reverse order of class init args: unit is higher priority

pioreactor/actions/leader/experiment_profile.py

@@ -220,7 +220,7 @@ def execute_experiment_profile(profile_filename: str, dry_run: bool = False) ->
                     timer.cancel()
                 logger.info(f"Exiting profile {profile.experiment_profile_name} early.")
             else:
-                logger.info(f"Finished at commands in profile {profile.experiment_profile_name}.")
+                logger.info(f"Finished executing profile {profile.experiment_profile_name}.")
 
 
 @click.group(name="experiment_profile")
@@ -242,6 +242,6 @@ def click_execute_experiment_profile(filename: str, dry_run: bool) -> None:
 @click.argument("filename", type=click.Path(exists=True))
 def click_verify_experiment_profile(filename: str) -> None:
     """
-    (leader only) Verify an experiment profile.
+    (leader only) Verify an experiment profile for correctness.
     """
     load_and_verify_profile_file(filename)

pioreactor/automations/__init__.py

@@ -1,13 +1,26 @@
 # -*- coding: utf-8 -*-
 from __future__ import annotations
 
-from . import dosing
-from . import events
-from . import led
-from . import temperature
-from .dosing.base import DosingAutomationJob
-from .dosing.base import DosingAutomationJobContrib
-from .led.base import LEDAutomationJob
-from .led.base import LEDAutomationJobContrib
-from .temperature.base import TemperatureAutomationJob
-from .temperature.base import TemperatureAutomationJobContrib
+from pioreactor.background_jobs.subjobs import BackgroundSubJob
+
+DISALLOWED_AUTOMATION_NAMES = {
+    "config",
+}
+
+
+class BaseAutomationJob(BackgroundSubJob):
+    automation_name = "base_automation_job"
+
+    def __init__(self, unit: str, experiment: str):
+        super(BaseAutomationJob, self).__init__(unit, experiment)
+
+        if self.automation_name in DISALLOWED_AUTOMATION_NAMES:
+            raise NameError(f"{self.automation_name} is not allowed.")
+
+        self.add_to_published_settings(
+            "latest_event",
+            {
+                "datatype": "AutomationEvent",
+                "settable": False,
+            },
+        )

pioreactor/automations/dosing/base.py

@@ -238,7 +238,7 @@ def __init__(
         ),
         **kwargs,
     ) -> None:
-        super(DosingAutomationJob, self).__init__(unit=unit, experiment=experiment)
+        super(DosingAutomationJob, self).__init__(unit, experiment)
         self.skip_first_run = skip_first_run
 
         self._latest_settings_started_at = current_utc_datetime()

pioreactor/automations/led/base.py

@@ -15,9 +15,9 @@
 from pioreactor import structs
 from pioreactor import types as pt
 from pioreactor.actions.led_intensity import led_intensity
+from pioreactor.automations import BaseAutomationJob
 from pioreactor.automations import events
 from pioreactor.background_jobs.led_control import LEDController
-from pioreactor.background_jobs.subjobs import BackgroundSubJob
 from pioreactor.pubsub import QOS
 from pioreactor.utils import is_pio_job_running
 from pioreactor.utils.timing import current_utc_datetime
@@ -30,7 +30,7 @@ def brief_pause() -> float:
     return d
 
 
-class LEDAutomationJob(BackgroundSubJob):
+class LEDAutomationJob(BaseAutomationJob):
     """
     This is the super class that LED automations inherit from. The `run` function will
     execute every `duration` minutes (selected at the start of the program), and call the `execute` function
@@ -79,22 +79,14 @@ def __init__(
         skip_first_run: bool = False,
         **kwargs,
     ) -> None:
-        super(LEDAutomationJob, self).__init__(unit=unit, experiment=experiment)
+        super(LEDAutomationJob, self).__init__(unit, experiment)
 
         self.skip_first_run = skip_first_run
         self._latest_settings_started_at: datetime = current_utc_datetime()
         self.latest_normalized_od_at: datetime = current_utc_datetime()
         self.latest_growth_rate_at: datetime = current_utc_datetime()
         self.edited_channels: set[pt.LedChannel] = set()
 
-        self.add_to_published_settings(
-            "latest_event",
-            {
-                "datatype": "AutomationEvent",
-                "settable": False,
-            },
-        )
-
         self.set_duration(duration)
 
     def on_init_to_ready(self):

pioreactor/automations/temperature/base.py

@@ -61,7 +61,7 @@ def __init__(
         temperature_control_parent: TemperatureController,
         **kwargs,
     ) -> None:
-        super(TemperatureAutomationJob, self).__init__(unit=unit, experiment=experiment)
+        super(TemperatureAutomationJob, self).__init__(unit, experiment)
 
         self.latest_normalized_od_at: datetime = current_utc_datetime()
         self.latest_growth_rate_at: datetime = current_utc_datetime()

pioreactor/automations/temperature/only_record_temperature.py

@@ -13,5 +13,6 @@ def __init__(self, **kwargs) -> None:
         self.update_heater(0)
 
     def execute(self) -> NoEvent:
-        self.update_heater(0)
+        if self.heater_duty_cycle != 0:
+            self.update_heater(0)
         return NoEvent()

pioreactor/background_jobs/base.py

@@ -35,6 +35,16 @@
 T = t.TypeVar("T")
 BJT = t.TypeVar("BJT", bound="_BackgroundJob")
 
+# these are used elsewhere in our software
+DISALLOWED_JOB_NAMES = {
+    "run",
+    "dosing_events",
+    "leds",
+    "led_change_events",
+    "unit_label",
+    "pwm",
+}
+
 
 def cast_bytes_to_type(value: bytes, type_: str):
     try:
@@ -90,17 +100,6 @@ def __call__(cls, *args, **kwargs):
         return obj
 
 
-# these are used elsewhere in our software
-DISALLOWED_JOB_NAMES = {
-    "run",
-    "dosing_events",
-    "leds",
-    "led_change_events",
-    "unit_label",
-    "pwm",
-}
-
-
 class _BackgroundJob(metaclass=PostInitCaller):
 
     """
@@ -249,7 +248,7 @@ class _BackgroundJob(metaclass=PostInitCaller):
     # See pt.PublishableSetting type
     published_settings: dict[str, pt.PublishableSetting] = dict()
 
-    def __init__(self, experiment: str, unit: str, source: str = "app") -> None:
+    def __init__(self, unit: str, experiment: str, source: str = "app") -> None:
         if self.job_name in DISALLOWED_JOB_NAMES:
             raise ValueError("Job name not allowed.")
         if not self.job_name.islower():
@@ -958,17 +957,17 @@ class BackgroundJob(_BackgroundJob):
     Native jobs should inherit from this class.
     """
 
-    def __init__(self, experiment: str, unit: str) -> None:
-        super().__init__(experiment=experiment, unit=unit, source="app")
+    def __init__(self, unit: str, experiment: str) -> None:
+        super().__init__(unit, experiment, source="app")
 
 
 class BackgroundJobContrib(_BackgroundJob):
     """
     Plugin jobs should inherit from this class.
     """
 
-    def __init__(self, experiment: str, unit: str, plugin_name: str) -> None:
-        super().__init__(experiment=experiment, unit=unit, source=plugin_name)
+    def __init__(self, unit: str, experiment: str, plugin_name: str) -> None:
+        super().__init__(unit, experiment, source=plugin_name)
 
 
 class BackgroundJobWithDodging(_BackgroundJob):
@@ -1165,5 +1164,5 @@ class BackgroundJobWithDodgingContrib(BackgroundJobWithDodging):
     Plugin jobs should inherit from this class.
     """
 
-    def __init__(self, experiment: str, unit: str, plugin_name: str) -> None:
-        super().__init__(source=plugin_name, experiment=experiment, unit=unit)
+    def __init__(self, unit: str, experiment: str, plugin_name: str) -> None:
+        super().__init__(unit=unit, experiment=experiment, source=plugin_name)

pioreactor/background_jobs/leader/mqtt_to_db_streaming.py

@@ -66,9 +66,12 @@ class MqttToDBStreamer(BackgroundJob):
     _inserts_in_last_60s = 0
 
     def __init__(
-        self, topics_to_tables: list[TopicToParserToTable], unit: str, experiment: str
+        self,
+        unit: str,
+        experiment: str,
+        topics_to_tables: list[TopicToParserToTable],
     ) -> None:
-        super().__init__(experiment=experiment, unit=unit)
+        super().__init__(unit, experiment)
         self.logger.debug(f'Streaming MQTT data to {config["storage"]["database"]}.')
         self.sqliteworker = Sqlite3Worker(
             config["storage"]["database"], max_queue_size=250, raise_on_error=False
@@ -459,7 +462,7 @@ def register_source_to_sink(t2p2t: TopicToParserToTable | list[TopicToParserToTa
 
 def start_mqtt_to_db_streaming() -> MqttToDBStreamer:
     source_to_sinks = add_default_source_to_sinks()
-    return MqttToDBStreamer(source_to_sinks, experiment=UNIVERSAL_EXPERIMENT, unit=get_unit_name())
+    return MqttToDBStreamer(get_unit_name(), UNIVERSAL_EXPERIMENT, source_to_sinks)
 
 
 @click.command(name="mqtt_to_db_streaming")

pioreactor/background_jobs/stirring.py

@@ -356,7 +356,7 @@ def poll(self, poll_for_seconds: float) -> Optional[structs.MeasuredRPM]:
         if self.rpm_calculator is None:
             return None
 
-        recent_rpm = round(self.rpm_calculator(poll_for_seconds), 1)
+        recent_rpm = round(self.rpm_calculator(poll_for_seconds), 2)
 
         self._measured_rpm = recent_rpm
         self.measured_rpm = structs.MeasuredRPM(

pioreactor/background_jobs/temperature_control.py

@@ -434,7 +434,7 @@ def infer_temperature(self) -> None:
 
         try:
             self.temperature = Temperature(
-                temperature=self.approximate_temperature(features),
+                temperature=round(self.approximate_temperature(features), 2),
                 timestamp=current_utc_datetime(),
             )
 

pioreactor/tests/test_dosing_control.py

@@ -16,9 +16,9 @@
 from pioreactor import exc
 from pioreactor import pubsub
 from pioreactor import structs
-from pioreactor.automations import DosingAutomationJob
 from pioreactor.automations import events
 from pioreactor.automations.dosing.base import AltMediaFractionCalculator
+from pioreactor.automations.dosing.base import DosingAutomationJob
 from pioreactor.automations.dosing.base import VialVolumeCalculator
 from pioreactor.automations.dosing.pid_morbidostat import PIDMorbidostat
 from pioreactor.automations.dosing.silent import Silent

pioreactor/tests/test_mqtt_to_db_streaming.py

@@ -48,7 +48,7 @@ def parse_setting(topic, payload) -> dict:
         )
     ]
 
-    with m2db.MqttToDBStreamer(parsers, unit=unit, experiment=exp):
+    with m2db.MqttToDBStreamer(unit, exp, parsers):
         with collect_all_logs_of_level("ERROR", unit, exp) as bucket:
             t = TestJob(unit=unit, experiment=exp)
             t.clean_up()
@@ -80,7 +80,7 @@ def test_updated_heater_dc() -> None:
         ),
     ]
 
-    with m2db.MqttToDBStreamer(parsers, unit=unit, experiment=exp):
+    with m2db.MqttToDBStreamer(unit, exp, parsers):
         sleep(1)
         publish(
             f"pioreactor/{unit}/test/temperature_automation/latest_event",
@@ -122,7 +122,7 @@ def test_dosing_events_land_in_db() -> None:
         ),
     ]
 
-    with m2db.MqttToDBStreamer(parsers, unit=unit, experiment=exp):
+    with m2db.MqttToDBStreamer(unit, exp, parsers):
         from pioreactor.actions.pump import add_media
 
         add_media(
@@ -197,7 +197,7 @@ def test_kalman_filter_entries() -> None:
         )
     ]
 
-    m = m2db.MqttToDBStreamer(parsers, unit=unit, experiment=exp)
+    m = m2db.MqttToDBStreamer(unit, exp, parsers)
 
     # let data collect
     sleep(10)
@@ -259,7 +259,7 @@ def parse_setting(topic, payload) -> dict:
         )
     ]
 
-    with m2db.MqttToDBStreamer(parsers, unit=unit, experiment=exp):
+    with m2db.MqttToDBStreamer(unit, exp, parsers):
         with collect_all_logs_of_level("ERROR", unit, exp) as bucket:
             t = TestJob(unit=unit, experiment=exp)
             t.clean_up()

pioreactor/utils/streaming_calculations.py

@@ -535,4 +535,6 @@ def publish_pid_stats(self) -> None:
             "job_name": self.job_name,
             "target_name": self.target_name,
         }
-        self.client.publish(f"pioreactor/{self.unit}/{self.experiment}/pid_log", dumps(to_send))
+        self.client.publish(
+            f"pioreactor/{self.unit}/{self.experiment}/pid_log/{self.target_name}", dumps(to_send)
+        )

pioreactor/version.py

@@ -5,7 +5,7 @@
 
 # Append "dev" if a dev version
 # Append "rc0" if a rc version
-__version__ = "23.8.29"
+__version__ = "23.8.29dev"
 
 
 def _get_hardware_version() -> tuple[int, int] | tuple[int, int, str]: