBATCH --get-user-env=L
#SBATCH --ntasks={{cores}}

{{command}}
"""


@unittest.skipIf(
skip_slurm_test, "SLURM is not installed, so the slurm tests are skipped.",
)
class TestSlurm(unittest.TestCase):
def test_slurm(self):
slurm_dynamic = QueueAdapter(queue_type="slurm")
job_id = slurm_dynamic.submit_job(command="sleep 1", cores=1, submission_template=submission_template)
self.assertEqual(slurm_dynamic.get_status_of_job(process_id=job_id), "pending")
slurm_dynamic.delete_job(process_id=job_id)
self.assertIsNone(slurm_dynamic.get_status_of_job(process_id=job_id))
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