pid morbidostat uses nOD, so make sure the class uses it explcitly

CHANGELOG.md

@@ -4,7 +4,7 @@
  - Fix for Ngrok remote access
  - Merged the turbidostat automations into one. You can either select target target nOD or target OD, but not both!
  - Both "Target OD" and "Target nOD" are available to be changed in the UI.
-
+ - `pid_morbidostat` now explicitly uses the keyword arg `target_normalized_od`, instead of `target_od`. It always has been nOD.
 
 ### 23.11.18
  - No more waiting around for growth-rate-calculating to get to "Ready" state

pioreactor/automations/dosing/pid_morbidostat.py

@@ -20,14 +20,16 @@ class PIDMorbidostat(DosingAutomationJob):
     automation_name = "pid_morbidostat"
     published_settings = {
         "volume": {"datatype": "float", "settable": True, "unit": "mL"},
-        "target_od": {"datatype": "float", "settable": True, "unit": "AU"},
+        "target_normalized_od": {"datatype": "float", "settable": True, "unit": "AU"},
         "target_growth_rate": {"datatype": "float", "settable": True, "unit": "h⁻¹"},
         "duration": {"datatype": "float", "settable": True, "unit": "min"},
     }
 
-    def __init__(self, target_growth_rate: float | str, target_od: float | str, **kwargs):
+    def __init__(
+        self, target_growth_rate: float | str, target_normalized_od: float | str, **kwargs
+    ):
         super(PIDMorbidostat, self).__init__(**kwargs)
-        assert target_od is not None, "`target_od` must be set"
+        assert target_normalized_od is not None, "`target_normalized_od` must be set"
         assert target_growth_rate is not None, "`target_growth_rate` must be set"
 
         with local_persistant_storage("current_pump_calibration") as cache:
@@ -39,7 +41,7 @@ def __init__(self, target_growth_rate: float | str, target_od: float | str, **kw
                 raise CalibrationError("Alt-Media pump calibration must be performed first.")
 
         self.set_target_growth_rate(target_growth_rate)
-        self.target_od = float(target_od)
+        self.target_normalized_od = float(target_normalized_od)
 
         Kp = config.getfloat("dosing_automation.pid_morbidostat", "Kp")
         Ki = config.getfloat("dosing_automation.pid_morbidostat", "Ki")
@@ -105,11 +107,11 @@ def execute(self) -> events.AutomationEvent:
 
     @property
     def min_od(self):
-        return 0.7 * self.target_od
+        return 0.7 * self.target_normalized_od
 
     @property
     def max_od(self):
-        return 1.25 * self.target_od
+        return 1.25 * self.target_normalized_od
 
     def set_target_growth_rate(self, value: str | float | int):
         self.target_growth_rate = float(value)

pioreactor/tests/test_dosing_control.py

@@ -322,7 +322,7 @@ def test_pid_morbidostat_automation() -> None:
     experiment = "test_pid_morbidostat_automation"
     target_growth_rate = 0.09
     with PIDMorbidostat(
-        target_od=1.0,
+        target_normalized_od=1.0,
         target_growth_rate=target_growth_rate,
         duration=60,
         unit=unit,
@@ -375,7 +375,7 @@ def test_changing_morbidostat_parameters_over_mqtt() -> None:
     target_growth_rate = 0.05
     algo = PIDMorbidostat(
         target_growth_rate=target_growth_rate,
-        target_od=1.0,
+        target_normalized_od=1.0,
         duration=60,
         unit=unit,
         experiment=experiment,
@@ -527,7 +527,7 @@ def test_throughput_calculator() -> None:
         experiment,
         "pid_morbidostat",
         target_growth_rate=0.05,
-        target_od=1.0,
+        target_normalized_od=1.0,
         duration=60,
     ) as algo:
         assert algo.automation_job.media_throughput == 0
@@ -765,7 +765,7 @@ def test_execute_io_action_outputs_will_shortcut_if_disconnected() -> None:
 def test_PIDMorbidostat() -> None:
     experiment = "test_PIDMorbidostat"
     algo = PIDMorbidostat(
-        target_od=1.0,
+        target_normalized_od=1.0,
         target_growth_rate=0.01,
         duration=5 / 60,
         unit=unit,
@@ -801,7 +801,7 @@ def test_PIDMorbidostat() -> None:
 def test_changing_duration_over_mqtt() -> None:
     experiment = "test_changing_duration_over_mqtt"
     with PIDMorbidostat(
-        target_od=1.0,
+        target_normalized_od=1.0,
         target_growth_rate=0.01,
         duration=5 / 60,
         unit=unit,
@@ -831,7 +831,7 @@ def test_changing_duration_over_mqtt() -> None:
 def test_changing_duration_over_mqtt_will_start_next_run_earlier() -> None:
     experiment = "test_changing_duration_over_mqtt_will_start_next_run_earlier"
     with PIDMorbidostat(
-        target_od=1.0,
+        target_normalized_od=1.0,
         target_growth_rate=0.01,
         duration=10 / 60,
         unit=unit,
@@ -879,7 +879,7 @@ def test_changing_algo_over_mqtt_with_wrong_automation_type() -> None:
                     "type": "led",
                     "args": {
                         "duration": 60,
-                        "target_od": 1.0,
+                        "target_normalized_od": 1.0,
                         "target_growth_rate": 0.07,
                     },
                 }
@@ -909,7 +909,7 @@ def test_changing_algo_over_mqtt_solo() -> None:
                     "type": "dosing",
                     "args": {
                         "duration": 60,
-                        "target_od": 1.0,
+                        "target_normalized_od": 1.0,
                         "target_growth_rate": 0.07,
                     },
                 }