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fix tests
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@CamDavidsonPilon
CamDavidsonPilon committed Sep 8, 2023
1 parent d775799 commit 49173d6
Showing 1 changed file with 34 additions and 36 deletions.
70 changes: 34 additions & 36 deletions pioreactor/tests/test_dosing_control.py
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Original file line number Diff line number Diff line change
Expand Up @@ -372,12 +372,12 @@ def test_pause_in_dosing_automation() -> None:
def test_pause_in_dosing_control_also_pauses_automation() -> None:
experiment = "test_pause_in_dosing_control_also_pauses_automation"
algo = DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
)
pause()
pubsub.publish(f"pioreactor/{unit}/{experiment}/dosing_control/$state/set", "sleeping")
Expand Down Expand Up @@ -424,12 +424,12 @@ def test_throughput_calculator() -> None:
c[experiment] = 0.0

with DosingController(
unit,
experiment,
"pid_morbidostat",
target_growth_rate=0.05,
target_od=1.0,
duration=60,
unit=unit,
experiment=experiment,
) as algo:
assert algo.automation_job.media_throughput == 0
pause()
Expand Down Expand Up @@ -493,12 +493,12 @@ def test_throughput_calculator_restart() -> None:
c[experiment] = 1.5

with DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
pause()
assert algo.automation_job.media_throughput == 1.0
Expand All @@ -514,12 +514,12 @@ def test_throughput_calculator_manual_set() -> None:
c[experiment] = 1.5

with DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
pause()
assert algo.automation_job.media_throughput == 1.0
Expand All @@ -544,7 +544,7 @@ def test_execute_io_action() -> None:
with local_persistant_storage("alt_media_throughput") as c:
c[experiment] = 0.0

with DosingController("silent", unit=unit, experiment=experiment) as ca:
with DosingController(unit, experiment, "silent") as ca:
ca.automation_job.execute_io_action(media_ml=0.50, alt_media_ml=0.35, waste_ml=0.50 + 0.35)
pause()
assert ca.automation_job.media_throughput == 0.50
Expand Down Expand Up @@ -577,9 +577,7 @@ def test_execute_io_action2() -> None:
with local_persistant_storage("alt_media_fraction") as c:
c[experiment] = 0.0

with DosingController(
"silent", unit=unit, experiment=experiment, initial_vial_volume=14.0
) as ca:
with DosingController(unit, experiment, "silent", initial_vial_volume=14.0) as ca:
ca.automation_job.execute_io_action(media_ml=1.25, alt_media_ml=0.01, waste_ml=1.26)
pause()
assert ca.automation_job.media_throughput == 1.25
Expand Down Expand Up @@ -784,12 +782,12 @@ def test_changing_duration_over_mqtt_will_start_next_run_earlier() -> None:
def test_changing_algo_over_mqtt_with_wrong_automation_type() -> None:
experiment = "test_changing_algo_over_mqtt_with_wrong_automation_type"
with DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
assert algo.automation.automation_name == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
Expand All @@ -814,12 +812,12 @@ def test_changing_algo_over_mqtt_with_wrong_automation_type() -> None:
def test_changing_algo_over_mqtt_solo() -> None:
experiment = "test_changing_algo_over_mqtt_solo"
with DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
assert algo.automation.automation_name == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
Expand Down Expand Up @@ -847,12 +845,12 @@ def test_changing_algo_over_mqtt_solo() -> None:
def test_changing_algo_over_mqtt_when_it_fails_will_rollback() -> None:
experiment = "test_changing_algo_over_mqtt_when_it_fails_will_rollback"
with DosingController(
unit,
experiment,
"turbidostat",
target_normalized_od=1.0,
duration=5 / 60,
volume=1.0,
unit=unit,
experiment=experiment,
) as algo:
assert algo.automation.automation_name == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
Expand Down Expand Up @@ -888,12 +886,12 @@ def test_changing_algo_over_mqtt_will_not_produce_two_dosing_jobs() -> None:
c[experiment] = 0.0

algo = DosingController(
unit,
experiment,
"turbidostat",
volume=1.0,
target_normalized_od=0.4,
duration=60,
unit=unit,
experiment=experiment,
)
assert algo.automation.automation_name == "turbidostat"
pause()
Expand Down Expand Up @@ -945,12 +943,12 @@ def test_changing_algo_over_mqtt_with_wrong_type_is_okay() -> None:
c[experiment] = 0.0

algo = DosingController(
unit,
experiment,
"turbidostat",
volume=1.0,
target_normalized_od=0.4,
duration=2 / 60,
unit=unit,
experiment=experiment,
)
assert algo.automation.automation_name == "turbidostat"
assert algo.automation_name == "turbidostat"
Expand All @@ -974,12 +972,12 @@ def test_changing_algo_over_mqtt_with_wrong_type_is_okay() -> None:
def test_disconnect_cleanly() -> None:
experiment = "test_disconnect_cleanly"
algo = DosingController(
experiment,
unit,
"turbidostat",
target_normalized_od=1.0,
duration=50,
unit=unit,
volume=1.0,
experiment=experiment,
)
assert algo.automation.automation_name == "turbidostat"
assert isinstance(algo.automation_job, Turbidostat)
Expand All @@ -991,11 +989,11 @@ def test_disconnect_cleanly() -> None:
def test_disconnect_cleanly_during_pumping_execution() -> None:
experiment = "test_disconnect_cleanly_during_pumping_execution"
algo = DosingController(
unit,
experiment,
"chemostat",
volume=5.0,
duration=10,
unit=unit,
experiment=experiment,
)
assert algo.automation.automation_name == "chemostat"
time.sleep(4)
Expand Down Expand Up @@ -1024,11 +1022,11 @@ def execute(self) -> None:
self.execute_io_action(media_ml=1.0, waste_ml=1.0)

with DosingController(
get_unit_name(),
experiment,
"naive_turbidostat",
target_od=2.0,
duration=10,
unit=get_unit_name(),
experiment=experiment,
):
pass

Expand Down Expand Up @@ -1124,10 +1122,10 @@ def execute(self):
return events.NoEvent(message="demo", data={"d": 1.0, "s": "test"})

with DosingController(
get_unit_name(),
experiment,
"fake_automation",
duration=0.1,
unit=get_unit_name(),
experiment=experiment,
) as dc:
assert "latest_event" in dc.automation_job.published_settings

Expand Down Expand Up @@ -1506,9 +1504,9 @@ def test_execute_io_action_errors() -> None:
experiment = "test_execute_io_action_errors"

with DosingController(
unit,
experiment,
"silent",
unit=unit,
experiment=experiment,
) as ca:
with pytest.raises(ValueError):
# missing _ml
Expand All @@ -1528,7 +1526,7 @@ def test_timeout_in_run() -> None:
experiment = "test_timeout_in_run"

with pubsub.collect_all_logs_of_level("DEBUG", unit, experiment) as bucket:
with DosingController("silent", unit=unit, experiment=experiment, duration=5) as ca:
with DosingController(unit, experiment, "silent", duration=5) as ca:
ca.automation_job.set_state(ca.automation_job.SLEEPING)
time.sleep(70)

Expand All @@ -1543,11 +1541,11 @@ def test_automation_will_pause_itself_if_pumping_goes_above_safety_threshold() -
del c[experiment]

with DosingController(
unit,
experiment,
"chemostat",
duration=0.05,
volume=0.5,
unit=unit,
experiment=experiment,
initial_vial_volume=17.95,
) as dc:
job = dc.automation_job
Expand Down Expand Up @@ -1585,7 +1583,7 @@ def execute(self):
return

with pubsub.collect_all_logs_of_level("WARNING", unit, experiment) as bucket:
with DosingController("bad_waste_removal", unit=unit, experiment=experiment, duration=5):
with DosingController(unit, experiment, "bad_waste_removal", duration=5):
time.sleep(30)

assert len(bucket) >= 1
Expand Down

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