bump adafruit libs, new kalman filter

Author: CamDavidsonPilon

CHANGELOG.md

@@ -1,6 +1,9 @@
 ### Upcoming
 
  - adding dirs to exported data zips
+ - new kalman filter
+ - new system logs
+ - fixed stirrer not spinning on Pioreactor page (UI)
 
 ### 25.5.1
 

pioreactor/background_jobs/growth_rate_calculating.py

@@ -299,6 +299,13 @@ def get_precomputed_values(
 
         od_blank = self.get_od_blank_from_cache()
 
+        # check that od_variances is not zero:
+        # this means that the sensor is not working properly.
+        if any(v == 0.0 for v in od_variances.values()):
+            raise ValueError(
+                "OD variance is zero - this means that the sensor is not working properly. Please check the sensor."
+            )
+
         # what happens if od_blank is near / less than od_normalization_factors?
         # this means that the inoculant had near 0 impact on the turbidity => very dilute.
         # I think we should not use od_blank if so

pioreactor/background_jobs/leader/mqtt_to_db_streaming.py

@@ -120,7 +120,7 @@ def callback(message: pt.MQTTMessage) -> None:
             except Exception as e:
                 self.logger.warning(f"Encountered error in saving to DB: {e}. See logs.")
                 self.logger.debug(
-                    f"Error in {parser.__name__}. Payload that caused error: `{message.payload.decode()}`. Topic: `{message.topic}`",
+                    f"Error in {parser.__name__}. Payload: `{message.payload.decode()}`. Topic: `{message.topic}`",
                     exc_info=True,
                 )
                 return

pioreactor/background_jobs/od_reading.py

@@ -1317,19 +1317,18 @@ def click_od_reading(
     """
 
     if snapshot:
-        od = start_od_reading(
+        with start_od_reading(
             od_angle_channel1,
             od_angle_channel2,
             fake_data=fake_data or whoami.is_testing_env(),
             interval=None,
-        )
-        od.logger.debug(od.record_from_adc())
-        # end early
-        return
+        ) as od:
+            od.logger.debug(od.record_from_adc())
+            # end early
     else:
-        od = start_od_reading(
+        with start_od_reading(
             od_angle_channel1,
             od_angle_channel2,
             fake_data=fake_data or whoami.is_testing_env(),
-        )
-        od.block_until_disconnected()
+        ) as od:
+            od.block_until_disconnected()

pioreactor/background_jobs/stirring.py

@@ -596,6 +596,6 @@ def click_stirring(target_rpm: float, use_rpm: bool) -> None:
     """
     Start the stirring of the Pioreactor.
     """
-    st = start_stirring(target_rpm=target_rpm, use_rpm=use_rpm)
-    st.block_until_rpm_is_close_to_target()
-    st.block_until_disconnected()
+    with start_stirring(target_rpm=target_rpm, use_rpm=use_rpm) as st:
+        st.block_until_rpm_is_close_to_target()
+        st.block_until_disconnected()

pioreactor/background_jobs/temperature_automation.py

@@ -597,7 +597,7 @@ def start_temperature_automation(
         )
 
     except Exception as e:
-        logger = create_logger("temperature_automation")
+        logger = create_logger("temperature_automation", experiment=experiment)
         logger.error(e)
         logger.debug(e, exc_info=True)
         raise e

pioreactor/cluster_management/__init__.py

@@ -44,11 +44,11 @@ def get_active_workers_in_experiment(experiment: str) -> tuple[str, ...]:
 @click.command(name="add", short_help="add a pioreactor worker")
 @click.argument("hostname")
 @click.option("--password", "-p", default="raspberry")
-@click.option("--model-version", "-v", required=True, type=click.STRING)
 @click.option("--model-name", "-m", type=click.Choice(["pioreactor_20ml", "pioreactor_40ml"]), required=True)
+@click.option("--model-version", "-v", required=True, type=click.Choice(["1.0", "1.1"]))
 @click.option("--address", "-a")
 def add_worker(
-    hostname: str, password: str, model_version: str, model_name: str, address: str | None
+    hostname: str, password: str, model_name: str, model_version: str, address: str | None
 ) -> None:
     """
     Add a new pioreactor worker to the cluster. The pioreactor should already have the worker image installed and is turned on.

pioreactor/hardware.py

@@ -45,8 +45,8 @@
 
 if rpi_version_info.startswith("Raspberry Pi 5"):
     GPIOCHIP = 4
-    SDA = (4, 2)
-    SCL = (4, 3)
+    SDA = 2
+    SCL = 3
 else:
     GPIOCHIP = 0
     SDA = 2

pioreactor/utils/streaming_calculations.py

@@ -274,8 +274,14 @@ def update(self, observation_: list[float], dt: float, recent_dilution=False):
             kalman_gain_[1:, 0] = 0
 
         ### update estimates
-        self.state_ = state_prediction + kalman_gain_ @ residual_state
-        self.covariance_ = (np.eye(self.n_states) - kalman_gain_ @ H) @ covariance_prediction
+        state_ = state_prediction + kalman_gain_ @ residual_state
+        covariance_ = (np.eye(self.n_states) - kalman_gain_ @ H) @ covariance_prediction
+
+        if np.isnan(state_).any():
+            raise ValueError("NaNs detected after calculation.")
+
+        self.state_ = state_
+        self.covariance_ = covariance_
 
         return self.state_, self.covariance_
 

requirements/requirements_worker.txt

@@ -1,11 +1,11 @@
 -r requirements.txt
-Adafruit-Blinka==8.43.0
+Adafruit-Blinka==8.57.0
 adafruit-circuitpython-ads1x15==2.2.23
 adafruit-circuitpython-busdevice==5.2.9
 adafruit-circuitpython-connectionmanager==3.1.1
 adafruit-circuitpython-requests==4.1.3
 adafruit-circuitpython-typing==1.10.3
-Adafruit-PlatformDetect==3.71.0
+Adafruit-PlatformDetect==3.78.0
 Adafruit-PureIO==1.1.11
 DAC43608==0.2.7
 plotext==5.2.8