Fix CI with postgres

[tcompa]

See failures in #953.

For the record, as of #949 we are using sqlalchemy 1.4.50 in the CI (while we were using 1.4.41 before that PR).

Ref:

• https://docs.sqlalchemy.org/en/20/changelog/changelog_14.html

[tcompa]

A sample traceback from https://pipelinesghubeus12.actions.githubusercontent.com/IMqMjycCLBE0AibOdlE9KqIzP2XzCrYHTi7wHEWdbQzDFyFwBI/_apis/pipelines/1/runs/4819/signedlogcontent/2?urlExpires=2023-11-10T14%3A04%3A11.1235309Z&urlSigningMethod=HMACV1&urlSignature=lTGd5iZHnmQYw11bV03I7lHRqKeYHvOM49MaFl6XwbE%3D

2023-11-10T13:51:23.2861997Z tests/test_alive.py .                                                    [  0%]
2023-11-10T13:51:27.9952067Z tests/test_backend_local.py .........                                    [  3%]
2023-11-10T13:51:30.4547390Z tests/test_backend_local_custom_task.py .                                [  3%]
2023-11-10T13:52:48.4764275Z tests/test_backend_runners.py ..                                         [  4%]
2023-11-10T13:53:19.0700901Z tests/test_backend_slurm.py .........                                    [  7%]
2023-11-10T13:53:30.7329445Z tests/test_backend_slurm_shutdown.py ...                                 [  8%]
2023-11-10T13:53:31.0413328Z tests/test_background_tasks.py ..                                        [  8%]
2023-11-10T13:54:12.3007006Z tests/test_commands.py ..........                                        [ 11%]
2023-11-10T13:54:32.5687820Z tests/test_dataset_api.py ...........                                    [ 15%]
2023-11-10T13:54:32.9849319Z tests/test_db.py ...                                                     [ 16%]
2023-11-10T13:54:34.1934238Z tests/test_db_project.py .                                               [ 16%]
2023-11-10T13:54:34.2185183Z tests/test_fixtures_settings_factory.py ..                               [ 17%]
2023-11-10T13:56:00.0667358Z tests/test_full_workflow.py .............                                [ 21%]
2023-11-10T13:56:11.3182802Z tests/test_history.py .....                                              [ 23%]
2023-11-10T13:56:25.1764134Z tests/test_job_api.py .....                                              [ 24%]
2023-11-10T13:56:26.7560823Z tests/test_link_project_user.py .                                        [ 25%]
2023-11-10T13:56:46.3710485Z tests/test_project_api.py ...........                                    [ 28%]
2023-11-10T13:57:06.9872547Z tests/test_project_apply_api.py .....                                    [ 30%]
2023-11-10T13:57:19.7657612Z tests/test_security.py ...............                                   [ 34%]
2023-11-10T13:57:33.8949644Z tests/test_task_api.py .............F                                    [ 39%]
2023-11-10T13:57:34.2997104Z tests/test_task_api.py:318 test_delete_task - pytest.PytestUnraisabl…
2023-11-10T13:57:34.2998460Z tests/test_task_api.py .                                                 [ 39%]
2023-11-10T13:58:51.4910273Z tests/test_task_collection_api.py .............                          [ 43%]
2023-11-10T13:59:26.9185982Z tests/test_task_collection_pypi.py ............                          [ 47%]
2023-11-10T13:59:34.5638360Z tests/test_unit_aux_functions.py .......                                 [ 50%]
2023-11-10T13:59:34.8118913Z tests/test_unit_config.py .................                              [ 55%]
2023-11-10T13:59:34.9210815Z tests/test_unit_coroutine_never_awaited.py .xx                           [ 56%]
2023-11-10T13:59:35.0621833Z tests/test_unit_custom_subprocess_module.py ..                           [ 57%]
2023-11-10T13:59:44.0211257Z tests/test_unit_db_models.py ........                                    [ 59%]
2023-11-10T13:59:44.5211876Z tests/test_unit_dummytasks.py .....                                      [ 61%]
2023-11-10T13:59:44.6294480Z tests/test_unit_fractal_thread_pool_executor.py ................         [ 66%]
2023-11-10T13:59:44.6555695Z tests/test_unit_injection.py ...                                         [ 67%]
2023-11-10T13:59:44.6587692Z tests/test_unit_json_schemas.py .                                        [ 67%]
2023-11-10T13:59:44.7827526Z tests/test_unit_local_config.py ..                                       [ 68%]
2023-11-10T13:59:45.7918136Z tests/test_unit_schemas.py .......................                       [ 75%]
2023-11-10T13:59:45.8420132Z tests/test_unit_set_start_and_last_task_index.py .......                 [ 77%]
2023-11-10T13:59:46.2536560Z tests/test_unit_slurm_batching.py ................................       [ 88%]
2023-11-10T13:59:46.8052709Z tests/test_unit_slurm_config.py ......                                   [ 90%]
2023-11-10T13:59:49.4175545Z tests/test_unit_submit_workflow.py ...                                   [ 91%]
2023-11-10T13:59:49.4712381Z tests/test_unit_utils.py ...                                             [ 91%]
2023-11-10T14:01:24.2363055Z tests/test_workflow_api.py .........................                     [100%]
2023-11-10T14:01:24.2363889Z 
2023-11-10T14:01:24.2364211Z =================================== FAILURES ===================================
2023-11-10T14:01:24.2365172Z _______________________________ test_delete_task _______________________________
2023-11-10T14:01:24.2366201Z 
2023-11-10T14:01:24.2366729Z cls = <class '_pytest.runner.CallInfo'>
2023-11-10T14:01:24.2367679Z func = <function call_runtest_hook.<locals>.<lambda> at 0x7f77dc144ca0>
2023-11-10T14:01:24.2368619Z when = 'call'
2023-11-10T14:01:24.2369410Z reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)
2023-11-10T14:01:24.2370131Z 
2023-11-10T14:01:24.2370300Z     @classmethod
2023-11-10T14:01:24.2370730Z     def from_call(
2023-11-10T14:01:24.2371166Z         cls,
2023-11-10T14:01:24.2371616Z         func: "Callable[[], TResult]",
2023-11-10T14:01:24.2372532Z         when: "Literal['collect', 'setup', 'call', 'teardown']",
2023-11-10T14:01:24.2373353Z         reraise: Optional[
2023-11-10T14:01:24.2374099Z             Union[Type[BaseException], Tuple[Type[BaseException], ...]]
2023-11-10T14:01:24.2374900Z         ] = None,
2023-11-10T14:01:24.2375453Z     ) -> "CallInfo[TResult]":
2023-11-10T14:01:24.2376107Z         """Call func, wrapping the result in a CallInfo.
2023-11-10T14:01:24.2376798Z     
2023-11-10T14:01:24.2377193Z         :param func:
2023-11-10T14:01:24.2378087Z             The function to call. Called without arguments.
2023-11-10T14:01:24.2378860Z         :param when:
2023-11-10T14:01:24.2379450Z             The phase in which the function is called.
2023-11-10T14:01:24.2380165Z         :param reraise:
2023-11-10T14:01:24.2380892Z             Exception or exceptions that shall propagate if raised by the
2023-11-10T14:01:24.2381855Z             function, instead of being wrapped in the CallInfo.
2023-11-10T14:01:24.2382574Z         """
2023-11-10T14:01:24.2384550Z         excinfo = None
2023-11-10T14:01:24.2385058Z         start = timing.time()
2023-11-10T14:01:24.2385680Z         precise_start = timing.perf_counter()
2023-11-10T14:01:24.2386325Z         try:
2023-11-10T14:01:24.2386812Z >           result: Optional[TResult] = func()
2023-11-10T14:01:24.2387596Z 
2023-11-10T14:01:24.2388749Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/_pytest/runner.py:341: 
2023-11-10T14:01:24.2390269Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2023-11-10T14:01:24.2392109Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/_pytest/runner.py:262: in <lambda>
2023-11-10T14:01:24.2393752Z     lambda: ihook(item=item, **kwds), when=when, reraise=reraise
2023-11-10T14:01:24.2395543Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/pluggy/_hooks.py:433: in __call__
2023-11-10T14:01:24.2397269Z     return self._hookexec(self.name, self._hookimpls, kwargs, firstresult)
2023-11-10T14:01:24.2399203Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/pluggy/_manager.py:112: in _hookexec
2023-11-10T14:01:24.2400928Z     return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
2023-11-10T14:01:24.2403061Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/_pytest/unraisableexception.py:88: in pytest_runtest_call
2023-11-10T14:01:24.2404824Z     yield from unraisable_exception_runtest_hook()
2023-11-10T14:01:24.2405700Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2023-11-10T14:01:24.2406337Z 
2023-11-10T14:01:24.2406922Z     def unraisable_exception_runtest_hook() -> Generator[None, None, None]:
2023-11-10T14:01:24.2407886Z         with catch_unraisable_exception() as cm:
2023-11-10T14:01:24.2408540Z             yield
2023-11-10T14:01:24.2408984Z             if cm.unraisable:
2023-11-10T14:01:24.2409618Z                 if cm.unraisable.err_msg is not None:
2023-11-10T14:01:24.2410367Z                     err_msg = cm.unraisable.err_msg
2023-11-10T14:01:24.2411029Z                 else:
2023-11-10T14:01:24.2411565Z                     err_msg = "Exception ignored in"
2023-11-10T14:01:24.2412426Z                 msg = f"{err_msg}: {cm.unraisable.object!r}\n\n"
2023-11-10T14:01:24.2413154Z                 msg += "".join(
2023-11-10T14:01:24.2413752Z                     traceback.format_exception(
2023-11-10T14:01:24.2414448Z                         cm.unraisable.exc_type,
2023-11-10T14:01:24.2415144Z                         cm.unraisable.exc_value,
2023-11-10T14:01:24.2415864Z                         cm.unraisable.exc_traceback,
2023-11-10T14:01:24.2416515Z                     )
2023-11-10T14:01:24.2416947Z                 )
2023-11-10T14:01:24.2417647Z >               warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2023-11-10T14:01:24.2419464Z E               pytest.PytestUnraisableExceptionWarning: Exception ignored in: <function Connection.__del__ at 0x7f77df2000d0>
2023-11-10T14:01:24.2420743Z E               
2023-11-10T14:01:24.2421255Z E               Traceback (most recent call last):
2023-11-10T14:01:24.2423278Z E                 File "/home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/asyncpg/connection.py", line 132, in __del__
2023-11-10T14:01:24.2424980Z E                   self.terminate()
2023-11-10T14:01:24.2426899Z E                 File "/home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/asyncpg/connection.py", line 1344, in terminate
2023-11-10T14:01:24.2428728Z E                   self._abort()
2023-11-10T14:01:24.2430588Z E                 File "/home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/asyncpg/connection.py", line 1371, in _abort
2023-11-10T14:01:24.2432312Z E                   self._protocol.abort()
2023-11-10T14:01:24.2433808Z E                 File "asyncpg/protocol/protocol.pyx", line 571, in asyncpg.protocol.protocol.BaseProtocol.abort
2023-11-10T14:01:24.2435881Z E                 File "/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/selector_events.py", line 686, in abort
2023-11-10T14:01:24.2437177Z E                   self._force_close(None)
2023-11-10T14:01:24.2438521Z E                 File "/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/selector_events.py", line 737, in _force_close
2023-11-10T14:01:24.2440000Z E                   self._loop.call_soon(self._call_connection_lost, exc)
2023-11-10T14:01:24.2441486Z E                 File "/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/base_events.py", line 755, in call_soon
2023-11-10T14:01:24.2442756Z E                   self._check_thread()
2023-11-10T14:01:24.2444041Z E                 File "/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/base_events.py", line 792, in _check_thread
2023-11-10T14:01:24.2445366Z E                   raise RuntimeError(
2023-11-10T14:01:24.2446650Z E               RuntimeError: Non-thread-safe operation invoked on an event loop other than the current one
2023-11-10T14:01:24.2447575Z 
2023-11-10T14:01:24.2449139Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/_pytest/unraisableexception.py:78: PytestUnraisableExceptionWarning
2023-11-10T14:01:24.2451204Z ----------------------------- Captured stderr call -----------------------------
2023-11-10T14:01:24.2459022Z WARNING:asyncio:Executing <Task pending name='Task-2513' coro=<_create_ssl_connection() running at /home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/asyncpg/connect_utils.py:684> wait_for=<Future pending cb=[_chain_future.<locals>._call_check_cancel() at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/futures.py:385, Task.task_wakeup()] created at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/base_events.py:429> cb=[_release_waiter(<Future pendi...events.py:429>)() at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/tasks.py:387] created at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/tasks.py:636> took 0.171 seconds
2023-11-10T14:01:24.2465962Z ------------------------------ Captured log call -------------------------------
2023-11-10T14:01:24.2473748Z WARNING  asyncio:base_events.py:1904 Executing <Task pending name='Task-2513' coro=<_create_ssl_connection() running at /home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/asyncpg/connect_utils.py:684> wait_for=<Future pending cb=[_chain_future.<locals>._call_check_cancel() at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/futures.py:385, Task.task_wakeup()] created at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/base_events.py:429> cb=[_release_waiter(<Future pendi...events.py:429>)() at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/tasks.py:387] created at /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/asyncio/tasks.py:636> took 0.171 seconds
2023-11-10T14:01:24.2480631Z =============================== warnings summary ===============================
2023-11-10T14:01:24.2482205Z ../../../.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/passlib/pwd.py:16
2023-11-10T14:01:24.2485608Z   /home/runner/.cache/pypoetry/virtualenvs/fractal-server-21eqDTaF-py3.10/lib/python3.10/site-packages/passlib/pwd.py:16: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
2023-11-10T14:01:24.2488043Z     import pkg_resources
2023-11-10T14:01:24.2488371Z 
2023-11-10T14:01:24.2488803Z tests/test_unit_coroutine_never_awaited.py::test_harmless_warning
2023-11-10T14:01:24.2490832Z   /home/runner/work/fractal-server/fractal-server/tests/test_unit_coroutine_never_awaited.py:12: UserWarning: This is a dummy harmless warning, to be ignored
2023-11-10T14:01:24.2493071Z     warnings.warn("This is a dummy harmless warning, to be ignored")
2023-11-10T14:01:24.2493736Z 
2023-11-10T14:01:24.2494312Z -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
2023-11-10T14:01:24.2495587Z                               Summary of Failures                               
2023-11-10T14:01:24.2496765Z ┏━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
2023-11-10T14:01:24.2498051Z ┃               ┃               ┃  Function     ┃              ┃               ┃
2023-11-10T14:01:24.2499176Z ┃  File         ┃  Function     ┃  Line         ┃  Error Line  ┃  Error        ┃
2023-11-10T14:01:24.2500366Z ┡━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━┩
2023-11-10T14:01:24.2501693Z │  tests/test…  │  test_delet…  │  319          │  341         │  PytestUnra…  │
2023-11-10T14:01:24.2502940Z └───────────────┴───────────────┴───────────────┴──────────────┴───────────────┘
2023-11-10T14:01:24.2503776Z Results (607.09s):
2023-11-10T14:01:24.2523323Z          1 failed
2023-11-10T14:01:24.2530786Z        309 passed
2023-11-10T14:01:24.2538503Z          2 xfailed
2023-11-10T14:01:24.2545379Z          2 warnings
2023-11-10T14:01:25.3288611Z ##[error]Process completed with exit code 1.

[tcompa]

Cannot reproduce any more.

[tcompa]

Re-opening, see e.g.

• https://github.com/fractal-analytics-platform/fractal-server/actions/runs/6879852902/job/18712722944
• https://github.com/fractal-analytics-platform/fractal-server/actions/runs/6879848351/job/18712708586

[tcompa]

Perhaps fixed with 1008? To be verified.

EDIT: no