Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

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c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all \u003cpre\u003e\u003ccode\u003e blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks"); } } catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); } })(); (function(){ try { var __m = "github.com"; var __re = new RegExp('^' + "github\\.com" + '
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

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12 commits
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c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

Show file tree
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Commits
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12 commits
Select commit Hold shift + click to select a range
c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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Contributor

Choose a reason for hiding this comment

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length \u003e 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
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Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

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c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

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12 commits
Select commit Hold shift + click to select a range
c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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Contributor

Choose a reason for hiding this comment

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

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c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

Add terminate_tasks_in_cache() function to kill remaining tasks#739

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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Merged
jan-janssen merged 12 commits into from
Jul 16, 2025
Merged

Add terminate_tasks_in_cache() function to kill remaining tasks #739

Show file tree
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Changes from all commits
Commits
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12 commits
Select commit Hold shift + click to select a range
c2ad089
Add terminate_tasks_in_cache() function to kill remaining tasks
jan-janssen Jul 16, 2025
a8b8c8c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
a6dffc5
Remove unused variable
jan-janssen Jul 16, 2025
cb90f60
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
f1cc703
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2025
689cc57
fix type hint
jan-janssen Jul 16, 2025
2dde569
Merge remote-tracking branch 'origin/terminate_tasks_in_cache' into t…
jan-janssen Jul 16, 2025
9fac1f8
Merge branch 'main' into terminate_tasks_in_cache
jan-janssen Jul 16, 2025
d535493
Add Docstrings
jan-janssen Jul 16, 2025
8aad240
Add flux based tests
jan-janssen Jul 16, 2025
3d82db4
fix tests
jan-janssen Jul 16, 2025
b276552
functions need to be named test
jan-janssen Jul 16, 2025
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -36,4 +36,11 @@
"SlurmClusterExecutor",
]

try:
from executorlib.task_scheduler.file.queue_spawner import terminate_tasks_in_cache

__all__ += ["terminate_tasks_in_cache"]
except ImportError:
pass

__version__ = _version.__version__
31 changes: 29 additions & 2 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,7 +33,7 @@ def execute_with_pysqa(
cwd: None,
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].

Returns:
int: queuing system ID
Expand DownExpand Up@@ -102,7 +102,7 @@ def terminate_with_pysqa(
Args:
queue_id (int): Queuing system ID of the job to delete.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
qa = QueueAdapter(
directory=config_directory,
Expand All@@ -115,6 +115,33 @@ def terminate_with_pysqa(
qa.delete_job(process_id=queue_id)


def terminate_tasks_in_cache(
cache_directory: str,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
):
"""
Delete all jobs stored in the cache directory from the queuing system

Args:
cache_directory (str): The directory to store cache files.
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks ["slurm", "flux"].
"""
hdf5_file_lst = []
for root, _, files in os.walk(cache_directory):
hdf5_file_lst += [os.path.join(root, f) for f in files if f[-5:] == "_i.h5"]

for f in hdf5_file_lst:
queue_id = get_queue_id(f)
if queue_id is not None:
terminate_with_pysqa(
queue_id=queue_id,
config_directory=config_directory,
backend=backend,
)


def _pysqa_execute_command(
commands: str,
working_directory: Optional[str] = None,
Expand Down
12 changes: 12 additions & 0 deletions tests/test_fluxclusterexecutor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,6 +9,7 @@
try:
import flux.job
from executorlib.task_scheduler.file.hdf import dump
from executorlib.task_scheduler.file.queue_spawner import terminate_with_pysqa, terminate_tasks_in_cache

skip_flux_test = "FLUX_URI" not in os.environ
pmi = os.environ.get("EXECUTORLIB_PMIX", None)
Expand DownExpand Up@@ -58,6 +59,9 @@ def test_executor_no_cwd(self):
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def test_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
Comment on lines +62 to +63

@coderabbitaicoderabbitaiBotJul 16, 2025

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Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🛠️ Refactor suggestion

Enhance test coverage for better validation.

The current test only verifies that the function executes without errors, but doesn't validate the actual termination behavior. Consider:

  1. Mock the QueueAdapter: Use mocking to verify that get_status_of_job and delete_job are called appropriately
  2. Test edge cases: Test scenarios where the job doesn't exist or is already finished
  3. Parameterize backends: Test both "slurm" and "flux" backends if possible

Example improvement:

+ @unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')+ def test_terminate_with_pysqa(self, mock_qa_class):+ mock_qa = mock_qa_class.return_value+ mock_qa.get_status_of_job.return_value = "running"++ result = terminate_with_pysqa(queue_id=1, backend="flux")++ self.assertIsNone(result)+ mock_qa.get_status_of_job.assert_called_once_with(process_id=1)+ mock_qa.delete_job.assert_called_once_with(process_id=1)- def test_terminate_with_pysqa(self):- self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="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
deftest_terminate_with_pysqa(self):
self.assertIsNone(terminate_with_pysqa(queue_id=1, backend="flux"))
@unittest.mock.patch('executorlib.task_scheduler.file.queue_spawner.QueueAdapter')
deftest_terminate_with_pysqa(self, mock_qa_class):
mock_qa=mock_qa_class.return_value
mock_qa.get_status_of_job.return_value="running"
result=terminate_with_pysqa(queue_id=1, backend="flux")
self.assertIsNone(result)
mock_qa.get_status_of_job.assert_called_once_with(process_id=1)
mock_qa.delete_job.assert_called_once_with(process_id=1)
🤖 Prompt for AI Agents
In tests/test_fluxclusterexecutor.py around lines 62 to 63, the test for
terminate_with_pysqa only checks for no errors but does not verify the
function's behavior. Enhance the test by mocking the QueueAdapter to assert that
get_status_of_job and delete_job are called correctly. Add tests for edge cases
such as when the job does not exist or is already finished. Also, parameterize
the test to cover both "slurm" and "flux" backends to ensure broader coverage.


def test_executor_existing_files(self):
with FluxClusterExecutor(
resource_dict={"cores": 2, "cwd": "executorlib_cache"},
Expand DownExpand Up@@ -89,5 +93,13 @@ def test_executor_existing_files(self):
self.assertTrue(fs1.done())
self.assertEqual(len(os.listdir("executorlib_cache")), 4)

def test_terminate_tasks_in_cache(self):
file = os.path.join("executorlib_cache", "test_i.h5")
dump(file_name=file, data_dict={"queue_id": 1})
self.assertIsNone(terminate_tasks_in_cache(
cache_directory="executorlib_cache",
backend="flux",
))

def tearDown(self):
shutil.rmtree("executorlib_cache", ignore_errors=True)