types and tests

pioreactor/actions/self_test.py

@@ -24,6 +24,7 @@
 from pioreactor.background_jobs import stirring
 from pioreactor.background_jobs.od_reading import ADCReader
 from pioreactor.background_jobs.od_reading import ALL_PD_CHANNELS
+from pioreactor.background_jobs.od_reading import average_over_pd_channel_to_voltages
 from pioreactor.background_jobs.od_reading import IR_keyword
 from pioreactor.background_jobs.od_reading import REF_keyword
 from pioreactor.background_jobs.od_reading import start_od_reading
@@ -153,13 +154,13 @@ def test_all_positive_correlations_between_pds_and_leds(
             )
 
             # record from ADC, we'll average them
-            readings1 = adc_reader.take_reading()
-            readings2 = adc_reader.take_reading()
+            avg_reading = average_over_pd_channel_to_voltages(
+                adc_reader.take_reading(), adc_reader.take_reading()
+            )
 
             # Add to accumulating list
             for pd_channel in ALL_PD_CHANNELS:
-                reading = 0.5 * (readings1[pd_channel] + readings2[pd_channel])
-                varying_intensity_results[pd_channel].append(reading)
+                varying_intensity_results[pd_channel].append(avg_reading[pd_channel])
 
         # compute the linear correlation between the intensities and observed PD measurements
         for pd_channel in ALL_PD_CHANNELS:

pioreactor/automations/led/base.py

@@ -174,7 +174,7 @@ def execute(self) -> Optional[events.AutomationEvent]:
     def most_stale_time(self) -> datetime:
         return min(self.latest_normalized_od_at, self.latest_growth_rate_at)
 
-    def set_led_intensity(self, channel: pt.LedChannel, intensity: float) -> bool:
+    def set_led_intensity(self, channel: pt.LedChannel, intensity: pt.LedIntensityValue) -> bool:
         """
         This first checks the lock on the LED channel, and will wait a few seconds for it to clear,
         and error out if it waits too long.
@@ -262,7 +262,7 @@ def on_disconnected(self) -> None:
             self.run_thread.join()
 
         led_intensity(
-            {channel: 0 for channel in self.edited_channels},
+            {channel: 0.0 for channel in self.edited_channels},
             unit=self.unit,
             experiment=self.experiment,
             source_of_event=f"{self.job_name}:{self.automation_name}",

pioreactor/background_jobs/od_reading.py

@@ -825,7 +825,7 @@ def __init__(
 
         # setup the ADC by turning off all LEDs.
         with led_utils.change_leds_intensities_temporarily(
-            self.ir_led_on_and_rest_off_state,
+            {ch: 0.0 for ch in led_utils.ALL_LED_CHANNELS},
             unit=self.unit,
             experiment=self.experiment,
             source_of_event=self.job_name,
@@ -834,19 +834,19 @@ def __init__(
         ):
             with led_utils.lock_leds_temporarily(self.non_ir_led_channels):
                 # IR led is on
-                sleep(0.1)
-
+                self.start_ir_led()
+                sleep(0.10)
                 self.adc_reader.setup_adc()  # determine best gain, max-signal, etc.
 
+                # IR led is off so we can set blanks
                 self.stop_ir_led()
-                sleep(0.15)
+                sleep(0.10)
 
-                blank_reading = average_over_pd_channel_to_voltages(
-                    self.adc_reader.take_reading(),
+                avg_blank_reading = average_over_pd_channel_to_voltages(
                     self.adc_reader.take_reading(),
                     self.adc_reader.take_reading(),
                 )
-                self.adc_reader.set_offsets(blank_reading)  # determine offset
+                self.adc_reader.set_offsets(avg_blank_reading)  # set dark offset
 
                 # clear the history in adc_reader, so that we don't blank readings in later inference.
                 self.adc_reader.clear_batched_readings()

pioreactor/pubsub.py

@@ -397,7 +397,7 @@ def publish_to_pioreactor_cloud(
     from pioreactor.utils.timing import current_utc_timestamp
     from json import dumps
 
-    assert data_dict is not None and data_str is not None
+    assert (data_dict is not None) or (data_str is not None)
 
     if is_testing_env():
         return

pioreactor/tests/test_dosing_control.py

@@ -278,7 +278,7 @@ def test_changing_morbidostat_parameters_over_mqtt() -> None:
     )
     pause()
     assert algo.target_growth_rate == new_target
-    assert algo.pid.pid.setpoint == new_target
+    assert algo.pid.setpoint == new_target
     algo.clean_up()
 
 

pioreactor/tests/test_temperature_control.py

@@ -115,7 +115,11 @@ def test_heating_is_reduced_when_set_temp_is_exceeded() -> None:
     with temperature_control.TemperatureController(
         "only_record_temperature", unit=unit, experiment=experiment
     ) as t:
-        setattr(t.tmp_driver, "get_temperature", lambda *args: t.MAX_TEMP_TO_REDUCE_HEATING + 0.1)
+        setattr(
+            t.heating_pcb_tmp_driver,
+            "get_temperature",
+            lambda *args: t.MAX_TEMP_TO_REDUCE_HEATING + 0.1,
+        )
         pause()
         t._update_heater(50)
         pause()
@@ -146,7 +150,11 @@ def test_heating_stops_when_max_temp_is_exceeded() -> None:
         target_temperature=25,
     ) as t:
         # monkey patch the driver
-        setattr(t.tmp_driver, "get_temperature", lambda *args: t.MAX_TEMP_TO_DISABLE_HEATING + 0.1)
+        setattr(
+            t.heating_pcb_tmp_driver,
+            "get_temperature",
+            lambda *args: t.MAX_TEMP_TO_DISABLE_HEATING + 0.1,
+        )
         pause()
         pause()
         t._update_heater(50)