Fix CI

CHANGELOG.md

@@ -34,6 +34,7 @@
 * Testing:
     * Improve `test_full_workflow.py` (\#971).
     * Update `pytest-asyncio` to v0.21 (\#1008).
+    * Fix CI issue related to event loop and asyncpg (\#1012).
 
 # 1.3.14 (do not use!)
 

tests/conftest.py

@@ -21,18 +21,12 @@ def check_basetemp(tpath: Path):
         )
 
 
-def pytest_configure(config):
-    """
-    See https://docs.pytest.org/en/stable/how-to/mark.html#registering-marks
-    """
-    config.addinivalue_line("markers", "slow: marks tests as slow")
-
-
 @pytest.fixture(scope="session")
 def event_loop():
     _event_loop = asyncio.new_event_loop()
     _event_loop.set_debug(True)
     yield _event_loop
+    _event_loop.close()
 
 
 @pytest.fixture(scope="session")

tests/test_backend_slurm_shutdown.py

@@ -1,8 +1,6 @@
-import asyncio
-import logging
-import threading
+import shlex
+import subprocess
 import time
-from pathlib import Path
 
 import pytest
 from devtools import debug
@@ -114,33 +112,6 @@ def _sleep_and_return(sleep_time):
         raise e
 
 
-async def _write_shutdown_file(shutdown_file: Path, sleep_time):
-    # The _auxiliary_scancel and _auxiliary_run functions are used as in
-    # https://stackoverflow.com/a/59645689/19085332
-    logging.warning(f"[_write_shutdown_file] run START {time.perf_counter()=}")
-    # Wait `scancel_sleep_time` seconds, to let the SLURM job pass from PENDING
-    # to RUNNING
-    time.sleep(sleep_time)
-
-    debug(run_squeue())
-    # Scancel all jobs of the current SLURM user
-    logging.warning(f"[_write_shutdown_file] run WRITE {time.perf_counter()=}")
-    # Trigger shutdown
-    with shutdown_file.open("w") as f:
-        f.write("")
-    assert shutdown_file.exists()
-    logging.warning(f"[_write_shutdown_file] run END {time.perf_counter()=}")
-
-
-def _auxiliary_run(shutdown_file: Path, sleep_time):
-    # The _write_shutdown_file and _auxiliary_run functions are used as in
-    # https://stackoverflow.com/a/59645689/19085332
-    loop = asyncio.new_event_loop()
-    asyncio.set_event_loop(loop)
-    loop.run_until_complete(_write_shutdown_file(shutdown_file, sleep_time))
-    loop.close()
-
-
 def test_indirect_shutdown_during_map(
     monkey_slurm,
     monkey_slurm_user,
@@ -154,18 +125,23 @@ def fun_sleep(dummy):
 
     shutdown_file = tmp_path / "shutdown"
 
-    # NOTE: the executor.map call below is blocking. For this reason, we call
-    # the scancel function from a different thread, so that we can make it
-    # happen during the workflow execution The following block is based on
-    # https://stackoverflow.com/a/59645689/19085332
-
+    # NOTE: the executor.map call below is blocking. For this reason, we write
+    # the shutdown file from a subprocess.Popen, so that we can make it happen
+    # during the execution.
     shutdown_sleep_time = 2
-    logging.warning(f"PRE THREAD START {time.perf_counter()=}")
-    _thread = threading.Thread(
-        target=_auxiliary_run, args=(shutdown_file, shutdown_sleep_time)
+    tmp_script = (tmp_path / "script.sh").as_posix()
+    debug(tmp_script)
+    with open(tmp_script, "w") as f:
+        f.write(f"sleep {shutdown_sleep_time}\n")
+        f.write(f"cat NOTHING > {shutdown_file.as_posix()}\n")
+
+    tmp_stdout = open((tmp_path / "stdout").as_posix(), "w")
+    tmp_stderr = open((tmp_path / "stderr").as_posix(), "w")
+    subprocess.Popen(
+        shlex.split(f"bash {tmp_script}"),
+        stdout=tmp_stdout,
+        stderr=tmp_stderr,
     )
-    _thread.start()
-    logging.warning(f"POST THREAD START {time.perf_counter()=}")
 
     with FractalSlurmExecutor(
         slurm_user=monkey_slurm_user,
@@ -186,3 +162,6 @@ def fun_sleep(dummy):
             list(res)
         debug(e.value)
         assert "shutdown" in str(e.value)
+
+    tmp_stdout.close()
+    tmp_stderr.close()

tests/test_full_workflow.py

@@ -13,18 +13,15 @@
 Institute for Biomedical Research and Pelkmans Lab from the University of
 Zurich.
 """
-import asyncio
 import glob
-import logging
 import os
-import threading
-import time
+import shlex
+import subprocess
 from pathlib import Path
 
 import pytest
 from devtools import debug
 
-from .fixtures_slurm import scancel_all_jobs_of_a_slurm_user
 from fractal_server.app.runner import _backends
 
 PREFIX = "/api/v1"
@@ -33,7 +30,6 @@
 backends_available = list(_backends.keys())
 
 
-@pytest.mark.slow
 @pytest.mark.parametrize("backend", backends_available)
 async def test_full_workflow(
     db,
@@ -48,7 +44,6 @@ async def test_full_workflow(
     request,
     override_settings_factory,
 ):
-
     override_settings_factory(
         FRACTAL_RUNNER_BACKEND=backend,
         FRACTAL_RUNNER_WORKING_BASE_DIR=tmp777_path / f"artifacts-{backend}",
@@ -231,7 +226,6 @@ async def test_full_workflow(
         assert "index" in list(output_dataset_json["meta"].keys())
 
 
-@pytest.mark.slow
 @pytest.mark.parametrize("backend", backends_available)
 async def test_failing_workflow_UnknownError(
     client,
@@ -332,7 +326,6 @@ async def test_failing_workflow_UnknownError(
         print(job_status_data["log"])
 
 
-@pytest.mark.slow
 @pytest.mark.parametrize("backend", backends_available)
 @pytest.mark.parametrize("failing_task", ["parallel", "non_parallel"])
 async def test_failing_workflow_TaskExecutionError(
@@ -350,7 +343,6 @@ async def test_failing_workflow_TaskExecutionError(
     override_settings_factory,
     resource_factory,
 ):
-
     override_settings_factory(
         FRACTAL_RUNNER_BACKEND=backend,
         FRACTAL_RUNNER_WORKING_BASE_DIR=tmp777_path
@@ -500,30 +492,7 @@ async def test_failing_workflow_TaskExecutionError(
             assert "index" in list(output_dataset_json["meta"].keys())
 
 
-async def _auxiliary_scancel(slurm_user, sleep_time):
-    # The _auxiliary_scancel and _auxiliary_run functions are used as in
-    # https://stackoverflow.com/a/59645689/19085332
-    logging.warning(f"[scancel_thread] run START {time.perf_counter()=}")
-    # Wait `scancel_sleep_time` seconds, to let the SLURM job pass from PENDING
-    # to RUNNING
-    time.sleep(sleep_time)
-    # Scancel all jobs of the current SLURM user
-    logging.warning(f"[scancel_thread] run SCANCEL {time.perf_counter()=}")
-    scancel_all_jobs_of_a_slurm_user(slurm_user=slurm_user, show_squeue=True)
-    logging.warning(f"[scancel_thread] run END {time.perf_counter()=}")
-
-
-def _auxiliary_run(slurm_user, sleep_time):
-    # The _auxiliary_scancel and _auxiliary_run functions are used as in
-    # https://stackoverflow.com/a/59645689/19085332
-    loop = asyncio.new_event_loop()
-    asyncio.set_event_loop(loop)
-    loop.run_until_complete(_auxiliary_scancel(slurm_user, sleep_time))
-    loop.close()
-
-
 @pytest.mark.parametrize("backend", ["slurm"])
-@pytest.mark.slow
 async def test_failing_workflow_JobExecutionError(
     backend,
     client,
@@ -541,8 +510,8 @@ async def test_failing_workflow_JobExecutionError(
     relink_python_interpreter,
     cfut_jobs_finished,
     resource_factory,
+    tmp_path,
 ):
-
     override_settings_factory(
         FRACTAL_RUNNER_BACKEND=backend,
         FRACTAL_RUNNER_WORKING_BASE_DIR=tmp777_path
@@ -603,19 +572,31 @@ async def test_failing_workflow_JobExecutionError(
         debug(wftask1_id)
 
         # NOTE: the client.post call below is blocking, due to the way we are
-        # running tests. For this reason, we call the scancel functionfrom a
-        # different thread, so that we can make it happen during the workflow
-        # execution
-        # The following block is based on
-        # https://stackoverflow.com/a/59645689/19085332
+        # running tests. For this reason, we call the scancel function from a
+        # from a subprocess.Popen, so that we can make it happen during the
+        # execution.
         scancel_sleep_time = 10
         slurm_user = monkey_slurm_user
-        logging.warning(f"PRE THREAD START {time.perf_counter()=}")
-        _thread = threading.Thread(
-            target=_auxiliary_run, args=(slurm_user, scancel_sleep_time)
+
+        tmp_script = (tmp_path / "script.sh").as_posix()
+        debug(tmp_script)
+        with open(tmp_script, "w") as f:
+            f.write(f"sleep {scancel_sleep_time}\n")
+            f.write(
+                (
+                    f"sudo --non-interactive -u {slurm_user} "
+                    f"scancel -u {slurm_user} -v"
+                    "\n"
+                )
+            )
+
+        tmp_stdout = open((tmp_path / "stdout").as_posix(), "w")
+        tmp_stderr = open((tmp_path / "stderr").as_posix(), "w")
+        subprocess.Popen(
+            shlex.split(f"bash {tmp_script}"),
+            stdout=tmp_stdout,
+            stderr=tmp_stderr,
         )
-        _thread.start()
-        logging.warning(f"POST THREAD START {time.perf_counter()=}")
 
         # Re-submit the modified workflow
         res_second_apply = await client.post(
@@ -656,6 +637,9 @@ async def test_failing_workflow_JobExecutionError(
             str(wftask1_id): "failed",
         }
 
+        tmp_stdout.close()
+        tmp_stderr.close()
+
 
 async def test_non_python_task(
     client,
@@ -925,7 +909,6 @@ async def test_non_executable_task_command(
         user_kwargs = {}
 
     async with MockCurrentUser(persist=True, user_kwargs=user_kwargs) as user:
-
         # Create task
         task = await task_factory(
             name="invalid-task-command",