wip

Author: CamDavidsonPilon

CHANGELOG.md

@@ -1,3 +1,12 @@
+### Upcoming
+
+ - new upload calibration dialog
+
+#### Bug fixes
+ - stirring calibration was using too many points from the lower bound, this is fixed.
+ - fix for stirring calibration in the self-test creating an empty file
+ - Fix custom charts that were not fetching from the database correctly due to the backend table being a sqlite3 view (VIEWs don't have ROWID, which was breaking a filter).
+
 ### 25.4.11
 
 #### Bug fixes

config.dev.ini

@@ -169,7 +169,3 @@ ekf_variance_shift_post_dosing_minutes=0.40
 ekf_variance_shift_post_dosing_factor=2500
 ekf_outlier_std_threshold=3.0
 samples_for_od_statistics=35
-
-[pioreactor]
-model=pioreactor_20ml
-version=1.0

pioreactor/actions/self_test.py

@@ -101,6 +101,8 @@ def test_REF_is_in_correct_position(managed_state, logger: CustomLogger, unit: s
             if i == 25:
                 break
 
+    logger.debug(f"{signal1=}, {signal2=}")
+
     norm_variance_per_channel = {
         "1": variance(signal1) / trimmed_mean(signal1) ** 2,
         "2": variance(signal2) / trimmed_mean(signal2) ** 2,
@@ -375,7 +377,9 @@ def test_run_stirring_calibration(managed_state, logger: CustomLogger, unit: str
     from pioreactor.calibrations.stirring_calibration import run_stirring_calibration
 
     cal = run_stirring_calibration()
+    cal.save_to_disk_for_device("stirring")
     cal.set_as_active_calibration_for_device("stirring")
+    return
 
 
 def test_positive_correlation_between_temperature_and_heating(

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()}`",
+                    f"Error in {parser.__name__}. Payload that caused error: `{message.payload.decode()}`. Topic: `{message.topic}`",
                     exc_info=True,
                 )
                 return
@@ -178,7 +178,7 @@ def parse_od(topic: str, payload: pt.MQTTMessagePayload) -> dict:
 
 def parse_raw_od(topic: str, payload: pt.MQTTMessagePayload) -> dict:
     metadata = produce_metadata(topic)
-    od_reading = msgspec_loads(payload, type=structs.ODReading)
+    od_reading = msgspec_loads(payload, type=structs.RawODReading)
     return {
         "experiment": metadata.experiment,
         "pioreactor_unit": metadata.pioreactor_unit,

pioreactor/calibrations/__init__.py

@@ -44,7 +44,7 @@ def __init_subclass__(cls, **kwargs):
         else:
             raise ValueError("target_device must be a string or a list of strings")
 
-    def run(self, *args, **kwargs):
+    def run(self, *args, **kwargs) -> structs.CalibrationBase:
         raise NotImplementedError("Subclasses must implement this method.")
 
 
@@ -128,6 +128,8 @@ def load_calibration(device: Device, calibration_name: str) -> structs.AnyCalibr
         raise FileNotFoundError(
             f"Calibration {calibration_name} was not found in {CALIBRATION_PATH / device}"
         )
+    elif target_file.stat().st_size == 0:
+        raise FileNotFoundError(f"Calibration {calibration_name} is empty")
 
     try:
         data = yaml_decode(target_file.read_bytes(), type=structs.subclass_union(structs.CalibrationBase))

pioreactor/calibrations/stirring_calibration.py

@@ -31,7 +31,7 @@ def run_stirring_calibration(
     if max_dc is None and min_dc is None:
         # seed with initial_duty_cycle
         config_initial_duty_cycle = config.getfloat("stirring.config", "initial_duty_cycle", fallback=30)
-        min_dc, max_dc = config_initial_duty_cycle * 0.5, clamp(0, config_initial_duty_cycle * 1.5, 100)
+        min_dc, max_dc = config_initial_duty_cycle * 0.66, clamp(0, config_initial_duty_cycle * 1.33, 100)
     elif (max_dc is not None) and (min_dc is not None):
         assert min_dc < max_dc, "min_dc >= max_dc"
     else:
@@ -52,7 +52,7 @@ def run_stirring_calibration(
         measured_rpms = []
 
         # go up and down to observe any hysteresis.
-        dcs = linspace(max_dc, min_dc, 5) + linspace(min_dc, min_dc, 5) + linspace(max_dc, min_dc, 5)
+        dcs = linspace(max_dc, min_dc, 5) + linspace(min_dc, max_dc, 5) + linspace(max_dc, min_dc, 5)
         n_samples = len(dcs)
 
         with temporary_config_change(config, "stirring.config", "enable_dodging_od", "False"):

pioreactor/calibrations/utils.py

@@ -67,6 +67,9 @@ def curve_callable(x):
 
 
 def linspace(start: float, stop: float, num: int = 50) -> list[float]:
+    assert start < stop
+    assert num > 0
+
     def linspace_(start: float, stop: float, num: int = 50):
         num = int(num)
         start = start * 1.0

pioreactor/structs.py

@@ -304,8 +304,8 @@ class ODCalibration(CalibrationBase, kw_only=True, tag="od"):
     ir_led_intensity: float
     angle: t.Literal["45", "90", "135", "180"]
     pd_channel: t.Literal["1", "2"]
-    x: str = "OD600"
     y: str = "Voltage"
+    x: str = "OD600"
 
 
 class SimplePeristalticPumpCalibration(CalibrationBase, kw_only=True, tag="simple_peristaltic_pump"):

update_scripts/25.4.11/post_update.sh

@@ -17,9 +17,29 @@ if [ "$HOSTNAME" = "$LEADER_HOSTNAME" ]; then
     for config_file in "$CONFIG_DIR"/config_*.ini; do
         if [[ -f "$config_file" ]]; then
             pioreactor_unit=$(basename "$config_file" | sed 's/config_\(.*\)\.ini/\1/')
+
+            # Check if the [pioreactor] section exists
+            if ! crudini --get "$config_file" pioreactor &> /dev/null; then
+                echo "Skipping $config_file: Missing [pioreactor] section"
+                continue
+            fi
+
+            # Check if the 'model' and 'version' parameters are present
+            if ! crudini --get "$config_file" pioreactor model &> /dev/null; then
+                echo "Skipping $config_file: Missing 'model' parameter in [pioreactor] section"
+                continue
+            fi
+
+            if ! crudini --get "$config_file" pioreactor version &> /dev/null; then
+                echo "Skipping $config_file: Missing 'version' parameter in [pioreactor] section"
+                continue
+            fi
+
+            # Retrieve parameters
             model_name=$(crudini --get "$config_file" pioreactor model 2>/dev/null)
             model_version=$(crudini --get "$config_file" pioreactor version 2>/dev/null)
 
+            # Double-check that both values are non-empty before updating
             if [[ -n "$model_name" && -n "$model_version" ]]; then
                 sqlite3 "$DB_PATH" <<EOF
 UPDATE workers SET
@@ -30,10 +50,11 @@ EOF
                 echo "Updated: $pioreactor_unit ($model_name, $model_version)"
                 crudini --del "$config_file" pioreactor
             else
-                echo "Skipping $config_file: Missing model or version"
+                echo "Skipping $config_file: One or more parameter values are empty"
             fi
         fi
     done
+
     sudo -u pioreactor pios sync-configs || :
 
     # restart mqtt to db