adding stirring cal to self_test

pioreactor/actions/self_test.py

@@ -179,9 +179,18 @@ def test_all_positive_correlations_between_pds_and_leds(
                     adc_reader.take_reading(),
                     adc_reader.take_reading(),
                     adc_reader.take_reading(),
-                    adc_reader.take_reading(),
                 )
 
+                # turn off led to cool it down
+                led_intensity(
+                    {led_channel: 0},
+                    unit=unit,
+                    experiment=experiment,
+                    verbose=False,
+                    source_of_event="self_test",
+                )
+                sleep(intensity / 100)  # let it cool down in proportion to the intensity
+
                 # Add to accumulating list
                 for pd_channel in ALL_PD_CHANNELS:
                     varying_intensity_results[pd_channel].append(avg_reading[pd_channel])
@@ -359,6 +368,13 @@ def test_detect_heating_pcb(managed_state, logger: CustomLogger, unit: str, expe
     assert is_heating_pcb_present(), "Heater PCB is not connected, or i2c is not working."
 
 
+def test_run_stirring_calibration(managed_state, logger: CustomLogger, unit: str, experiment: str) -> None:
+    from pioreactor.calibrations.stirring_calibration import run_stirring_calibration
+
+    cal = run_stirring_calibration()
+    cal.set_as_active_calibration_for_device("stirring")
+
+
 def test_positive_correlation_between_temperature_and_heating(
     managed_state, logger: CustomLogger, unit: str, experiment: str
 ) -> None:
@@ -499,6 +515,7 @@ def click_self_test(k: Optional[str], retry_failed: bool) -> int:
         test_REF_is_in_correct_position,
         test_PD_is_near_0_volts_for_blank,
         test_positive_correlation_between_rpm_and_stirring,
+        test_run_stirring_calibration,
     )
 
     with managed_lifecycle(unit, experiment, "self_test") as managed_state, temporary_config_change(

pioreactor/background_jobs/od_reading.py

@@ -198,12 +198,13 @@ def set_offsets(self, batched_readings: PdChannelToVoltage) -> None:
         )
 
     def check_on_max(self, value: pt.Voltage) -> None:
-        unit = whoami.get_unit_name()
-        exp = whoami.get_assigned_experiment_name(unit)
-
         if value <= 3.0:
             return
         elif value > 3.2:
+            # TODO: sometimes we use ADC in self-tests or calibrations, and it might not be assigned. This will fail if that's the case.
+            unit = whoami.get_unit_name()
+            exp = whoami.get_assigned_experiment_name(unit)
+
             self.logger.error(
                 f"An ADC channel is recording a very high voltage, {round(value, 2)}V. We are shutting down components and jobs to keep the ADC safe."
             )
@@ -235,6 +236,9 @@ def check_on_max(self, value: pt.Voltage) -> None:
             return
 
         elif value > 3.0:
+            unit = whoami.get_unit_name()
+            exp = whoami.get_assigned_experiment_name(unit)
+
             self.logger.warning(
                 f"An ADC channel is recording a very high voltage, {round(value, 2)}V. It's recommended to keep it less than 3.0V. Suggestion: decrease the IR intensity, or change the PD angle to a lower angle."
             )

pioreactor/cli/calibrations.py

@@ -21,6 +21,10 @@ def green(string: str) -> str:
     return click.style(string, fg="green")
 
 
+def bold(string: str) -> str:
+    return click.style(string, bold=True)
+
+
 @click.group(short_help="calibration utils")
 def calibration() -> None:
     """
@@ -35,11 +39,14 @@ def list_calibrations(device: str | None) -> None:
     """
     List existing calibrations for the given device if provided, else all.
     """
+
+    header = f"{'Device':<25}{'Name':<50}{'Created At':<25}{'Active?':<10}"
+    click.echo(header)
+    click.echo("-" * len(header))
+
     if device is None:
         for device in list_devices():
             _display_calibrations_by_device(device)
-            click.echo()
-            click.echo()
     else:
         _display_calibrations_by_device(device)
 
@@ -50,19 +57,21 @@ def _display_calibrations_by_device(device: str) -> None:
         click.echo(f"No calibrations found for device '{device}'. Directory does not exist.")
         raise click.Abort()
 
-    header = f"{'Device':<25}{'Name':<50}{'Created At':<25}{'Active?':<10}{'Location':<75}"
-    click.echo(header)
-    click.echo("-" * len(header))
+    calibrations_by_device = list_of_calibrations_by_device(device)
 
-    for name in list_of_calibrations_by_device(device):
+    if len(calibrations_by_device) == 0:
+        return
+
+    for name in calibrations_by_device:
         try:
             location = (calibration_dir / name).with_suffix(".yaml")
             data = yaml_decode(location.read_bytes(), type=structs.subclass_union(structs.CalibrationBase))
-            row = f"{device:<25}{data.calibration_name:<50}{data.created_at.strftime('%Y-%m-%d %H:%M:%S'):<25}{'✅' if data.is_active(device) else '':<10}{location}"
+            row = f"{device:<25}{data.calibration_name:<50}{data.created_at.strftime('%Y-%m-%d %H:%M:%S'):<25}{'✅' if data.is_active(device) else '':<10}"
             click.echo(row)
-        except Exception as e:
-            error_message = f"Error reading {name}: {e}"
-            click.echo(f"{error_message:<60}")
+        except Exception:
+            pass
+            # error_message = f"Error reading {name}: {e}"
+            # click.echo(f"{error_message:<60}")
 
 
 @calibration.command(name="run", context_settings=dict(ignore_unknown_options=True, allow_extra_args=True))
@@ -83,6 +92,11 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
 
     # Dispatch to the assistant function for that device
     if protocol_name is None:
+        if len(calibration_protocols.get(device, {}).keys()) == 0:
+            click.echo(
+                f"No protocols found for device '{device}'. Try `pio calibrations protocols` to see available protocols."
+            )
+            raise click.Abort()
         if len(calibration_protocols.get(device, {}).keys()) == 1:
             protocol_name = list(calibration_protocols.get(device, {}).keys())[0]
         else:
@@ -92,7 +106,7 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
             click.echo(f"Available protocols for {device}:")
             click.echo()
             for protocol in calibration_protocols.get(device, {}).values():
-                click.echo(click.style(f"  • {protocol.protocol_name}", bold=True))
+                click.echo(bold(f"  • {protocol.protocol_name}"))
                 click.echo(f"        Description: {protocol.description}")
             click.echo()
             protocol_name = click.prompt(
@@ -137,9 +151,11 @@ def run_calibration(ctx, device: str, protocol_name: str | None, y: bool) -> Non
 
 @calibration.command(name="protocols")
 def list_protocols() -> None:
+    """
+    List available protocols for device calibrations.
+    """
     for device, protocols in calibration_protocols.items():
-        for protocol in protocols:
-            click.echo(f"{device}: {protocol}")
+        click.echo(f"{bold(device)}: {', '.join(protocols.keys())}")
 
 
 @calibration.command(name="display")