small changes

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
     hooks:
     -   id: mypy
         additional_dependencies: [
-            msgspec==0.15.1
+            msgspec==0.16.0
         ]
 
 

CHANGELOG.md

@@ -3,17 +3,29 @@
 #### Highlights
  - The UI now offers a way to upgrade to the bleeding-edge Pioreactor app and UI software, called "development". This software is unstable (and fun!).
 
+#### Better thermostat
+
+ - Improved temperature inference accuracy.
+ - After some testing, we've found that the following set of PID parameters for `temperature_automation.thermostat` works better¹ than the previous set of parameters:
+```
+Kp=3.0
+Ki=0.0
+Kd=4.5
+```
+
+This set now ships with all new installations of Pioreactor software. **Existing users can update their parameters in the config.ini**
+
+¹ Better == less thermal runaways, slightly less overshooting.
+
 #### Everything else
+ - On startup, the Raspberry Pi will write its IP address to a text file `/boot/ip`. This means that if you (carefully) remove the SD card, you should be able see the IP address (hopefully it hasn't changed).
  - Fixed `source` in `BackgroundJobContrib` - thanks @odcambc!
  - `pio add-pioreactor` will now accept an option that is the password of the RPi being added (default: `raspberry`). Ex: `pio add-pioreactor worker1 -p mypass`
  - Improved some warning and error messages.
  - Improved watchdog detecting and fixing "lost" Pioreactors.
- - Improved temperature inference accuracy.
  - Starting to test software against Python 3.11, in anticipation of a Python 3.11 coming to Raspberry Pi OS.
  - Improvements to bash scripts to make them more robust.
 
-
-
 ### 23.6.7
 
 #### Highlights

pioreactor/actions/self_test.py

@@ -60,6 +60,8 @@ def test_REF_is_in_correct_position(
     # this _also_ uses stirring to increase the variance in the non-REF, so...
     from statistics import variance
 
+    reference_channel = cast(PdChannel, config["od_config.photodiode_channel_reverse"][REF_keyword])
+
     signal1 = []
     signal2 = []
 
@@ -86,18 +88,16 @@ def test_REF_is_in_correct_position(
         "2": variance(signal2) / trimmed_mean(signal2) ** 2,
     }
 
-    ref_channel = config["od_config.photodiode_channel_reverse"][REF_keyword]
-
     THRESHOLD = 1.0
-    if ref_channel == "1":
+    if reference_channel == "1":
         assert (
             THRESHOLD * norm_variance_per_channel["1"] < norm_variance_per_channel["2"]
-        ), f"{ref_channel=}, {norm_variance_per_channel=}"
+        ), f"{reference_channel=}, {norm_variance_per_channel=}"
 
-    elif ref_channel == "2":
+    elif reference_channel == "2":
         assert (
             THRESHOLD * norm_variance_per_channel["2"] < norm_variance_per_channel["1"]
-        ), f"{ref_channel=}, {norm_variance_per_channel=}"
+        ), f"{reference_channel=}, {norm_variance_per_channel=}"
 
 
 def test_all_positive_correlations_between_pds_and_leds(

pioreactor/background_jobs/base.py

@@ -20,6 +20,7 @@
 from pioreactor.logging import create_logger
 from pioreactor.pubsub import Client
 from pioreactor.pubsub import create_client
+from pioreactor.pubsub import MQTT_TOPIC
 from pioreactor.pubsub import QOS
 from pioreactor.pubsub import subscribe
 from pioreactor.utils import append_signal_handlers
@@ -424,7 +425,7 @@ def publish(
     def subscribe_and_callback(
         self,
         callback: t.Callable[[pt.MQTTMessage], None],
-        subscriptions: list[str] | str,
+        subscriptions: list[str | MQTT_TOPIC] | str | MQTT_TOPIC,
         allow_retained: bool = True,
         qos: int = QOS.AT_MOST_ONCE,
     ) -> None:
@@ -462,9 +463,9 @@ def _callback(client, userdata, message: pt.MQTTMessage) -> t.Optional[T]:
 
         subscriptions = [subscriptions] if isinstance(subscriptions, str) else subscriptions
 
-        for sub in subscriptions:
-            self.sub_client.message_callback_add(sub, wrap_callback(callback))
-            self.sub_client.subscribe(sub, qos=qos)
+        for topic in subscriptions:
+            self.sub_client.message_callback_add(str(topic), wrap_callback(callback))
+            self.sub_client.subscribe(str(topic), qos=qos)
         return
 
     def set_state(self, new_state: pt.JobState) -> None:

pioreactor/background_jobs/growth_rate_calculating.py

@@ -239,6 +239,7 @@ def _compute_and_cache_od_statistics(
         means, variances = od_statistics(
             self._yield_od_readings_from_mqtt(),
             action_name="od_normalization",
+            n_samples=35,
             unit=self.unit,
             experiment=self.experiment,
             logger=self.logger,

pioreactor/background_jobs/leader/mqtt_to_db_streaming.py

@@ -17,6 +17,7 @@
 from pioreactor.background_jobs.base import BackgroundJob
 from pioreactor.config import config
 from pioreactor.hardware import PWM_TO_PIN
+from pioreactor.pubsub import MQTT_TOPIC
 from pioreactor.pubsub import QOS
 from pioreactor.utils.sqlite_worker import Sqlite3Worker
 from pioreactor.utils.timing import current_utc_datetime
@@ -44,13 +45,13 @@ class TopicToParserToTable(Struct):
      - parsers can return None as well, to skip adding the row to the database.
     """
 
-    topic: str | list[str]
+    topic: str | MQTT_TOPIC | list[str | MQTT_TOPIC]
     parser: Callable[[str, pt.MQTTMessagePayload], Optional[dict | list[dict]]]
     table: str
 
 
 class TopicToCallback(Struct):
-    topic: str | list[str]
+    topic: str | MQTT_TOPIC | list[str | MQTT_TOPIC]
     callback: Callable[[pt.MQTTMessage], None]
 
 
@@ -145,7 +146,7 @@ def initialize_callbacks(self, topics_and_callbacks: list[TopicToCallback]) -> N
         for topic_and_callback in topics_and_callbacks:
             self.subscribe_and_callback(
                 topic_and_callback.callback,
-                topic_and_callback.topic,
+                str(topic_and_callback.topic),
                 qos=QOS.EXACTLY_ONCE,
                 allow_retained=False,
             )

pioreactor/background_jobs/od_reading.py

@@ -130,7 +130,7 @@ def __init__(
         fake_data: bool = False,
         interval: Optional[float] = 1.0,
         dynamic_gain: bool = True,
-        penalizer: float = 525.0,
+        penalizer: float = 625.0,
         oversampling_count: int = 28,
     ) -> None:
         super().__init__()

pioreactor/cli/pio.py

@@ -747,7 +747,9 @@ def display_data_for(hostname_status: tuple[str, str]) -> bool:
 
             ip, state, reachable = get_network_metadata(hostname)
 
-            statef = click.style(f"{state:15s}", fg="green" if state == "ready" else "red")
+            statef = click.style(
+                f"{state:15s}", fg="green" if state in ("ready", "init") else "red"
+            )
             ipf = f"{ip if (ip is not None) else 'unknown':20s}"
 
             is_leaderf = f"{('Y' if hostname==get_leader_hostname() else 'N'):15s}"

pioreactor/pubsub.py

@@ -17,28 +17,24 @@
 from pioreactor.types import MQTTMessage
 
 
-class PIOREACTOR:
-    """
-    Use to construct MQTT paths like Pathlib in Python core.
-
-    > PIOREACTOR() / unit / experiment / "+" / "$state" / "set"
-    >> "pioreactor/test_unit/test_experiment/+/$state/set"
+class MQTT_TOPIC:
+    def __init__(self, init: str):
+        self.body = init
 
-    BETA: may be deleted in the future.
+    def __truediv__(self, other: str | MQTT_TOPIC) -> MQTT_TOPIC:
+        return MQTT_TOPIC(self.body + "/" + str(other))
 
-    """
+    def __str__(self) -> str:
+        return self.body
 
-    def __init__(self, body="pioreactor"):
-        self.body = body
+    def __repr__(self) -> str:
+        return str(self)
 
-    def __truediv__(self, other):
-        return PIOREACTOR(self.body + "/" + other)
+    def __iter__(self):
+        return iter(str(self))
 
-    def __str__(self):
-        return self.body
 
-    def __repr__(self):
-        return str(self)
+PIOREACTOR = MQTT_TOPIC("pioreactor")
 
 
 def add_hash_suffix(s: str) -> str:
@@ -364,7 +360,7 @@ def __init__(self, log_level: str, unit: str, experiment: str) -> None:
         # subscribe to the logs
         self.client: Client = subscribe_and_callback(
             self._collect_logs_into_bucket,
-            str(PIOREACTOR() / self.unit / self.experiment / "logs" / "app"),
+            str(PIOREACTOR / self.unit / self.experiment / "logs" / "app"),
         )
 
     def _collect_logs_into_bucket(self, message):

update_scripts/upcoming/update.sh

@@ -7,4 +7,11 @@ export LC_ALL=C
 
 wget -O /usr/local/bin/install_pioreactor_plugin.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/install_pioreactor_plugin.sh
 wget -O /usr/local/bin/uninstall_pioreactor_plugin.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/uninstall_pioreactor_plugin.sh
+
+# adding bounds to the while loops
 wget -O /usr/local/bin/add_new_pioreactor_worker_from_leader.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/add_new_pioreactor_worker_from_leader.sh
+
+
+# we write the IP address to /boot/ip
+wget -O /usr/local/bin/everyboot.sh https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/bash/everyboot.sh
+wget -O /lib/systemd/system/everyboot.service https://raw.githubusercontent.com/Pioreactor/CustoPiZer/pioreactor/workspace/scripts/files/system/systemd/everyboot.service